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R/generaltoolsmenu.R
In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
Defines functions
genomeStudioReformat
setBinDir
tuxedoSetup
openPdf
closePdf
Documented in
closePdf
genomeStudioReformat
openPdf
setBinDir
tuxedoSetup
#set of functions, directly/indirectly involved, in oneChannelGUI generalToolMenu
#oneChannelGUI filteringTable filtering a tab delimited file on the basis of a list of probesets
#oneChannelGUI colExtract extract a user defined colum from a tab delimited file with header
#oneChannelGUI geneExonLibs queries affymetrix web site to download exon and gene 1.0 ST WT library files
#RETIRED oneChannelGUI ngsperlDownload creating dir with ngs perl scripts
#oneChannelGUI bowtieDownload download bowtie and picard tools and build a binary form of ref genome for non coding precursors
# alos downloading tophat and cufflinks for linux and mac
# bowtiesGenomes downloades and builds chromosome level genomes references for bowtie
# embeds also makeGeneScaffold for gene level analysis, which creates gene-level oriented scaffolds
# bowtieBuilt downloads prebuilt cromosome oriented bowtie references from:
# http://sourceforge.net/p/ochguiextras/home/oneChannelGUI.extras/
#oneChannelGUI aptFolder setting the folder were apt tools are located (save data in localdata.txt in etc)
#oneChannelGUI javaFolder setting the folder were java is located
#oneChannelGUI deleteLocalData delete data in localdata.txt resetting aptDir and libDirLocation
#oneChannelGUI buildingLocalAnnotation updates gene level annotation using the netaffx annotation data
# exon level annotation is done using the UCSC exon-level annotation data
#oneChannelGUI refseqDownload retrieve the latest Hs, Mm, Rn refseq fasta file
#oneChannelGUI madscrosshybDownload and creation of mads derived mps file only available for Hs and Mm core NOT FINISHED
#oneChannelGUI updateLibs run an update of the Bioconductor libraries
#oneChannelGUI variantExons the function updates the table available in oneChannelGUI that contains only variant exons
# for the core set. variant exons are those that are present only in a subset of isoforms associated to a gene to the UCSC browser
#oneChannelGUI exportFASTA Export non-coding RNA fasta file for RNA-seq
#oneChannelGUI meVDownload setting the folder were meV software (http://www.tm4.org/mev/) is located (save data in localdata.txt in etc)
#oneChannelGUI extPckInfo show which external software are available and in which dir
#oneChannelGUI combining2eSet combine two tables with the same row names
#oneChannelGUI wrapNGS wrapping function to install all expernal software needed for RNA-seq
#oneChannelGUI makeGeneScaffold creating Grange object for UCSC browser needed to map reads on UCSC genes located in stand alone functions
# part of the bowtiesGenomes function it returns a list of GRanges chromosomes encompassing the positions of all annotated USCS genes that encode for a protein
#oneChannelGUI genomeStudioReformat the function convert a genomestudio output in a format suitable to be loaded on oneChannelGUI
#oneChannelGUI setBinDir setting the dir in which create the soft lnks for tuxido suite
#oneChannelGUI openPdf needed under linux to print pdf
#oneChannelGUI closePdf needed under linux to print pdf
#################################################################################
#################################################################################
#this file contains a set of function that perfomr basic R function useful for handlying microarray data.
#this function filter a table on the basis of a vector of data present in an other file
"filteringTable" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Table subsetting",message="Open the file to be filtered. This file should be tab delimited with an header."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(saving.file <- paste(tempFileName, ".filtered.by.",sep=""))
Try(mySel<-read.table(tempFileName, sep="\t", header=T, as.is=TRUE, quote=""))
Try(tkmessageBox(title="Table subsetting",message="Open the file to be used to filter the previous file.\nThis file should contain a single column with an header equal to \nthe one that should be used for filtering in the tab delimited file."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(tmp <- as.vector(unlist(strsplit(tempFileName , "/"))))
Try(saving.file <- paste(saving.file, tmp[length(tmp)],sep=""))
Try(myFilter<-read.table(tempFileName, sep="\t", header=T, as.is=TRUE, quote=""))
Try(col.for.filter <- which(names(mySel)==names(myFilter)[1]))
Try(mySel <- mySel[which(mySel[,col.for.filter]%in%myFilter[,1]),])
Try(tkmessageBox(title="Table subsetting",message="Saving the filtered table."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=saving.file, filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if(!nchar(FileName))
return())
Try(write.table(mySel,file=FileName,quote=FALSE,col.names=NA,sep="\t"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
"colExtract" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Column extraction",message="Open the file to be manipulated. This file should be tab delimited with an header."))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(mySel<-read.table(tempFileName, sep="\t", header=T, as.is=TRUE, quote=""))
Try(mycol <- names(mySel))
Try(mycol <- paste(mycol, "=",seq(1, length(mycol)), sep="", collapse=" "))
#selecting the column to be removed
Try(ttcolExtract<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttcolExtract))
Try(tkgrab.set(ttcolExtract))
Try(tkfocus(ttcolExtract))
Try(tkwm.title(ttcolExtract,"Defining the column to be estracted"))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(colnum <- "1")
Try(Local.colExtract <- tclVar(init=colnum))
Try(entry.colExtract <-tkentry(ttcolExtract,width="4",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.colExtract,bg="white"))
Try(tkgrid(tklabel(ttcolExtract,text=paste("Please enter the number associated to the columnof interest\n", mycol,collapse=" "),font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.colExtract))
onOK <- function()
{
Try(colnum <- as.numeric(tclvalue(Local.colExtract)))
Try(assign("colnum", as.numeric(tclvalue(Local.colExtract)),affylmGUIenvironment))
Try(tkgrab.release(ttcolExtract));Try(tkdestroy(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttcolExtract,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkfocus(entry.colExtract))
Try(tkbind(entry.colExtract, "<Return>",onOK))
Try(tkbind(ttcolExtract, "<Destroy>", function(){Try(tkgrab.release(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttcolExtract))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(colnum <- get("colnum", affylmGUIenvironment))
if(colnum > length(names(mySel))){
Try(tkmessageBox(title="Column extraction",message="You have selected a non existing column!"))
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
Try(tempFileName <- as.vector(unlist(strsplit(tempFileName, "/"))))
Try(if(length(tempFileName) > 1) tempFileName <- tempFileName[length(tempFileName)])
Try(saving.file <- paste("col.",colnum,".from.",tempFileName,".txt",sep=""))
Try(tkmessageBox(title="Column extraction",message="Saving the extracted column."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=saving.file, filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if(!nchar(FileName))
return())
Try(myout <- as.character(as.vector(mySel[,colnum])))
Try(zz <- file(FileName, "w"))
Try(writeLines(myout, con = zz, sep = "\n"))
Try(close(zz))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
#save affy libraries in allylibs dir as new dir in oneChannelPath
"geneExonLibs" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Gene Exon 1.0 ST libraries",message="This routine installs, in a user defined folder,\nall library files needed for analysis of Gene/Exon Affymetrix arrays."))
Try(myWD <- getwd())
#Try(SetWD())
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(libDirLocation <- myinfo[which(myinfo[,1]=="libDirLocation"),2])
Try(if(is.na(libDirLocation)) libDirLocation <- "")
if(libDirLocation != ""){
Try(assign("libDirLocation", libDirLocation, affylmGUIenvironment))
Try(mbVal <- tkmessageBox(title="Gene Exon 1.0 ST libraries",
message="There already a folder defined for Affymetrix libraries.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
} else{
Try(.downloadLibs())
Try(setwd(myWD))
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
Try(.downloadLibs())
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
}
".downloadLibs" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(libDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/affylibs", sep=""))
Try(dir.create(libDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(libDirLocation))
Try(assign("libDirLocation", libDirLocation, affylmGUIenvironment))#directory where affy library files are located
Try(cat("\nBegin downloads of library files.....\n"))
Try(cat("Be patient!\n"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/HuEx.zip", "HuEx.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/HuGene.zip","HuGene.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/MoEx.zip", "MoEx.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/MoGene.zip","MoGene.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/RaEx.zip","RaEx.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/RaGene.zip","RaGene.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/HTA_2.0.zip","HTA_2.0.zip", mode="wb"))
#in file exondata.zip are located transcripts annotation and variant exons
#generated with the function buildingLocalAnnotation()
#and with the function variantExons()
#are zipped and loaded on www.bioinformatica.unito.it to be downloaded in oneChannelGUI affylibs dir
#the first time an exon array is loaded (to be made)
Try(download.file("http://www.bioinformatica.unito.it/downloads/exondata.zip","exondata.zip", mode="wb"))
Try(cat("\nEnd downloads of 7 library files.....\n"))
Try(cat("\nBegin unzip library files.....\n"))
if(.Platform$OS.type=="windows"){
Try(unzip("exondata.zip"))
Try(unzip("HuGene.zip"))
Try(unzip("HuEx.zip"))
Try(unzip("MoEx.zip"))
Try(unzip("MoGene.zip"))
Try(unzip("RaEx.zip"))
Try(unzip("RaGene.zip"))
Try(unzip("HTA_2.0.zip"))
} else{
Try(system(paste("unzip exondata.zip", sep="")))
Try(system(paste("unzip HuGene.zip", sep="")))
Try(system(paste("unzip HuEx.zip")))
Try(system(paste("unzip MoEx.zip")))
Try(system(paste("unzip MoGene.zip")))
Try(system(paste("unzip RaEx.zip")))
Try(system(paste("unzip RaGene.zip")))
Try(system(paste("unzip HTA_2.0.zip")))
}
Try(cat("\nEnd unzip library files.....\n"))
Try(cat("\nLibrary files are ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="libDirLocation"),2] <- libDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
#######################################################################################################
#define the folder where apt tools are locate
"aptFolder" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="APT tools folder",message="Please select the folder where APT tools are located."))
Try(myWD <- getwd())
#Try(SetWD())
Try(aptDir <- get("aptDir",envir=affylmGUIenvironment))
if(is.na(aptDir)){aptDir <- ""}
if(aptDir == ""){
Try(SetED())
Try(aptDir <- getwd())
if(length(grep("apt-probeset-summarize", dir(paste(aptDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="APT tools dir ",message="You have not correctly defined the main folder where APT tools are located!",icon="error"))
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="aptDir"),2] <- aptDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
} else{
Try(mbVal <- tkmessageBox(title="APT tools folder",
message="There already a folder defined for APT tools.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
if(tclvalue(mbVal)=="yes"){
Try(SetED())
Try(aptDir <- getwd())
if(length(grep("apt-probeset-summarize", dir(paste(aptDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="APT tools dir ",message="You have not correctly defined the main folder where APT tools are located!",icon="error"))
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="aptDir"),2] <- aptDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
}
}
# Try(mbVal <- tkmessageBox(title="RefSeq Fasta",
# message="Do you wish to download reference sequence for exon-level analysis?\nIf you answer NO oneChannelGUI you can also do it later. Be patient!",
# icon="question",type="yesno",default="no"
# )#end of tkmessageBox
# )#end of Try(mbVal..
# if(tclvalue(mbVal)=="yes"){
# Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(refseqDownload())
# Try(tkmessageBox(title="APT tools folder",message="Please install the BLAST executable in the apt/blast dir.\nDownload the BAST from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"))
# }
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
###########################################################################################
#define the folder where apt tools are locate
"javaFolder" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="JAVA folder",message="Please select the folder where JAVA is located."))
Try(myWD <- getwd())
#Try(SetWD())
Try(javaDir <- get("javaDir",envir=affylmGUIenvironment))
if(is.na(javaDir)){javaDir <- ""}
if(javaDir == ""){
Try(SetED())
Try(javaDir <- getwd())
#javaDir <- paste('"',javaDir,"/bin/",'"', sep="")
#javabin <- paste(javaDir, "/java -version", sep="")
if(length(grep("java", dir(paste(javaDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="Java dir ",message="You have not correctly defined the main folder where java binary is located!\nIn windows should be C:/somewhere/Java/jre6",icon="error"))
assign("javaDir.Available",FALSE,affylmGUIenvironment)
assign("javaDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="javaDir"),2] <- javaDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("javaDir.Available",TRUE,affylmGUIenvironment)
assign("javaDir", javaDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
} else{
Try(mbVal <- tkmessageBox(title="Java folder",
message="There already a folder defined for Java.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
if(tclvalue(mbVal)=="yes"){
Try(SetED())
Try(javaDir <- getwd())
if(length(grep("java", dir(paste(javaDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="Java dir ",message="You have not correctly defined the main folder where java binary is located!\nIn windows should be C:/somewhere/Java/jre6",icon="error"))
assign("javaDir.Available",FALSE,affylmGUIenvironment)
assign("javaDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="javaDir"),2] <- javaDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("javaDir.Available",TRUE,affylmGUIenvironment)
assign("javaDir", javaDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
}
}
# Try(mbVal <- tkmessageBox(title="RefSeq Fasta",
# message="Do you wish to download reference sequence for exon-level analysis?\nIf you answer NO oneChannelGUI you can also do it later. Be patient!",
# icon="question",type="yesno",default="no"
# )#end of tkmessageBox
# )#end of Try(mbVal..
# if(tclvalue(mbVal)=="yes"){
# Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(refseqDownload())
# Try(tkmessageBox(title="APT tools folder",message="Please install the BLAST executable in the apt/blast dir.\nDownload the BAST from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"))
# }
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
###########################################################################################
"deleteLocalData" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(mbVal <- tkmessageBox(title="Local setting",
message="Do you want to the delete the local setting for Gene Exon arrays analysis?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
} else{
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="libDirLocation"),2] <- "")
Try(myinfo[which(myinfo[,1]=="aptDir"),2] <- "")
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names= F, quote=F))
Try(tkmessageBox(title="Local settings",message="Local setting were reset."))
return()
}
}
################################################################################
#building gene and exon annotation for oneChannelGUI
"buildingLocalAnnotation" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(libDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/affylibs/", sep = ""))
#gathering affy libs and apt tools folders
Try(netaffxUpdates <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/netaffxUpdates.txt", sep=""))
Try(cat(readLines(netaffxUpdates), sep="\n"))
#username
Try(ttGetUserName<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetUserName))
Try(tkgrab.set(ttGetUserName))
Try(tkfocus(ttGetUserName))
Try(tkwm.title(ttGetUserName,"NetAffx User Name"))
Try(tkgrid(tklabel(ttGetUserName,text=" ")))
Try(UserNameText <- "")
Try(Local.UserName <- tclVar(init=UserNameText))
Try(entry.UserName <-tkentry(ttGetUserName,width="30",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.UserName,bg="white"))
Try(tkgrid(tklabel(ttGetUserName,text="Please enter your NetAffx User Name.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.UserName))
onOK <- function()
{
Try(UserNameText <- tclvalue(Local.UserName))
if(nchar(UserNameText)==0)
UserNameText <- "Unselected"
Try(assign("UserNameText",UserNameText,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$UserNameTcl) <- UserNameText)
Try(tkgrab.release(ttGetUserName));Try(tkdestroy(ttGetUserName));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetUserName,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetUserName,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetUserName,text=" ")))
Try(tkfocus(entry.UserName))
Try(tkbind(entry.UserName, "<Return>",onOK))
Try(tkbind(ttGetUserName, "<Destroy>", function(){Try(tkgrab.release(ttGetUserName));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetUserName))
Try(tkfocus(.affylmGUIglobals$ttMain))
#########################
#password
Try(ttGetUserPw<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetUserPw))
Try(tkgrab.set(ttGetUserPw))
Try(tkfocus(ttGetUserPw))
Try(tkwm.title(ttGetUserPw,"NetAffx User Password"))
Try(tkgrid(tklabel(ttGetUserPw,text=" ")))
Try(UserPwText <- "")
Try(Local.UserPw <- tclVar(init=UserPwText))
Try(entry.UserPw <-tkentry(ttGetUserPw,width="20",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.UserPw,bg="white"))
Try(tkgrid(tklabel(ttGetUserPw,text="Please enter your NetAffx User Password.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.UserPw))
onOK <- function()
{
Try(UserPwText <- tclvalue(Local.UserPw))
if(nchar(UserPwText)==0)
UserPwText <- "Unselected"
Try(assign("UserPwText",UserPwText,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$UserPwTcl) <- UserPwText)
Try(tkgrab.release(ttGetUserPw));Try(tkdestroy(ttGetUserPw));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetUserPw,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetUserPw,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetUserPw,text=" ")))
Try(tkfocus(entry.UserPw))
Try(tkbind(entry.UserPw, "<Return>",onOK))
Try(tkbind(ttGetUserPw, "<Destroy>", function(){Try(tkgrab.release(ttGetUserPw));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetUserPw))
Try(tkfocus(.affylmGUIglobals$ttMain))
#########################
Try(username.tmp <- get("UserNameText", env=affylmGUIenvironment))
Try(userpw.tmp <- get("UserPwText", env=affylmGUIenvironment))
if(username.tmp != "Unselected" & userpw.tmp != "Unselected"){
Try(rsrc <- NetAffxResource(user = username.tmp, password = userpw.tmp, affxLicence = "BIOCON0808"))
Try(rsrc)
#selecting the annotation to be updated
Try(ttIfDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttIfDialog))
Try(tkgrab.set(ttIfDialog))
Try(tkfocus(ttIfDialog))
Try(tkwm.title(ttIfDialog,"Defining the Gene level annotation file to be updated"))
Try(tkgrid(tklabel(ttIfDialog,text=" ")))
Try(frame1 <- tkframe(ttIfDialog,relief="groove",borderwidth=2))
Try(HowManyQuestion1 <- tklabel(frame1,text="Select the genechip of interest",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(HowManyQuestion1))
Try(tkgrid.configure(HowManyQuestion1,columnspan=2,sticky="w"))
Try(netaffxTcl <- tclVar("none"))
Try(I1.but <- tkradiobutton(frame1,text="Human exon genechip: HuEx",variable=netaffxTcl,value="HuEx",font=.affylmGUIglobals$affylmGUIfont2))
# Try(I2.but <- tkradiobutton(frame1,text="Human gene genechip: HuGene",variable=netaffxTcl,value="HuGene-",font=.affylmGUIglobals$affylmGUIfont2))
Try(I3.but <- tkradiobutton(frame1,text="Mouse exon genechip: MoEx",variable=netaffxTcl,value="MoEx",font=.affylmGUIglobals$affylmGUIfont2))
# Try(I4.but <- tkradiobutton(frame1,text="Mouse gene genechip: MoGene",variable=netaffxTcl,value="MoGene-",font=.affylmGUIglobals$affylmGUIfont2))
Try(I5.but <- tkradiobutton(frame1,text="Rat exon genechip: RaEx",variable=netaffxTcl,value="RaEx",font=.affylmGUIglobals$affylmGUIfont2))
# Try(I6.but <- tkradiobutton(frame1,text="Rat gene genechip: RaGene",variable=netaffxTcl,value="RaGene-",font=.affylmGUIglobals$affylmGUIfont2))
Try(I7.but <- tkradiobutton(frame1,text="None",variable=netaffxTcl,value="none",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(I1.but,sticky="w"))
# Try(tkgrid(I2.but,sticky="w"))
Try(tkgrid(I3.but,sticky="w"))
# Try(tkgrid(I4.but,sticky="w"))
Try(tkgrid(I5.but,sticky="w"))
# Try(tkgrid(I6.but,sticky="w"))
Try(tkgrid(I7.but,sticky="w"))
Try(tkgrid.configure(HowManyQuestion1,I1.but,I3.but,I5.but,I7.but,sticky="w"))
Try(onOK <- function()
{
Try(ReturnNetaffx <<- as.character(tclvalue(netaffxTcl)))
Try(tkgrab.release(ttIfDialog))
Try(tkdestroy(ttIfDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
})
Try(frame3 <- tkframe(ttIfDialog,borderwidth=2))
Try(onCancel <- function() {
Try(tkgrab.release(ttIfDialog))
Try(tkdestroy(ttIfDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
})
Try(OK.but <-tkbutton(frame3,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(frame3,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(frame3,text=" "),OK.but,Cancel.but,tklabel(frame3,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" "),frame1,tklabel(ttIfDialog,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" "),frame3,tklabel(ttIfDialog,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" ")))
Try(tkgrid.configure(frame1,frame3,sticky="w"))
Try(tkfocus(ttIfDialog))
Try(tkbind(ttIfDialog, "<Destroy>", function() {Try(tkgrab.release(ttIfDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttIfDialog))
if(ReturnNetaffx == "none"){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(ReturnNetaffx != "none"){
Try(annos <- rsrc[[grep(ReturnNetaffx, names(rsrc))]])
#gene level
Try(anno <- affxAnnotation(annos)[[grep("Transcript Cluster Annotations, CSV", affxDescription(rsrc[[grep(ReturnNetaffx, names(rsrc))]]))]]) #"transcript clusters Annotation, CSV Format"
Try(df <- readAnnotation(rsrc, annotation = anno, content=FALSE))
Try(df1 <- as.character(unlist(strsplit(df, ".zip"))))
Try(df1 <- as.character(unlist(strsplit(df1,'/'))))
Try(df1 <- df1[length(df1)])
Try(conn <- unz(df, df1))
Try(tmp <- readLines(conn, n=500))
Try(myskip <- grep("transcript_cluster_id", tmp))
Try(df.ann <- read.csv(conn, skip= (myskip - 1), header=T, as.is=T))
Try(df.ann <- df.ann[,which(names(df.ann)%in%c("probeset_id", "gene_assignment"))])
#IMPORTANT to build the GENE level oneChannelGUI annotation file I use only the first assignment mapped on the gen_assignment field in the annotation files
geneAnnExtraction <- function(x){
mx <- strsplit(x, '//')
mx <- as.vector(unlist(mx))
if(length(mx) >= 4){
mx <- mx[1:4]
mxtmp <- gsub(" ", "", mx[c(1:2,4)])
mx <- c(mxtmp[1:2], mx[3], mxtmp[3])
return(mx)
} else{
mx <- rep(NA, 4)
return(mx)
}
}
myann <- sapply(df.ann[,2], geneAnnExtraction)
myann <- t(myann)
rownames(myann) <- df.ann[,1]
df.ann <- cbind(df.ann[,1], myann)
df.ann <- as.data.frame(df.ann)
names(df.ann) <- c("PROBESETID","ACC","SYMBOL","DESCRIPTION","CYTOBAND")
#exon level
if(length(grep("Probeset Annotations, CSV Format", affxDescription(rsrc[[grep(ReturnNetaffx, names(rsrc))]]))) > 0){
Try(annops <- affxAnnotation(annos)[[grep("Probeset Annotations, CSV Format", affxDescription(rsrc[[grep(ReturnNetaffx, names(rsrc))]]))]]) #"exon probe set level Annotation, CSV Format"
Try(dfps <- readAnnotation(rsrc, annotation = annops, content=FALSE))
Try(df1ps <- as.character(unlist(strsplit(dfps, ".zip"))))
Try(df1ps <- as.character(unlist(strsplit(df1ps,'/'))))
Try(df1ps <- df1ps[length(df1ps)])
Try(connps <- unz(dfps, df1ps))
Try(tmpps <- readLines(connps, n=500))
Try(myskipps <- grep("probeset_id", tmpps))
Try(df.annps <- read.csv(connps, skip= (myskipps - 1), header=T, as.is=T))
Try(df.annps <- df.annps[,which(names(df.annps)%in%c("probeset_id", "seqname", "strand", "start", "stop", "transcript_cluster_id","level"))])
Try(names(df.annps) <- c("EPROBESETID", "CHR", "STRAND", "START", "STOP", "GPROBESETID","ANNLEVEL"))
}
####
if(ReturnNetaffx == "HuEx"){
huex.annotation <- df.ann
save(huex.annotation, file="huex.annotation.rda", ascii=T)
#hs exon-level probesets
cat("\nCreating annotation for Hs exon-level probesets. \nBased on USCS golden path data from hg19 genome release\n")
download.file("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/affyAllExonProbes.txt.gz", "affyAllExonProbes.txt.gz", mode="wb")
cat(".")
zz <- gzfile("affyAllExonProbes.txt.gz","r")
cat(".")
tmp <- readLines(con=zz)
cat(".")
close(zz)
tmp <- strsplit(tmp, "\t")
cat(".")
tmp <- as.data.frame(do.call(rbind, tmp), stringsAsFactors=F)
cat(".")
names(tmp) <- c("X", "CHR", "START", "STOP", "NAME", "SCORE", "STRAND")
tmp1 <- tmp$NAME
tmp1 <- strsplit(as.character(tmp1), "\\|")
cat(".")
eid <- sapply(tmp1, function(x)x[1])
cat(".")
eann <- sapply(tmp1, function(x)x[2])
cat(".")
crosshybhuex.annotation <- data.frame(eid, as.character(tmp[,2]), as.character(tmp[,3]), as.character(tmp[,4]), as.character(tmp[,7]), eann, as.character(tmp[,6]), stringsAsFactors=F)
names(crosshybhuex.annotation) <- c("EPROBESETID", "CHR", "START", "STOP", "STRAND", "ANNLEVEL", "SCORE")
cat(".")
df.annps <- df.annps[which(df.annps$EPROBESETID %in% crosshybhuex.annotation$EPROBESETID),]
crosshybhuex.annotation <- crosshybhuex.annotation[which(crosshybhuex.annotation$EPROBESETID %in% df.annps$EPROBESETID),]
df.annps <- df.annps[order(df.annps$EPROBESETID),]
crosshybhuex.annotation <- crosshybhuex.annotation[order(crosshybhuex.annotation$EPROBESETID),]
if(identical(as.character(df.annps$EPROBESETID), crosshybhuex.annotation$EPROBESETID)){
crosshybhuex.annotation <- cbind(crosshybhuex.annotation$EPROBESETID, as.character(df.annps$GPROBESETID), crosshybhuex.annotation[,2:dim(crosshybhuex.annotation)[2]])
names(crosshybhuex.annotation)[1] <- "EPROBESETID"
names(crosshybhuex.annotation)[2] <- "GPROBESETID"
save(crosshybhuex.annotation, file="crosshybhuex.annotation.rda")
} else{
cat("\nInternal error in buildingLocalAnnotation function. \nPlease report to oneChannelGUI maintainer raffaele.calogero@unito.it\n")
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
if(ReturnNetaffx == "HuGene-"){
hugene.annotation <- df.ann
save(hugene.annotation, file="hugene.annotation.rda", ascii=T)
}
if(ReturnNetaffx == "MoEx"){
moex.annotation <- df.ann
save(moex.annotation, file="moex.annotation.rda", ascii=T)
#mm exon-level probesets
cat("\nCreating annotation for Mm exon-level probesets. \nBased on USCS golden path data from mm9 genome release\n")
download.file("ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/affyAllExonProbes.txt.gz", "affyAllExonProbes.txt.gz", mode="wb")
cat(".")
zz <- gzfile("affyAllExonProbes.txt.gz","r")
cat(".")
tmp <- readLines(con=zz)
cat(".")
close(zz)
tmp <- strsplit(tmp, "\t")
cat(".")
tmp <- as.data.frame(do.call(rbind, tmp), stringsAsFactors=F)
cat(".")
names(tmp) <- c("X", "CHR", "START", "STOP", "NAME", "SCORE", "STRAND")
tmp1 <- tmp$NAME
tmp1 <- strsplit(as.character(tmp1), "\\|")
cat(".")
eid <- sapply(tmp1, function(x)x[1])
cat(".")
eann <- sapply(tmp1, function(x)x[2])
cat(".")
crosshybmoex.annotation <- data.frame(eid, as.character(tmp[,2]), as.character(tmp[,3]), as.character(tmp[,4]), as.character(tmp[,7]), eann, as.character(tmp[,6]), stringsAsFactors=F)
names(crosshybmoex.annotation) <- c("EPROBESETID", "CHR", "START", "STOP", "STRAND", "ANNLEVEL", "SCORE")
cat(".")
df.annps <- df.annps[which(df.annps$EPROBESETID %in% crosshybmoex.annotation$EPROBESETID),]
crosshybmoex.annotation <- crosshybmoex.annotation[which(crosshybmoex.annotation$EPROBESETID %in% df.annps$EPROBESETID),]
df.annps <- df.annps[order(df.annps$EPROBESETID),]
crosshybmoex.annotation <- crosshybmoex.annotation[order(crosshybmoex.annotation$EPROBESETID),]
if(identical(as.character(df.annps$EPROBESETID), crosshybmoex.annotation$EPROBESETID)){
crosshybmoex.annotation <- cbind(crosshybmoex.annotation$EPROBESETID, as.character(df.annps$GPROBESETID), crosshybmoex.annotation[,2:dim(crosshybmoex.annotation)[2]])
names(crosshybmoex.annotation)[1] <- "EPROBESETID"
names(crosshybmoex.annotation)[2] <- "GPROBESETID"
save(crosshybmoex.annotation, file="crosshybmoex.annotation.rda")
} else{
cat("\nInternal error in buildingLocalAnnotation function. \nPlease report to oneChannelGUI maintainer raffaele.calogero@unito.it\n")
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
if(ReturnNetaffx == "MoGene-"){
mogene.annotation <- df.ann
save(mogene.annotation, file="mogene.annotation.rda", ascii=T)
}
if(ReturnNetaffx == "RaEx"){
raex.annotation <- df.ann
save(raex.annotation, file="raex.annotation.rda", ascii=T)
#rm exon-level probesets
cat("\nCreating annotation for Rn exon-level probesets. \nBased on USCS golden path data from rn4 genome release\n")
download.file("ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/affyAllExonProbes.txt.gz", "affyAllExonProbes.txt.gz", mode="wb")
cat(".")
zz <- gzfile("affyAllExonProbes.txt.gz","r")
cat(".")
tmp <- readLines(con=zz)
cat(".")
close(zz)
tmp <- strsplit(tmp, "\t")
cat(".")
tmp <- as.data.frame(do.call(rbind, tmp), stringsAsFactors=F)
cat(".")
names(tmp) <- c("X", "CHR", "START", "STOP", "NAME", "SCORE", "STRAND")
tmp1 <- tmp$NAME
tmp1 <- strsplit(as.character(tmp1), "\\|")
cat(".")
eid <- sapply(tmp1, function(x)x[1])
cat(".")
eann <- sapply(tmp1, function(x)x[2])
cat(".")
crosshybraex.annotation <- data.frame(eid, as.character(tmp[,2]), as.character(tmp[,3]), as.character(tmp[,4]), as.character(tmp[,7]), eann, as.character(tmp[,6]), stringsAsFactors=F)
names(crosshybraex.annotation) <- c("EPROBESETID", "CHR", "START", "STOP", "STRAND", "ANNLEVEL", "SCORE")
cat(".")
df.annps <- df.annps[which(df.annps$EPROBESETID %in% crosshybraex.annotation$EPROBESETID),]
crosshybraex.annotation <- crosshybraex.annotation[which(crosshybraex.annotation$EPROBESETID %in% df.annps$EPROBESETID),]
df.annps <- df.annps[order(df.annps$EPROBESETID),]
crosshybraex.annotation <- crosshybraex.annotation[order(crosshybraex.annotation$EPROBESETID),]
if(identical(as.character(df.annps$EPROBESETID), crosshybraex.annotation$EPROBESETID)){
crosshybraex.annotation <- cbind(crosshybraex.annotation$EPROBESETID, as.character(df.annps$GPROBESETID), crosshybraex.annotation[,2:dim(crosshybraex.annotation)[2]])
names(crosshybraex.annotation)[1] <- "EPROBESETID"
names(crosshybraex.annotation)[2] <- "GPROBESETID"
save(crosshybraex.annotation, file="crosshybraex.annotation.rda")
} else{
cat("\nInternal error in buildingLocalAnnotation function. \nPlease report to oneChannelGUI maintainer raffaele.calogero@unito.it\n")
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
if(ReturnNetaffx == "RaGene-"){
ragene.annotation <- df.ann
save(ragene.annotation, file="ragene.annotation.rda", ascii=T)
}
Try(tkmessageBox(title="Annotation data update",message=paste("\n", ReturnNetaffx, "annotation file was correctly updated in oneChannelGUI\n"),type="ok",icon="info"))
Try(zz <- file(netaffxUpdates, "a")) # open an output file connection
Try(writeLines(paste(ReturnNetaffx, "annotation file was updated on", as.character(Sys.Date())), zz))
Try(close(zz))
}
} else {
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkmessageBox(title="Annotation update",message="User or password for netaffx was not inserted!",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
################################################################################
"refseqDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(aptDir <- get("aptDir",envir=affylmGUIenvironment))
Try(home <- getwd())
Try(blastDir <- paste(aptDir, "/blast/", sep=""))
Try(setwd(blastDir))
Try(cat("\nBegin downloads of fasta files.....\n"))
Try(cat("Be patient!\n"))
#require(Biostrings) || stop("library Biostrings could not be found !")
Try(download.file("ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz", "human.rna.fna.gz", mode="wb"))
#Try(refseq <- read.DNAStringSet(zz, "fasta"))
#Try(write.XStringSet(refseq, file="hs.fa", format="fasta"))
Try(download.file("ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.rna.fna.gz", "mouse.rna.fna.gz", mode="wb"))
Try(download.file("ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.rna.fna.gz", "rat.rna.fna.gz", mode="wb"))
Try(cat("\nEnd downloads of 3 RefSeq fasta files.....\n"))
Try(mbVal <- tkmessageBox(title="RefSeq Fasta",
message=paste("Do you wish to unpack manually the gz files in ", getwd(), "\n If you answer NO oneChannelGUI will handle unpacking,\nbut the procedure can be quite long. Be patient!"),
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="yes"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(cat("\nRefSeq fasta gz files are located in ", getwd(),"\n"))
Try(setwd(home))
return()
}
Try(zz <- gzfile("human.rna.fna.gz", "r"))
Try(refseq <- readFASTA(zz, strip.desc=TRUE))
Try(writeFASTA(refseq, file="human.rna.fna", width=80))
Try(zz <- gzfile("mouse.rna.fna.gz", "r"))
Try(refseq <- readFASTA(zz, strip.desc=TRUE))
Try(writeFASTA(refseq, file="mouse.rna.fna", width=80))
Try(zz <- gzfile("rat.rna.fna.gz", "r"))
Try(refseq <- readFASTA(zz, strip.desc=TRUE))
Try(writeFASTA(refseq, file="rat.rna.fna", width=80))
Try(cat("\nRefSeq fasta files are ready to be used in ", getwd(),"\n"))
Try(setwd(home))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
#"madscrosshybDownload" <- function(){
# Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
# Try(home <- getwd())
# Try(libDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/affylibs/", sep = ""))
# Try(setwd(libDirLocation))
#gathering affy libs and apt tools folders
# Try(cat("\nBegin downloads of MADS CrossHyb data.....\n"))
# Try(cat("Be patient!\n"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Human_CrossHyb.txt", "Human_CrossHyb.txt", mode="w"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Mouse_CrossHyb.txt", "Mouse_CrossHyb.txt", mode="w"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Human_CrossHyb_core.txt", "Human_CrossHyb_core.txt", mode="w"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Mouse_CrossHyb_core.txt", "Mouse_CrossHyb_core.txt", mode="w"))
# Try(cat("\nEnd downloads of Human and Mouse MADS crosshyb files.....\n"))
# hs <- read.table("Human_CrossHyb_core.txt", sep="\t", header=T, as.is=T)
#building a mps without crosshyb exon probe sets, selecting bad probes on the basis of MADS approach
# mm <- read.table("Mouse_CrossHyb_core.txt", sep="\t", header=T, as.is=T)
# crossRefs <- which(mm$MaxCorrCrossHybRefseqEvidence > 0)
#hist(MaxCorrWithCrossHybTranscript[crossRefs])
# mm.cross <- mm[crossRefs,]
# mm.cross <- mm.cross[which(mm.cross$MaxCorrWithCrossHybTranscript >= 0.2),]
# mps <- mps[grep("core", mps)]
# mps <- mps[grep("mps$", mps)]
# mps.df <- read.table(mps, sep="\t", header=T, as.is=T)
# for(i in 1:dim(mm.cross)[1]){
# tmp <- mps.df[which(mps.df[,2] == mm.cross$TranscriptClusterId[1]),]
# tmp.p <- as.character(unlist(strsplit(as.character(tmp[3])," ")))
# tmp.p <- tmp.p[which(tmp.p != as.character(mm.cross$ProbesetId[1]))]
# tmp.p <- paste(tmp.p, collapse=" ")
# mps.df[which(mps.df[,2] == mm.cross$TranscriptClusterId[1]),3] <- tmp.p
#write.table.....
# }
# Try(setwd(home))
#}
################################################################################
"updateLibs" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(mbVal <- tkmessageBox(title="Updating Bioconductor Libraries",
message="You are updating all Bioconductor libraries files. \nThe process might take some time!", icon="question",type="yesno",default="yes"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
################################################################################
#inernal function used in variantExons
".outvsp" <- function(ov, affyR, vspR, chr, genome){
# myout <- list("affyname"=names(affyR)[ov[2]],"affystart"=start(affyR)[ov[2]],
# "affyend"=end(affyR)[ov[2]], "affywidth"=width(affyR)[ov[2]],
# "vspname"=names(vspR)[ov[1]],"vspstart"=start(vspR)[ov[1]],
# "vspend"=end(vspR)[ov[1]], "vspwidth"=width(vspR)[ov[1]])
affyname <- strsplit(names(affyR)[ov[2]],"\\.")[[1]][1]
affystrand <- strsplit(names(affyR)[ov[2]],"\\.")[[1]][2]
vspname <- strsplit(names(vspR)[ov[1]],"\\.")[[1]][1]
vspstrand <- strsplit(names(vspR)[ov[1]],"\\.")[[1]][2]
myout <- c(affyname,start(affyR)[ov[2]],end(affyR)[ov[2]], width(affyR)[ov[2]], affystrand,
vspname, start(vspR)[ov[1]], end(vspR)[ov[1]], width(vspR)[ov[1]], vspstrand,as.character(sub("chr","", chr)), genome)
}
"variantExons" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#require(IRanges) || stop("\nMissing IRanges library\n")
#loading exon level annotation
for(j in c("huex","moex","raex")){
out.all <- NULL
if(j=="huex"){
genome <- "organism=Human&version=hg19"
data(HuExExonProbesetLocation)
subject<- get("HuExExonProbesetLocation",envir=.GlobalEnv)
}
if(j=="moex"){
genome <- "organism=Mouse&version=mm9"
data(MoExExonProbesetLocation)
subject<- get("MoExExonProbesetLocation",envir=.GlobalEnv)
}
if(j=="raex"){
genome <- "organism=Rattus&version=rn4"
data(RaExExonProbesetLocation)
subject<- get("RaExExonProbesetLocation",envir=.GlobalEnv)
}
#retrieving variant exon file
vsp.file <- paste("http://www6.unito.it/RRE/Query/ensembleQuery.php?", genome, sep="")
tmpfile <- tempfile(tmpdir = getwd())
download.file(vsp.file, tmpfile, mode="w")
query <- read.table(tmpfile, header=T, as.is=T, sep="\t")
chr <- unique(query$chromosome)
chr <- chr[setdiff(seq(1,length(chr)),grep("_", chr))]
exoncore <- subject[which(subject$ANNLEVEL == "core"),]
for(i in chr){
vsp.tmp <- query[which(query$chromosome==i),]
vspRanges <- IRanges(start=vsp.tmp$start, end=vsp.tmp$end, names=paste(vsp.tmp$"transcript_id", vsp.tmp$"strand", sep="."))
#retrieving exon level annotation
exonchr <- subject[which(subject$CHR == i),]
affyRanges <- IRanges(start=as.numeric(exonchr$START), end=as.numeric(exonchr$STOP), names=paste(as.character(exonchr$EPROBESETID),exonchr$STRAND,sep="."))
ov <- findOverlaps(affyRanges, query=vspRanges)
ov <- matchMatrix(ov)
out <- apply(ov, 1,.outvsp, affyR=affyRanges, vspR=vspRanges, chr=i, genome=genome)
out <- t(out)
out <- out[which(out[,5] == out[,10]),]
out.all <- rbind(out.all, out)
}
dimnames(out.all)[[2]] <- c("affyname", "affystart", "affyend", "affywidth", "affystrand","vspname", "vspstart", "vspend", "vspwidth","vspstrand","chr","genome")
if(j == "huex"){
huex.variantexons <- out.all
save(huex.variantexons, file="huex.variantexons.rda", ascii=T)
cat("\n huex.variantexons.rda variant exons dataset is now ready to be now copied in oneChannelGUI data dir\n")
}
if(j == "moex"){
moex.variantexons <- out.all
save(moex.variantexons, file="moex.variantexons.rda", ascii=T)
cat("\n moex.variantexons.rda variant exons dataset is now ready to be now copied in oneChannelGUI data dir\n")
}
if(j == "raex"){
raex.variantexons <- out.all
save(raex.variantexons, file="raex.variantexons.rda", ascii=T)
cat("\n raex.variantexons.rda variant exons dataset is now ready to be now copied in oneChannelGUI data dir\n")
}
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
"exportFASTA" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#require(Biostrings) || stop("\nMissing Biostrings library\n")
#which organism
Try(ttGetOrganism <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetOrganism))
Try(tkgrab.set(ttGetOrganism))
Try(tkfocus(ttGetOrganism))
Try(tkwm.title(ttGetOrganism,"Which organism"))
Try(tkgrid(tklabel(ttGetOrganism,text=" ")))
Try(ttGetOrganismTcl <- tclVar("hs"))
Try(rbIQR.5 <- tkradiobutton(ttGetOrganism,text="H. sapiens",variable=ttGetOrganismTcl,value="hs",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.25<-tkradiobutton(ttGetOrganism,text="M. musculus",variable=ttGetOrganismTcl,value="mm",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.1<-tkradiobutton(ttGetOrganism,text="R. norvegicus",variable=ttGetOrganismTcl,value="rn",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.15<-tkradiobutton(ttGetOrganism,text="B. taurus",variable=ttGetOrganismTcl,value="bo",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.5))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.25))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.1))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.15))
Try(tkgrid.configure(rbIQR.5,rbIQR.25,rbIQR.1, rbIQR.15,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),tklabel(ttGetOrganism,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetOrganism));Try(tkdestroy(ttGetOrganism));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetOrganismTcl));Try(tkgrab.release(ttGetOrganism));Try(tkdestroy(ttGetOrganism));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetOrganism,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetOrganism,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),OK.but,Cancel.but, tklabel(ttGetOrganism,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetOrganism,text=" ")))
Try(tkbind(ttGetOrganism,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetOrganism));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetOrganism))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#miRbase19
Try(load(paste(find.package(package="oneChannelGUI"),"/data/hairpin.rda",sep="")))
if(ReturnVal == ""){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else if (ReturnVal == "hs"){
#hsa precursor
Try(hsfa <- hairpin[grep("^hsa-",names(hairpin))])
Try(writeXStringSet(hsfa, file="ncHs.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncHs.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
} else if (ReturnVal == "mm"){
#mmu precursor
Try(mmfa <- hairpin[grep("^hsa-",names(hairpin))])
Try(writeXStringSet(mmfa, file="ncMm.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncMm.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
} else if (ReturnVal == "rn"){
#rno precursor
Try(rnfa <- hairpin[grep("^rno-",names(hairpin))])
Try(writeXStringSet(rnfa, file="ncRn.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncRn.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
else if (ReturnVal == "bo"){
#bta precursor
Try(bofa <- hairpin[grep("^bta-",names(hairpin))])
Try(writeXStringSet(bofa, file="ncBo.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncBo.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
}
################################################################################
"ngsperlDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="NGS perl scripts",message="This routine creates a folder for the perl scripts used to reformat NGS primary mapping output."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(myWD <- getwd())
#Try(SetWD())
Try(perlDirLocation <- get("perlDirLocation",envir=affylmGUIenvironment))
if(perlDirLocation != ""){
Try(mbVal <- tkmessageBox(title="NGS perl scripts",
message="There already a folder defined for NGS perl scripts.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
}
Try(perlDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/ngsperl", sep=""))
Try(dir.create(perlDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(perlDirLocation))
Try(assign("perlDirLocation", perlDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(cat("\nBegin downloads of NGS scripts.....\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/ngsperl.zip/download", "ngsperl.zip", mode="wb"))
if(.Platform$OS.type=="windows"){
Try(unzip("ngsperl.zip"))
# Try(setwd("ngsperl"))
# Try(system('XCOPY /S *.* ..'))
# Try(setwd(".."))
} else{
Try(system(paste("unzip ngsperl.zip", sep="")))
# Try(setwd("ngsperl"))
# Try(system("mv * .."))
# Try(setwd(".."))
}
Try(cat("\nEnd unzip NGS scripts.....\n"))
Try(cat("\nNGS scripts are ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="perlDirLocation"),2] <- perlDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("perlDirLocation", perlDirLocation, affylmGUIenvironment))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
}
################################################################################
"meVDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="meV software",message="This routine creates a folder to install the meV software."))
Try(myWD <- getwd())
#Try(SetWD())
Try(meVDirLocation.Available <- get("meVDirLocation.Available",envir=affylmGUIenvironment))
if(meVDirLocation.Available){
Try(mbVal <- tkmessageBox(title="meV software",
message="There already a folder defined for meV software.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
}
Try(meVDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/meV", sep=""))
Try(dir.create(meVDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(meVDirLocation))
Try(assign("meVDirLocation", meVDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(cat("\nBegin downloads of meV.....\n"))
#defining which program to be downloaded
Try(ttGetMev <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetMev))
Try(tkgrab.set(ttGetMev))
Try(tkfocus(ttGetMev))
Try(tkwm.title(ttGetMev,"Which OS are you using?"))
Try(tkgrid(tklabel(ttGetMev,text=" ")))
Try(ttGetMevTcl <- tclVar("win"))
Try(rbIQR.win <- tkradiobutton(ttGetMev,text="windows ",variable=ttGetMevTcl,value="win",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mac<-tkradiobutton(ttGetMev,text="mac ",variable=ttGetMevTcl,value="mac",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.linux<-tkradiobutton(ttGetMev,text="linux ",variable=ttGetMevTcl,value="linux",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetMev,text=" "),rbIQR.win))
Try(tkgrid(tklabel(ttGetMev,text=" "),rbIQR.mac))
Try(tkgrid(tklabel(ttGetMev,text=" "),rbIQR.linux))
Try(tkgrid.configure(rbIQR.win,rbIQR.mac,rbIQR.linux, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetMev,text=" "),tklabel(ttGetMev,text=" ")))
Try(ReturnVal <- "win")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetMev));Try(tkdestroy(ttGetMev));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetMevTcl));Try(tkgrab.release(ttGetMev));Try(tkdestroy(ttGetMev));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetMev,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetMev,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetMev,text=" "),OK.but,Cancel.but, tklabel(ttGetMev,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetMev,text=" ")))
Try(tkbind(ttGetMev,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetMev));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetMev))
if(ReturnVal=="win"){
Try(download.file("http://sourceforge.net/projects/mev-tm4/files/mev-tm4/MeV%204.8/MeV_4_8_0_r2721_win.zip/download", "mev.zip", mode="wb"))
Try(unzip("mev.zip"))
Try(setwd("MeV_4_8_0"))
Try(system('XCOPY /S *.* ..'))
Try(setwd(".."))
Try(cat("\nThe MeV downloaded version is MeV_4_8_0\n"))
} else if (ReturnVal=="mac"){
Try(download.file("http://sourceforge.net/projects/mev-tm4/files/mev-tm4/MeV%204.8/MeV_4_8_0_r2721_mac.tgz/download", "mev.tgz", mode="wb"))
Try(system(paste("gzip -d ","mev.tgz", sep="")))
Try(system(paste("tar xvf ","mev.tar", sep="")))
Try(cat("\nThe MeV downloaded version is MeV_4_8_0\n"))
Try(setwd("MeV_4_8_0"))
Try(system("cp -fR * .."))
Try(setwd(".."))
Try(system("rm -fR MeV_4_8_0"))
} else if (ReturnVal=="linux"){
Try(download.file("http://sourceforge.net/projects/mev-tm4/files/mev-tm4/MeV%204.8/MeV_4_8_0_r2721_linux.tar.gz/download", "mev.tar.gz", mode="wb"))
Try(system(paste("gzip -d ","mev.tar.gz", sep="")))
Try(system(paste("tar xvf ","mev.tar", sep="")))
Try(cat("\nThe MeV downloaded version is MeV_4_8_0\n"))
Try(setwd("MeV_4_8_0"))
Try(system("cp -fR * .."))
Try(setwd(".."))
}
Try(cat("\nEnd unzip meV files.....\n"))
Try(cat("\nMeV software is ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="meVDirLocation"),2] <- meVDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("meVDirLocation", meVDirLocation, affylmGUIenvironment))
assign("meVDirLocation.Available",TRUE,affylmGUIenvironment)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
}
################################################################################
#external package info
"extPckInfo" <- function(){
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(tmp <- system("perl -v 2>&1", intern = T))
Try(if(length(tmp) > 0) perl.version <- tmp[2])
# Try(tmp <- system("python -V 2>&1", intern = T))
# Try(if(length(tmp) > 0) python.version <- tmp)
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(perlDirLocation <- get("perlDirLocation",envir=affylmGUIenvironment))
# Try(pythonDirLocation <- get("pythonDirLocation",envir=affylmGUIenvironment))
Try(bowtieRefs <- get("bowtieRefs",envir=affylmGUIenvironment))
Try(installed <- names(bowtieRefs)[which(bowtieRefs=="Y")])
Try(tkmessageBox(title="External Packages associated to oneChannelGUI",message=paste("Affymetrix libraries: ", myinfo[1,2],
"\nAPT tools: ",myinfo[2,2],
"\nmeV clustering tool: ",myinfo[3,2],
"\nBowtie short reads aligner: ",myinfo[4,2],
"\nJava: ",myinfo[5,2],
"\nBowtie genomes: ", paste(installed, collapse=", "),
"\nPerl software: ", perl.version,
"\nPerl scripts: ", perlDirLocation,
"\n",sep="")))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
"combining2eSet" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="combining two datasets",message="This routine combines two matrices having the same number of row and the same row identifiers."))
Try(tempFileName1 <- tclvalue(tkgetOpenFile(filetypes = "{{Text Files} {.txt}} {{All files} *}")))
if (!nchar(tempFileName1)) {
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(mySel1 <- read.table(tempFileName1, sep = "\t", header = T, as.is = TRUE, row.names=1))
Try(tempFileName2 <- tclvalue(tkgetOpenFile(filetypes = "{{Text Files} {.txt}} {{All files} *}")))
if (!nchar(tempFileName2)) {
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(mySel2 <- read.table(tempFileName2, sep = "\t", header = T, as.is = TRUE, row.names=1))
Try(mySel1 <- mySel1[order(rownames(mySel1)),])
Try(mySel2 <- mySel2[order(rownames(mySel2)),])
if(identical(rownames(mySel1), rownames(mySel2))){
tempFileName1 <- unlist(strsplit(tempFileName1, "/"))
tempFileName1 <- tempFileName1[length(tempFileName1)]
tempFileName1 <- sub(".txt$", "", tempFileName1)
tempFileName2 <- unlist(strsplit(tempFileName2, "/"))
tempFileName2 <- tempFileName2[length(tempFileName2)]
tempFileName2 <- sub(".txt$", "", tempFileName2)
tempFileName <- paste(tempFileName1, "_", tempFileName2,".txt",sep="")
Try(mySel <- cbind(mySel1, mySel2))
Try(write.table(mySel, file = tempFileName, sep = "\t", quote = FALSE, col.names = NA))
Try(tkmessageBox(title="Combining two datasets",message=paste("The combined dataset is available in",getwd(),"as",tempFileName,sep="\n")))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
} else{
Try(tkmessageBox(title="Combining datasets",message="The two datasets do not have the same row identifiers.\nThey cannot be combined!",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
#using bowtieDownload I can also call the function to download or build the ref genomes for bowtie
#alos downloading tophat and cufflinks
"bowtieDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(require(Biostrings) || stop("library Biostrings could not be found !"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(myWD <- getwd())
Try(tkmessageBox(title="Bowtie primary mapping of short reads",message="This routine creates a folder to install the bowtie software and \nPicard tools to handle SAM files."))
# Try(libDirLocation <- get("libDirLocation",envir=affylmGUIenvironment))
# if(libDirLocation == ""){
# Try(.downloadLibs())
# Try(setwd(myWD))
# Try(tkfocus(.affylmGUIglobals$ttMain))
# }
Try(binDir.Available <- get("binDir.Available",envir=affylmGUIenvironment))
if(!binDir.Available){
Try(setBinDir())
}
#download fastQC
Try(cat("\nDownloading the fastQC java tool for qc analysis of fastq files\n"))
Try(fastqcDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/FastQC", sep=""))
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(setwd(path.package("oneChannelGUI", quiet = FALSE)))
Try(download.file("http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip", "fastqc.zip", mode="wb"))
Try(unzip("fastqc.zip"))
Try(cat("\nThe fastQC downloaded version is fastqc_v0.11.2\n"))
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",TRUE,affylmGUIenvironment))
#download bowtie
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(bowtieDirLocation.Available){
Try(mbVal <- tkmessageBox(title="Bowtie software",
message="There already a folder defined for bowtie software.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
Try(setwd(bowtieDirLocation))
Try(.bowtieGenomes())
Try(setwd(myWD))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
}
Try(bowtieDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/bowtie", sep=""))
Try(dir.create(bowtieDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(bowtieDirLocation))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(cat("\nBegin downloads of bowtie.....\n"))
#defining which program to be downloaded
Try(ttGetBowtie <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetBowtie))
Try(tkgrab.set(ttGetBowtie))
Try(tkfocus(ttGetBowtie))
Try(tkwm.title(ttGetBowtie,"Which OS are you using?"))
Try(tkgrid(tklabel(ttGetBowtie,text=" ")))
Try(ttGetBowtieTcl <- tclVar("win32"))
Try(rbIQR.win32 <- tkradiobutton(ttGetBowtie,text="windows ",variable=ttGetBowtieTcl,value="win32",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mac32<-tkradiobutton(ttGetBowtie,text="mac 32 bits ",variable=ttGetBowtieTcl,value="mac32",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mac64<-tkradiobutton(ttGetBowtie,text="mac 64 bits ",variable=ttGetBowtieTcl,value="mac64",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.linux32<-tkradiobutton(ttGetBowtie,text="linux 32 bits ",variable=ttGetBowtieTcl,value="linux32",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.linux64<-tkradiobutton(ttGetBowtie,text="linux 64 bits ",variable=ttGetBowtieTcl,value="linux64",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.win32))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.mac32))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.mac64))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.linux32))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.linux64))
Try(tkgrid.configure(rbIQR.win32,rbIQR.mac32,rbIQR.mac64,rbIQR.linux32,rbIQR.linux64, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),tklabel(ttGetBowtie,text=" ")))
Try(ReturnVal <- "win32")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetBowtie));Try(tkdestroy(ttGetBowtie));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetBowtieTcl));Try(tkgrab.release(ttGetBowtie));Try(tkdestroy(ttGetBowtie));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetBowtie,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetBowtie,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),OK.but,Cancel.but, tklabel(ttGetBowtie,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetBowtie,text=" ")))
Try(tkbind(ttGetBowtie,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetBowtie));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetBowtie))
#down-loading gene leve scaffolds
Try(cat("\nDownloading the gene-level scaffolds for human mouse and rat.\nThose scaffolds are used to build gne-oriented eSets containing RNA-seq mapped data\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/gene-level_USCS.GRanges/rn4_gene-level.scaffold.Rda/download", "rn4_gene-level.scaffold.Rda", mode="wb"))
Try(cat("\nThe The gene-level scaffolds for Rat genome were correctly downloaded\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/gene-level_USCS.GRanges/mm9_gene-level.scaffold.Rda/download", "mm9_gene-level.scaffold.Rda", mode="wb"))
Try(cat("\nThe The gene-level scaffolds for Mouse genome were correctly downloaded\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/gene-level_USCS.GRanges/hg19_gene-level.scaffold.Rda/download", "hg19_gene-level.scaffold.Rda", mode="wb"))
Try(cat("\nThe The gene-level scaffolds for Human genome were correctly downloaded\n"))
#download mirbase latest
Try(download.file("ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.zip", "hairpin.fa.zip", mode="wb"))
#Try(system("gzip -d hairpin.fa.gz"))
Try(unzip("hairpin.fa.zip"))
Try(cat("\nLatest miRbase was correctly downloaded\n"))
Try(hairpin <- readRNAStringSet("hairpin.fa"))
Try(hairpin <- DNAStringSet(hairpin))
Try(save(hairpin,file=paste(find.package(package="oneChannelGUI"),"/data/hairpin.rda",sep="")))
if(ReturnVal=="win32"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-mingw-x86_64.zip/download", "bowtie.zip", mode="wb"))
Try(unzip("bowtie.zip"))
Try(cat("\nThe Bowtie downloaded version is bowtie_1_1_1\n"))
Try(setwd("bowtie-1.1.1"))
Try(system('XCOPY /S *.* ..'))
Try(setwd(".."))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
} else if (ReturnVal=="mac32"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-macos-10.5-i386.zip/download", "bowtie.zip", mode="wb"))
Try(unzip("bowtie.zip"))
Try(cat("\nThe Bowtie downloaded version is bowtie_0_12_7\n"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(system("cp -fR ./bowtie-0.12.7/* ."))
Try(system("rm -fR ./bowtie-0.12.7/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
} else if (ReturnVal=="mac64"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-macos-x86_64.zip/download", "bowtie.zip", mode="wb"))
Try(unzip("bowtie.zip"))
Try(cat("\nThe Bowtie downloaded version is bowtie_1_1_1\n"))
Try(system("cp -fR ./bowtie-1.1.1/* ."))
Try(system("rm -fR ./bowtie-1.1.1/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
#tophat
Try(tophatDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/tophat", sep=""))
Try(dir.create(tophatDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(tophatDirLocation))
Try(cat("\nBegin downloads of tophat.....\n"))
Try(download.file("http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.OSX_x86_64.tar.gz", "tophat.tar.gz", mode="wb"))
Try(system("gzip -d tophat.tar.gz"))
Try(system("tar xvf tophat.tar"))
Try(cat("\nThe TopHat downloaded version is tophat-2.0.411.OSX_x86_64\n"))
Try(system("cp -fR ./tophat-2.0.13.OSX_x86_64/* ."))
Try(system("rm -fR ./tophat-2.0.13.OSX_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="tophatDirLocation"),2] <- tophatDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment))
#cufflinks
Try(cuffDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/cufflinks", sep=""))
Try(dir.create(cuffDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(cuffDirLocation))
Try(cat("\nBegin downloads of cufflinks.....\n"))
Try(download.file("http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz", "cufflinks.tar.gz", mode="wb"))
Try(system("gzip -d cufflinks.tar.gz"))
Try(system("tar xvf cufflinks.tar"))
Try(cat("\nThe Cufflinks downloaded version is cufflinks-2.1.1.OSX_x86_64\n"))
Try(system("cp -fR ./cufflinks-2.2.1.OSX_x86_64/* ."))
Try(system("rm -fR ./cufflinks-2.2.1.OSX_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="cuffDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment))
#samtools
Try(samtoolsDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/samtools", sep=""))
Try(dir.create(samtoolsDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(samtoolsDirLocation))
Try(cat("\nBegin downloads of samtools.....\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/tools/samtools_mac64.tar.gz/download", "samtools.tar.gz", mode="wb"))
Try(system("gzip -d samtools.tar.gz"))
Try(system("tar xvf samtools.tar"))
Try(cat("\nThe Samtools downloaded version is samtools-0.1.18\n"))
Try(system("cp -fR ./samtools-0.1.18/* ."))
Try(system("rm -fR ./samtools-0.1.18/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment))
Try(tuxedoSetup())
} else if (ReturnVal=="linux32"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-i386.zip/download", "bowtie.zip", mode="wb"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(cat("\nThe Bowtie downloaded version is bowtie_0_12_7\n"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(system("cp -fR ./bowtie-0.12.7/* ."))
Try(system("rm -fR ./bowtie-0.12.7/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
} else if (ReturnVal=="linux64"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-linux-x86_64.zip/download", "bowtie.zip", mode="wb"))
Try(cat("\nThe Bowtie downloaded version is bowtie_1_1_1\n"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(system("cp -fR ./bowtie-1.1.1/* ."))
Try(system("rm -fR ./bowtie-1.1.1/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
#tophat
Try(tophatDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/tophat", sep=""))
Try(dir.create(tophatDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(tophatDirLocation))
Try(cat("\nBegin downloads of tophat.....\n"))
Try(download.file("http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz", "tophat.tar.gz", mode="wb"))
Try(system("gzip -d tophat.tar.gz"))
Try(system("tar xvf tophat.tar"))
Try(cat("\nThe TopHat downloaded version is tophat-2.0.11.Linux_x86_64\n"))
Try(system("cp -fR ./tophat-2.0.13.Linux_x86_64/* ."))
Try(system("rm -fR ./tophat-2.0.13.Linux_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="tophatDirLocation"),2] <- tophatDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment))
Try(cat("\nEnd unzip tophat files.....\n"))
#cufflinks
Try(cuffDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/cufflinks", sep=""))
Try(dir.create(cuffDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(cuffDirLocation))
Try(cat("\nBegin downloads of cufflinks.....\n"))
Try(download.file("http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz", "cufflinks.tar.gz", mode="wb"))
Try(system("gzip -d cufflinks.tar.gz"))
Try(system("tar xvf cufflinks.tar"))
Try(cat("\nThe TopHat downloaded version is cufflinks-2.2.1.Linux_x86_64\n"))
Try(system("cp -fR ./cufflinks-2.2.1.Linux_x86_64/* ."))
Try(system("rm -fR ./ccufflinks-2.2.1.Linux_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="cuffDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment))
Try(cat("\nEnd unzip cufflinks files.....\n"))
#samtools
Try(samtoolsDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/samtools", sep=""))
Try(dir.create(samtoolsDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(samtoolsDirLocation))
Try(cat("\nBegin downloads of samtools.....\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/tools/samtools_linux64.tar.gz/download", "samtools.tar.gz", mode="wb"))
Try(system("gzip -d samtools.tar.gz"))
Try(system("tar xvf samtools.tar"))
Try(cat("\nThe Samtools downloaded version is samtools-0.1.18\n"))
Try(system("cp -fR ./samtools-0.1.18/* ."))
Try(system("rm -fR ./samtools-0.1.18/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment))
Try(tuxedoSetup())
}
Try(cat("\nEnd unzip Bowtie files.....\n"))
Try(cat("\nStart download of Picard tools for sam to bam conversion.....\n"))
#non ti dimenticare di aggiustare tuttui i nuovi nomi se modifichi la versione di picard
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/picard/files/picard-tools/1.119/picard-tools-1.119.zip/download", "picard.zip", mode="wb"))
Try(cat("\nThe Picard downloaded version is picard-tools-1.115\n"))
if(ReturnVal=="win32"){
Try(unzip("picard.zip"))
Try(setwd("picard-tools-1.119"))
Try(system('XCOPY /S *.* ..'))
Try(setwd(".."))
} else{
Try(system(paste("unzip picard.zip", sep="")))
Try(system("cp -fR ./picard-tools-1.119/* ."))
Try(system("rm -fR ./picard-tools-1.119/"))
Try(system("chmod -fR +x *"))
}
Try(cat("\nBowtie and Picard tools are ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="bowtieDirLocation"),2] <- bowtieDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(cat("\nInstalling bowtie reference sequences for miRNA analysis....\n"))
Try(cat("\nStart building Hs...\n"))
Try(hsfa <- hairpin[grep("^hsa-",names(hairpin))])
Try(writeXStringSet(hsfa, file="ncHs.fa"))
if(.Platform$OS.type=="windows"){
Try(system("bowtie-build.exe -f ncHs.fa hs_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncHs.fa hs_nc", sep="")))
}
Try(cat("\nThe fasta reference file for Hs miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(cat("\nStart building Mm...\n"))
Try(mmfa <- hairpin[grep("^mmu-",names(hairpin))])
Try(writeXStringSet(mmfa, file="ncMm.fa"))
if(.Platform$OS.type=="windows" ){
Try(system("bowtie-build.exe -f ncMm.fa mm_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncMm.fa mm_nc", sep="")))
}
Try(cat("\nThe fasta reference file for Mm miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(cat("\nStart building Rn...\n"))
Try(rnfa <- hairpin[grep("^rno-",names(hairpin))])
Try(writeXStringSet(rnfa, file="ncRn.fa"))
if(.Platform$OS.type=="windows" ){
Try(system("bowtie-build.exe -f ncRn.fa rn_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncRn.fa rn_nc",sep="")))
}
Try(cat("\nThe fasta reference file for Rn miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(cat("\nStart building Bo...\n"))
Try(bofa <- hairpin[grep("^bta-",names(hairpin))])
Try(writeXStringSet(bofa, file="ncBo.fa"))
if(.Platform$OS.type=="windows" ){
Try(system("bowtie-build.exe -f ncBo.fa bo_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncBo.fa bo_nc", sep="")))
}
Try(cat("\nThe fasta reference file for Bovine miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Bowtie primary mapping of short reads",message="Bowtie is installed with the miRNA precursors sets\nIf you wish to install other reference genomes, please use the function:\nDownload and build hs, mm, rn bowtie reference sets."))
Try(setwd(myWD))
#test if java path is defined
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
Try(javaDir <- myinfo[which(myinfo[,1]== "javaDir"),2])
if(is.na(javaDir)){javaDir <- ""}
if(javaDir == ""){
Try(tmp.java <- NULL)
Try(tmp.java <- system("java -version 2>&1", intern=T))
if(length(grep("Java", tmp.java)) == 0){
Try(tkmessageBox(title="Bowtie primary mapping of short reads",message="It seems that java dir is not defined in the system path.\nPlease provide the path for java.\nIn windows should be C:/somewhere/Java/jre6.", icon="error"))
Try(javaFolder())
}
}
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
################################################################################
"bowtieGenomes" <- function(){
Try(ptm <- proc.time())
# Try(require(R.utils) || stop("\nMissing R.utils library!\n"))
Try(tkfocus(.affylmGUIglobals$ttMain))
#Try(require(Biostrings) || stop("library Biostrings could not be found !"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
if(is.na(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2])){
Try(tkmessageBox(title="Bowtie",message="Bowtie cannot be found please go to the General tool menu and use the function:\nInstall Bowtie and Picard tools\nto install Bowtie.",icon="error",type="ok"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(setwd(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2]))
#which ref
Try(ttGetGenomes <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetGenomes))
Try(tkgrab.set(ttGetGenomes))
Try(tkfocus(ttGetGenomes))
Try(tkwm.title(ttGetGenomes,"Which genome do you want to use as reference?"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(ttGetGenomesTcl <- tclVar("hg19e"))
Try(rbIQR.hs <- tkradiobutton(ttGetGenomes,text="Human hg19 genome ",variable=ttGetGenomesTcl,value="hg19",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mm<-tkradiobutton(ttGetGenomes,text="Mouse mm9 genome ",variable=ttGetGenomesTcl,value="mm9",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.rn<-tkradiobutton(ttGetGenomes,text="Rat rn4 genome ",variable=ttGetGenomesTcl,value="rn4",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.hs))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.mm))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.rn))
Try(tkgrid.configure(rbIQR.hs,rbIQR.mm,rbIQR.rn, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),tklabel(ttGetGenomes,text=" ")))
Try(ReturnVal1 <- "")
Try(onCancel <- function() {Try(ReturnVal1 <<- "");Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal1 <<- tclvalue(ttGetGenomesTcl));Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetGenomes,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetGenomes,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),OK.but,Cancel.but, tklabel(ttGetGenomes,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(tkbind(ttGetGenomes,"<Destroy>",function() {ReturnVal1 <- "";Try(tkgrab.release(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetGenomes))
Try(cat("\nStart Downloading and building chromosome references for bowtie primary mapping.\n"))
Try(cat("\nBe patient! Download and installation will take a while...\n"))
Try(bowtieRefs <- get("bowtieRefs",envir=affylmGUIenvironment))
#creating the gene-level scaffold to upload the reads
Try(gene.scaffold <- makeGeneScaffold(whichRef = ReturnVal1))
#Please not that if bowtie annotation is available the corresponding gene-level scaffold is also present
#therefore for each bowtieRefs == Y there is also the gene-level scaffold
if(.Platform$OS.type=="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading Chr22\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_22/hs_ref_GRCh37.p2_chr22.fa.gz", "chr22.fa.gz", mode="wb"))
Try(gunzip("chr22.fa.gz"))
Try(system("bowtie-build.exe -f chr22.fa hs_chr22"))
Try(file.remove("chr22.fa"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_21/hs_ref_GRCh37.p2_chr21.fa.gz", "chr21.fa.gz", mode="wb"))
Try(gunzip("chr21.fa.gz"))
Try(system("bowtie-build.exe -f chr21.fa hs_chr21"))
Try(file.remove("chr21.fa"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_20/hs_ref_GRCh37.p2_chr20.fa.gz", "chr20.fa.gz", mode="wb"))
Try(gunzip("chr20.fa.gz"))
Try(system("bowtie-build.exe -f chr20.fa hs_chr20"))
Try(file.remove("chr20.fa"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/hs_ref_GRCh37.p2_chr19.fa.gz", "chr19.fa.gz", mode="wb"))
Try(gunzip("chr19.fa.gz"))
Try(system("bowtie-build.exe -f chr19.fa hs_chr19"))
Try(file.remove("chr19.fa"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_18/hs_ref_GRCh37.p2_chr18.fa.gz", "chr18.fa.gz", mode="wb"))
Try(gunzip("chr18.fa.gz"))
Try(system("bowtie-build.exe -f chr18.fa hs_chr18"))
Try(file.remove("chr18.fa"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_17/hs_ref_GRCh37.p2_chr17.fa.gz", "chr17.fa.gz", mode="wb"))
Try(gunzip("chr17.fa.gz"))
Try(system("bowtie-build.exe -f chr17.fa hs_chr17"))
Try(file.remove("chr17.fa"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_16/hs_ref_GRCh37.p2_chr16.fa.gz", "chr16.fa.gz", mode="wb"))
Try(gunzip("chr16.fa.gz"))
Try(system("bowtie-build.exe -f chr16.fa hs_chr16"))
Try(file.remove("chr16.fa"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_15/hs_ref_GRCh37.p2_chr15.fa.gz", "chr15.fa.gz", mode="wb"))
Try(gunzip("chr15.fa.gz"))
Try(system("bowtie-build.exe -f chr15.fa hs_chr15"))
Try(file.remove("chr15.fa"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_14/hs_ref_GRCh37.p2_chr14.fa.gz", "chr14.fa.gz", mode="wb"))
Try(gunzip("chr14.fa.gz"))
Try(system("bowtie-build.exe -f chr14.fa hs_chr14"))
Try(file.remove("chr14.fa"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_13/hs_ref_GRCh37.p2_chr13.fa.gz", "chr13.fa.gz", mode="wb"))
Try(gunzip("chr13.fa.gz"))
Try(system("bowtie-build.exe -f chr13.fa hs_chr13"))
Try(file.remove("chr13.fa"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_12/hs_ref_GRCh37.p2_chr12.fa.gz", "chr12.fa.gz", mode="wb"))
Try(gunzip("chr12.fa.gz"))
Try(system("bowtie-build.exe -f chr12.fa hs_chr12"))
Try(file.remove("chr12.fa"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_11/hs_ref_GRCh37.p2_chr11.fa.gz", "chr11.fa.gz", mode="wb"))
Try(gunzip("chr11.fa.gz"))
Try(system("bowtie-build.exe -f chr11.fa hs_chr11"))
Try(file.remove("chr11.fa"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_10/hs_ref_GRCh37.p2_chr10.fa.gz", "chr10.fa.gz", mode="wb"))
Try(gunzip("chr10.fa.gz"))
Try(system("bowtie-build.exe -f chr10.fa hs_chr10"))
Try(file.remove("chr10.fa"))
Try(cat("\nDownloading Chr9\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_09/hs_ref_GRCh37.p2_chr9.fa.gz", "chr09.fa.gz", mode="wb"))
Try(gunzip("chr09.fa.gz"))
Try(system("bowtie-build.exe -f chr09.fa hs_chr09"))
Try(file.remove("chr09.fa"))
Try(cat("\nDownloading Chr8\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_08/hs_ref_GRCh37.p2_chr8.fa.gz", "chr08.fa.gz", mode="wb"))
Try(gunzip("chr08.fa.gz"))
Try(system("bowtie-build.exe -f chr08.fa hs_chr08"))
Try(file.remove("chr08.fa"))
Try(cat("\nDownloading Chr7\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_07/hs_ref_GRCh37.p2_chr7.fa.gz", "chr07.fa.gz", mode="wb"))
Try(gunzip("chr07.fa.gz"))
Try(system("bowtie-build.exe -f chr07.fa hs_chr07"))
Try(file.remove("chr07.fa"))
Try(cat("\nDownloading Chr6\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_06/hs_ref_GRCh37.p2_chr6.fa.gz", "chr06.fa.gz", mode="wb"))
Try(gunzip("chr06.fa.gz"))
Try(system("bowtie-build.exe -f chr06.fa hs_chr06"))
Try(file.remove("chr06.fa"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_05/hs_ref_GRCh37.p2_chr5.fa.gz", "chr05.fa.gz", mode="wb"))
Try(gunzip("chr05.fa.gz"))
Try(system("bowtie-build.exe -f chr05.fa hs_chr05"))
Try(file.remove("chr05.fa"))
Try(cat("\nDownloading Chr4\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_04/hs_ref_GRCh37.p2_chr4.fa.gz", "chr04.fa.gz", mode="wb"))
Try(gunzip("chr04.fa.gz"))
Try(system("bowtie-build.exe -f chr04.fa hs_chr04"))
Try(file.remove("chr04.fa"))
Try(cat("\nDownloading Ch3\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_03/hs_ref_GRCh37.p2_chr3.fa.gz", "chr03.fa.gz", mode="wb"))
Try(gunzip("chr03.fa.gz"))
Try(system("bowtie-build.exe -f chr03.fa hs_chr03"))
Try(file.remove("chr03.fa"))
Try(cat("\nDownloading Ch2\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_02/hs_ref_GRCh37.p2_chr2.fa.gz", "chr02.fa.gz", mode="wb"))
Try(gunzip("chr02.fa.gz"))
Try(system("bowtie-build.exe -f chr02.fa hs_chr02"))
Try(file.remove("chr02.fa"))
Try(cat("\nDownloading Ch1\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_GRCh37.p2_chr1.fa.gz", "chr01.fa.gz", mode="wb"))
Try(gunzip("chr01.fa.gz"))
Try(system("bowtie-build.exe -f chr01.fa hs_chr01"))
Try(file.remove("chr01.fa"))
Try(cat("\nDownloading ChX\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_X/hs_ref_GRCh37.p2_chrX.fa.gz", "chrX.fa.gz", mode="wb"))
Try(gunzip("chrX.fa.gz"))
Try(system("bowtie-build.exe -f chrX.fa hs_chrX"))
Try(file.remove("chrX.fa"))
Try(cat("\nDownloading ChY\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_Y/hs_ref_GRCh37.p2_chrY.fa.gz", "chrY.fa.gz", mode="wb"))
Try(gunzip("chrY.fa.gz"))
Try(system("bowtie-build.exe -f chrY.fa hs_chrY"))
Try(file.remove("chrY.fa"))
Try(cat("\nDownloading ChMT\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_MT/hs_ref_GRCh37.p2_chrMT.fa.gz", "chrMT.fa.gz", mode="wb"))
Try(gunzip("chrMT.fa.gz"))
Try(system("bowtie-build.exe -f chrMT.fa hs_chrMT"))
Try(file.remove("chrMT.fa"))
Try(bowtieRefs[1] <- "Y")
} else if(.Platform$OS.type!="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading Chr22\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_22/hs_ref_GRCh37.p2_chr22.fa.gz", "chr22.fa.gz", mode="wb"))
Try(gunzip("chr22.fa.gz"))
Try(system("bowtie-build -f chr22.fa hs_chr22"))
Try(file.remove("chr22.fa"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_21/hs_ref_GRCh37.p2_chr21.fa.gz", "chr21.fa.gz", mode="wb"))
Try(gunzip("chr21.fa.gz"))
Try(system("bowtie-build -f chr21.fa hs_chr21"))
Try(file.remove("chr21.fa"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_20/hs_ref_GRCh37.p2_chr20.fa.gz", "chr20.fa.gz", mode="wb"))
Try(gunzip("chr20.fa.gz"))
Try(system("bowtie-build -f chr20.fa hs_chr20"))
Try(file.remove("chr20.fa"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/hs_ref_GRCh37.p2_chr19.fa.gz", "chr19.fa.gz", mode="wb"))
Try(gunzip("chr19.fa.gz"))
Try(system("bowtie-build -f chr19.fa hs_chr19"))
Try(file.remove("chr19.fa"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_18/hs_ref_GRCh37.p2_chr18.fa.gz", "chr18.fa.gz", mode="wb"))
Try(gunzip("chr18.fa.gz"))
Try(system("bowtie-build -f chr18.fa hs_chr18"))
Try(file.remove("chr18.fa"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_17/hs_ref_GRCh37.p2_chr17.fa.gz", "chr17.fa.gz", mode="wb"))
Try(gunzip("chr17.fa.gz"))
Try(system("bowtie-build -f chr17.fa hs_chr17"))
Try(file.remove("chr17.fa"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_16/hs_ref_GRCh37.p2_chr16.fa.gz", "chr16.fa.gz", mode="wb"))
Try(gunzip("chr16.fa.gz"))
Try(system("bowtie-build -f chr16.fa hs_chr16"))
Try(file.remove("chr16.fa"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_15/hs_ref_GRCh37.p2_chr15.fa.gz", "chr15.fa.gz", mode="wb"))
Try(gunzip("chr15.fa.gz"))
Try(system("bowtie-build -f chr15.fa hs_chr15"))
Try(file.remove("chr15.fa"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_14/hs_ref_GRCh37.p2_chr14.fa.gz", "chr14.fa.gz", mode="wb"))
Try(gunzip("chr14.fa.gz"))
Try(system("bowtie-build -f chr14.fa hs_chr14"))
Try(file.remove("chr14.fa"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_13/hs_ref_GRCh37.p2_chr13.fa.gz", "chr13.fa.gz", mode="wb"))
Try(gunzip("chr13.fa.gz"))
Try(system("bowtie-build -f chr13.fa hs_chr13"))
Try(file.remove("chr13.fa"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_12/hs_ref_GRCh37.p2_chr12.fa.gz", "chr12.fa.gz", mode="wb"))
Try(gunzip("chr12.fa.gz"))
Try(system("bowtie-build -f chr12.fa hs_chr12"))
Try(file.remove("chr12.fa"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_11/hs_ref_GRCh37.p2_chr11.fa.gz", "chr11.fa.gz", mode="wb"))
Try(gunzip("chr11.fa.gz"))
Try(system("bowtie-build -f chr11.fa hs_chr11"))
Try(file.remove("chr11.fa"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_10/hs_ref_GRCh37.p2_chr10.fa.gz", "chr10.fa.gz", mode="wb"))
Try(gunzip("chr10.fa.gz"))
Try(system("bowtie-build -f chr10.fa hs_chr10"))
Try(file.remove("chr10.fa"))
Try(cat("\nDownloading Chr09\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_09/hs_ref_GRCh37.p2_chr9.fa.gz", "chr09.fa.gz", mode="wb"))
Try(gunzip("chr09.fa.gz"))
Try(system("bowtie-build -f chr09.fa hs_chr09"))
Try(file.remove("chr09.fa"))
Try(cat("\nDownloading Chr08\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_08/hs_ref_GRCh37.p2_chr8.fa.gz", "chr08.fa.gz", mode="wb"))
Try(gunzip("chr08.fa.gz"))
Try(system("bowtie-build -f chr08.fa hs_chr08"))
Try(file.remove("chr08.fa"))
Try(cat("\nDownloading Chr07\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_07/hs_ref_GRCh37.p2_chr7.fa.gz", "chr07.fa.gz", mode="wb"))
Try(gunzip("chr07.fa.gz"))
Try(system("bowtie-build -f chr07.fa hs_chr7"))
Try(file.remove("chr07.fa"))
Try(cat("\nDownloading Chr06\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_06/hs_ref_GRCh37.p2_chr6.fa.gz", "chr06.fa.gz", mode="wb"))
Try(gunzip("chr06.fa.gz"))
Try(system("bowtie-build -f chr06.fa hs_chr6"))
Try(file.remove("chr06.fa"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_05/hs_ref_GRCh37.p2_chr5.fa.gz", "chr05.fa.gz", mode="wb"))
Try(gunzip("chr05.fa.gz"))
Try(system("bowtie-build -f chr05.fa hs_chr05"))
Try(file.remove("chr05.fa"))
Try(cat("\nDownloading Chr04\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_04/hs_ref_GRCh37.p2_chr4.fa.gz", "chr04.fa.gz", mode="wb"))
Try(gunzip("chr04.fa.gz"))
Try(system("bowtie-build -f chr04.fa hs_chr04"))
Try(file.remove("chr04.fa"))
Try(cat("\nDownloading Ch03\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_03/hs_ref_GRCh37.p2_chr3.fa.gz", "chr03.fa.gz", mode="wb"))
Try(gunzip("chr03.fa.gz"))
Try(system("bowtie-build -f chr03.fa hs_chr3"))
Try(file.remove("chr03.fa"))
Try(cat("\nDownloading Ch02\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_02/hs_ref_GRCh37.p2_chr2.fa.gz", "chr02.fa.gz", mode="wb"))
Try(gunzip("chr02.fa.gz"))
Try(system("bowtie-build -f chr02.fa hs_chr02"))
Try(file.remove("chr02.fa"))
Try(cat("\nDownloading Ch01\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_GRCh37.p2_chr1.fa.gz", "chr01.fa.gz", mode="wb"))
Try(gunzip("chr01.fa.gz"))
Try(system("bowtie-build -f chr01.fa hs_chr01"))
Try(file.remove("chr01.fa"))
Try(cat("\nDownloading ChX\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_X/hs_ref_GRCh37.p2_chrX.fa.gz", "chrX.fa.gz", mode="wb"))
Try(gunzip("chrX.fa.gz"))
Try(system("bowtie-build -f chrX.fa hs_chrX"))
Try(file.remove("chrX.fa"))
Try(cat("\nDownloading ChY\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_Y/hs_ref_GRCh37.p2_chrY.fa.gz", "chrY.fa.gz", mode="wb"))
Try(gunzip("chrY.fa.gz"))
Try(system("bowtie-build -f chrY.fa hs_chrY"))
Try(file.remove("chrY.fa"))
Try(cat("\nDownloading ChMT\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_MT/hs_ref_GRCh37.p2_chrMT.fa.gz", "chrMT.fa.gz", mode="wb"))
Try(gunzip("chrMT.fa.gz"))
Try(system("bowtie-build -f chrMT.fa hs_chrMT"))
Try(file.remove("chrMT.fa"))
Try(bowtieRefs[1] <- "Y")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
}
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
Try(bowtieRefs <- paste(bowtieRefs, collapse=","))
Try(myinfo[which(myinfo[,1]=="bowtieRefs"),2] <- bowtieRefs)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
Try(usedtime <- proc.time() - ptm)
Try(cat("\nUsed CPU time (min) ",usedtime[3]/60,"\n"))
Try(cat("\nEnd downloading and building chromosome references for bowtie primary mapping.\n"))
Try(return())
}
###############################################################################
"wrapNGS" <- function(){
Try(mbVal <- tkmessageBox(title="Installing external software for RNA-seq",
message="Do you wish to install all external software needed for RNA-seq?",
icon="question",type="yesno",default="yes"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="yes"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(myWD <-getwd())
#gathering affy libs and apt tools folders
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(bowtieDirLocation <- myinfo[which(myinfo[,1]=="bowtieDirLocation"),2]) #loacation of bowtie
if(bowtieDirLocation==""){
Try(bowtieDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/bowtie", sep=""))
Try(dir.create(bowtieDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(myinfo[which(myinfo[,1]=="bowtieDirLocation"),2] <- bowtieDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(setwd(myWD))
Try(bowtieDownload())
# ngsperlDownload()
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else{
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
}
################################################################################
"bowtieBuilt" <- function(){
# Try(require(R.utils) || stop("\nMissing R.utils library!\n"))
Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(require(Biostrings) || stop("library Biostrings could not be found !"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
if(is.na(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2])){
Try(tkmessageBox(title="Bowtie",message="Bowtie cannot be found please go to the General tool menu and use the function:\nInstall Bowtie and Picard tools\nto install Bowtie.",icon="error",type="ok"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(setwd(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2]))
#which ref
Try(ttGetGenomes <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetGenomes))
Try(tkgrab.set(ttGetGenomes))
Try(tkfocus(ttGetGenomes))
Try(tkwm.title(ttGetGenomes,"Which genome do you want to use as reference?"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(ttGetGenomesTcl <- tclVar("hg19"))
Try(rbIQR.hs <- tkradiobutton(ttGetGenomes,text="Human hg19 genome ",variable=ttGetGenomesTcl,value="hg19",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mm<-tkradiobutton(ttGetGenomes,text="Mouse mm9 genome ",variable=ttGetGenomesTcl,value="mm9",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.rn<-tkradiobutton(ttGetGenomes,text="Rat rn4 genome ",variable=ttGetGenomesTcl,value="rn4",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.hs))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.mm))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.rn))
Try(tkgrid.configure(rbIQR.hs,rbIQR.mm,rbIQR.rn, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),tklabel(ttGetGenomes,text=" ")))
Try(ReturnVal1 <- "")
Try(onCancel <- function() {Try(ReturnVal1 <<- "");Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal1 <<- tclvalue(ttGetGenomesTcl));Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetGenomes,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetGenomes,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),OK.but,Cancel.but, tklabel(ttGetGenomes,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(tkbind(ttGetGenomes,"<Destroy>",function() {ReturnVal1 <- "";Try(tkgrab.release(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetGenomes))
Try(cat("\nStart Downloading and building chromosome references for bowte primary mapping.\n"))
Try(cat("\nBe patient! Download and installation will take a while...\n"))
Try(bowtieRefs <- get("bowtieRefs",envir=affylmGUIenvironment))
#Please not that if bowtie annotation is available the corresponding gene-level scaffold is also present
#therefore for each bowtieRefs == Y there is also the gene-level scaffold
if(.Platform$OS.type=="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading ChrX and ChrY\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chrXY.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr22\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr22.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr21.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr20.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr19.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr18.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr17.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr16.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr15.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr14.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr13.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr12.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr11.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr10.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr9\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr9.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr8\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr8.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr7\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr7.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr6\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr6.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr5.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr4\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr4.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr3\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr3.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr2\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr2.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr1\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr1.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(bowtieRefs[1] <- "Y")
} else if(.Platform$OS.type!="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading ChrX and ChrY\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chrXY.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr22\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr22.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr21.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr20.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr19.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr18.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr17.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr16.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr15.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr14.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr13.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr12.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr11.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr10.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr9\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr9.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr8\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr8.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr7\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr7.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr6\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr6.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr5.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr4\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr4.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr3\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr3.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr2\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr2.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr1\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr1.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(bowtieRefs[1] <- "Y")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
}
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
Try(bowtieRefs <- paste(bowtieRefs, collapse=","))
Try(myinfo[which(myinfo[,1]=="bowtieRefs"),2] <- bowtieRefs)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
Try(cat("\nEnd downloading built chromosome references for bowtie primary mapping.\n"))
Try(return())
}
#####################################################################################
genomeStudioReformat <- function(){
#loading the tab delimited file
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="Reformat a GenomeStudio export file",message="Open the Genome Studio exported file."))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
##start grabbing the first 8 lines
Try(con <- file(tempFileName, "r", blocking = FALSE))
Try(gsInfo <- readLines(con, n=8))
Try(close(con))
Try(gsInfo <- gsub("\t","",gsInfo))
Try(mysel <- read.table(tempFileName, sep="\t", header=T, skip=8, fill=T))
Try(refined.df <- mysel[,grep("AVG_Signal",names(mysel))])
Try(refined.df <- refined.df[setdiff(seq(1,dim(mysel)[1]),which(duplicated(as.character(mysel$PROBE_ID)))),])
Try(rnames <- mysel$PROBE_ID[setdiff(seq(1,dim(mysel)[1]),which(duplicated(as.character(mysel$PROBE_ID))))])
Try(refined.df <- cbind(rnames,refined.df))
Try(tmp.df <- matrix(rep(" ", dim(refined.df)[2]*8), nrow=8))
Try(tmp.df[,1]<- gsInfo)
Try(tmp.df <- rbind(tmp.df, gsub("X","",names(refined.df))))
Try(tmp.df[9,1] <- "PROBE_ID")
Try(write.table(tmp.df, file = paste(tempFileName,"_reformatted.txt",sep=""), sep="\t", col.names=F,row.names=F, quote=F))
#Try(dimnames(tmp.df)[[2]] <- names(refined.df))
#Try(tmp.df <- rbind(tmp.df,refined.df))
Try(write.table(refined.df, file = paste(tempFileName,"_reformatted.txt",sep=""), sep="\t", col.names=F,row.names=F, append=T, quote=F))
Try(tkmessageBox(title="Reformat GenomeStudio output files",message=paste("The reformated file iis saved in your working directory as: ", paste(tempFileName,"_reformatted.txt",sep=""),"\nis made of ",dim(refined.df)[1]," rows and ",dim(refined.df)[2]," columns",sep=""),icon="info",type="ok"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
###############
setBinDir <- function(){
Try(wd <- tclVar(getwd()))
Try(
if(.Platform$OS.type=="windows"){
Try(tkmessageBox(title="Select user bin folder",message="Not implemented in windows",icon="info",type="ok"))
Try(return())
}
)
Try(ttChooseDir <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.title(ttChooseDir,"Choose Output directory"))
Try(tkwm.deiconify(ttChooseDir))
Try(tkgrab.set(ttChooseDir))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
Try(label1 <- tklabel(ttChooseDir,text="Choose user bin directory:",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttChooseDir,text=" "),label1,sticky="w"))
Try(tkgrid.configure(label1,columnspan=3))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
#
#
Try(
onBrowse <- function(){
Try(if(file.exists(gsub("\\\\","/",tclvalue(wd)))) initialdir<-gsub("\\\\","/",tclvalue(wd)) else initialdir<-getwd())
Try(dir1 <- tclvalue(tkchooseDirectory(title="Please choose the user bin dir",initialdir=initialdir)))
Try(if(nchar(dir1)>0) tclvalue(wd) <- dir1)
Try(
if(.Platform$OS.type=="windows"){
Try(tclvalue(wd) <- gsub("/","\\\\",tclvalue(wd)))
}
)
} #end of onBrowse <- function()
)# end of Try
#
#
Try(ReturnVal <- "")
#
#
Try(
onOK <- function(){
Try(DirChosen <- tclvalue(wd))
Try(tkgrab.release(ttChooseDir))
Try(tkdestroy(ttChooseDir))
Try(DirChosen <- gsub("\\\\","/",DirChosen))
Try(ReturnVal <<- DirChosen)
} #end of onOK <- function()
)
#
#
Try(
onCancel <- function(){
Try(tkgrab.release(ttChooseDir));
Try(tkdestroy(ttChooseDir))
} #end of onCancel <- function()
) #end of try
#
#
Try(Browse.but <- tkbutton(ttChooseDir,text="Browse",command=onBrowse,font=.affylmGUIglobals$affylmGUIfont2))
Try(OK.but <- tkbutton(ttChooseDir,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttChooseDir,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
#
Try(entry1 <- tkentry(ttChooseDir,textvariable=wd,width=40,font=.affylmGUIglobals$affylmGUIfont2))
#
Try(tkgrid(tklabel(ttChooseDir,text=" "),entry1))
Try(tkgrid.configure(entry1,columnspan=3))
Try(tkgrid(tklabel(ttChooseDir,text=" "),row=3,column=4))
Try(tkgrid(Browse.but,row=3,column=5))
Try(tkgrid(tklabel(ttChooseDir,text=" "),row=3,column=6))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
Try(tkgrid(tklabel(ttChooseDir,text=" "),tklabel(ttChooseDir,text=" "),OK.but,Cancel.but))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
#
Try(tkfocus(entry1))
Try(tkbind(ttChooseDir,"<Destroy>",function()tkgrab.release(ttChooseDir)))
Try(tkbind(entry1,"<Return>",onOK))
Try(tkwait.window(ttChooseDir))
Try(tkfocus(.affylmGUIglobals$ttMain))
#
Try(assign("binDir", ReturnVal, affylmGUIenvironment))#bin dir
Try(assign("binDir.Available",TRUE,affylmGUIenvironment))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
Try(myinfo[which(myinfo[,1]=="binDir"),2] <- ReturnVal)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
}
#################
tuxedoSetup<- function(){
Try(binDir.available <- get("binDir.Available",envir=affylmGUIenvironment))
if(!binDir.available){
setBinDir()
}
Try(binDir <- get("binDir",envir=affylmGUIenvironment))
#####bowtie
#already available in bowtieDirLocation
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(!bowtieDirLocation.Available){
bowtieDownload()
}
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",bowtieDirLocation, "/bowtie", sep="")))
Try(system(paste("ln -fs ",bowtieDirLocation,"/bowtie ", binDir, "/bowtie", sep="")))
Try(system(paste("chmod +x ",bowtieDirLocation, "/bowtie-build", sep="")))
Try(system(paste("ln -fs ",bowtieDirLocation,"/bowtie-build ", binDir, "/bowtie-build", sep="")))
Try(system(paste("chmod +x ",bowtieDirLocation, "/bowtie-inspect", sep="")))
Try(system(paste("ln -fs ",bowtieDirLocation,"/bowtie-inspect ", binDir, "/bowtie-inspect", sep="")))
#samtools dir
Try(samtoolsDirLocation.Available <- get("samtoolsDirLocation.Available",envir=affylmGUIenvironment))
if(!samtoolsDirLocation.Available){
bowtieDownload()
}
Try(samtoolsDirLocation <- get("samtoolsDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",samtoolsDirLocation, "/samtools", sep="")))
Try(system(paste("ln -fs ",samtoolsDirLocation,"/samtools ", binDir, "/samtools", sep="")))
#fastqc
Try(fastqcDirLocation.Available <- get("fastqcDirLocation.Available",envir=affylmGUIenvironment))
if(!fastqcDirLocation.Available){
bowtieDownload()
}
Try(fastqcDirLocation <- get("fastqcDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",fastqcDirLocation, "/fastqc", sep="")))
Try(system(paste("ln -fs ",fastqcDirLocation,"/fastqc ", binDir, "/fastqc", sep="")))
##tophat
Try(tophatDirLocation.Available <- get("tophatDirLocation.Available",envir=affylmGUIenvironment))
if(!tophatDirLocation.Available){
bowtieDownload()
}
Try(tophatDir <- get("tophatDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",tophatDir, "/bam2fastx", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/bam2fastx ", binDir, "/bam2fastx", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/bam_merge", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/bam_merge ", binDir, "/bam_merge", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/bed_to_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/bed_to_juncs ", binDir, "/bed_to_juncs", sep="")))
# Try(system(paste("chmod +x ",tophatDir, "/closure_juncs", sep="")))
# Try(system(paste("ln -fs ",tophatDir,"/closure_juncs ", binDir, "/closure_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/contig_to_chr_coords", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/contig_to_chr_coords ", binDir, "/contig_to_chr_coords", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/fix_map_ordering", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/fix_map_ordering ", binDir, "/fix_map_ordering", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/gtf_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/gtf_juncs ", binDir, "/gtf_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/gtf_to_fasta", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/gtf_to_fasta ", binDir, "/gtf_to_fasta", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/juncs_db", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/juncs_db ", binDir, "/juncs_db", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/long_spanning_reads", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/long_spanning_reads ", binDir, "/long_spanning_reads", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/map2gtf", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/map2gtf ", binDir, "/map2gtf", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/prep_reads", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/prep_reads ", binDir, "/prep_reads", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/sam_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/sam_juncs ", binDir, "/sam_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/segment_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/segment_juncs ", binDir, "/segment_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/sra_to_solid", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/sra_to_solid ", binDir, "/sra_to_solid", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat ", binDir, "/tophat", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat-fusion-post", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat-fusion-post ", binDir, "/tophat-fusion-post", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat2", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat2 ", binDir, "/tophat", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat2", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat2 ", binDir, "/tophat", sep="")))
#cufflinks
Try(cuffDirLocation.available <- get("cuffDirLocation.Available",envir=affylmGUIenvironment))
if(!cuffDirLocation.available){
bowtieDownload()
}
Try(cuffDir <- get("cuffDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",cuffDir, "/cuffcompare", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cuffcompare ", binDir, "/cuffcompare", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/cuffdiff", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cuffdiff ", binDir, "/cuffdiff", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/cufflinks", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cufflinks ", binDir, "/cufflinks", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/cuffmerge", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cuffmerge ", binDir, "/cuffmerge", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/gffread", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/gffread ", binDir, "/gffread", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/gtf_to_sam", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/gtf_to_sam ", binDir, "/gtf_to_sam", sep="")))
}
##############
openPdf <- function(){
while(as.numeric(dev.cur())> 1){
Try(dev.off())
}
#selecting a pdf file to save results
Try(ttpdf<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttpdf))
Try(tkgrab.set(ttpdf))
Try(tkfocus(ttpdf))
Try(tkwm.title(ttpdf,"Opening pdf output"))
Try(tkgrid(tklabel(ttpdf,text=" ")))
Try(pdfName<- "")
Try(Local.pdf <- tclVar(init=pdfName))
Try(entry.pdf <-tkentry(ttpdf,width="20",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.pdf,bg="white"))
Try(tkgrid(tklabel(ttpdf,text="Please enter the name of the pdf file to be created.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.pdf))
onOK <- function()
{
Try(pdfName <<- as.character(tclvalue(Local.pdf)))
Try(tkgrab.release(ttpdf));Try(tkdestroy(ttpdf));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttpdf,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttpdf,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttpdf,text=" ")))
Try(tkfocus(entry.pdf))
Try(tkbind(entry.pdf, "<Return>",onOK))
Try(tkbind(ttpdf, "<Destroy>", function(){Try(tkgrab.release(ttpdf));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttpdf))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(pdf(pdfName))
Try(return())
}
##############################################################################
closePdf <- function(){
while(as.numeric(dev.cur())> 1){
Try(dev.off())
}
Try(tkmessageBox(title="Closing pdf outputs",message="pdf files are closed",type="ok",icon="info"))
Try(return())
}
##############################################################################
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oneChannelGUI documentation built on Nov. 17, 2017, 11:02 a.m.
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Defines functions genomeStudioReformat setBinDir tuxedoSetup openPdf closePdf
Documented in closePdf genomeStudioReformat openPdf setBinDir tuxedoSetup
#set of functions, directly/indirectly involved, in oneChannelGUI generalToolMenu
#oneChannelGUI filteringTable filtering a tab delimited file on the basis of a list of probesets
#oneChannelGUI colExtract extract a user defined colum from a tab delimited file with header
#oneChannelGUI geneExonLibs queries affymetrix web site to download exon and gene 1.0 ST WT library files
#RETIRED oneChannelGUI ngsperlDownload creating dir with ngs perl scripts
#oneChannelGUI bowtieDownload download bowtie and picard tools and build a binary form of ref genome for non coding precursors
# alos downloading tophat and cufflinks for linux and mac
# bowtiesGenomes downloades and builds chromosome level genomes references for bowtie
# embeds also makeGeneScaffold for gene level analysis, which creates gene-level oriented scaffolds
# bowtieBuilt downloads prebuilt cromosome oriented bowtie references from:
# http://sourceforge.net/p/ochguiextras/home/oneChannelGUI.extras/
#oneChannelGUI aptFolder setting the folder were apt tools are located (save data in localdata.txt in etc)
#oneChannelGUI javaFolder setting the folder were java is located
#oneChannelGUI deleteLocalData delete data in localdata.txt resetting aptDir and libDirLocation
#oneChannelGUI buildingLocalAnnotation updates gene level annotation using the netaffx annotation data
# exon level annotation is done using the UCSC exon-level annotation data
#oneChannelGUI refseqDownload retrieve the latest Hs, Mm, Rn refseq fasta file
#oneChannelGUI madscrosshybDownload and creation of mads derived mps file only available for Hs and Mm core NOT FINISHED
#oneChannelGUI updateLibs run an update of the Bioconductor libraries
#oneChannelGUI variantExons the function updates the table available in oneChannelGUI that contains only variant exons
# for the core set. variant exons are those that are present only in a subset of isoforms associated to a gene to the UCSC browser
#oneChannelGUI exportFASTA Export non-coding RNA fasta file for RNA-seq
#oneChannelGUI meVDownload setting the folder were meV software (http://www.tm4.org/mev/) is located (save data in localdata.txt in etc)
#oneChannelGUI extPckInfo show which external software are available and in which dir
#oneChannelGUI combining2eSet combine two tables with the same row names
#oneChannelGUI wrapNGS wrapping function to install all expernal software needed for RNA-seq
#oneChannelGUI makeGeneScaffold creating Grange object for UCSC browser needed to map reads on UCSC genes located in stand alone functions
# part of the bowtiesGenomes function it returns a list of GRanges chromosomes encompassing the positions of all annotated USCS genes that encode for a protein
#oneChannelGUI genomeStudioReformat the function convert a genomestudio output in a format suitable to be loaded on oneChannelGUI
#oneChannelGUI setBinDir setting the dir in which create the soft lnks for tuxido suite
#oneChannelGUI openPdf needed under linux to print pdf
#oneChannelGUI closePdf needed under linux to print pdf
#################################################################################
#################################################################################
#this file contains a set of function that perfomr basic R function useful for handlying microarray data.
#this function filter a table on the basis of a vector of data present in an other file
"filteringTable" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Table subsetting",message="Open the file to be filtered. This file should be tab delimited with an header."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(saving.file <- paste(tempFileName, ".filtered.by.",sep=""))
Try(mySel<-read.table(tempFileName, sep="\t", header=T, as.is=TRUE, quote=""))
Try(tkmessageBox(title="Table subsetting",message="Open the file to be used to filter the previous file.\nThis file should contain a single column with an header equal to \nthe one that should be used for filtering in the tab delimited file."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(tmp <- as.vector(unlist(strsplit(tempFileName , "/"))))
Try(saving.file <- paste(saving.file, tmp[length(tmp)],sep=""))
Try(myFilter<-read.table(tempFileName, sep="\t", header=T, as.is=TRUE, quote=""))
Try(col.for.filter <- which(names(mySel)==names(myFilter)[1]))
Try(mySel <- mySel[which(mySel[,col.for.filter]%in%myFilter[,1]),])
Try(tkmessageBox(title="Table subsetting",message="Saving the filtered table."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=saving.file, filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if(!nchar(FileName))
return())
Try(write.table(mySel,file=FileName,quote=FALSE,col.names=NA,sep="\t"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
"colExtract" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Column extraction",message="Open the file to be manipulated. This file should be tab delimited with an header."))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(mySel<-read.table(tempFileName, sep="\t", header=T, as.is=TRUE, quote=""))
Try(mycol <- names(mySel))
Try(mycol <- paste(mycol, "=",seq(1, length(mycol)), sep="", collapse=" "))
#selecting the column to be removed
Try(ttcolExtract<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttcolExtract))
Try(tkgrab.set(ttcolExtract))
Try(tkfocus(ttcolExtract))
Try(tkwm.title(ttcolExtract,"Defining the column to be estracted"))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(colnum <- "1")
Try(Local.colExtract <- tclVar(init=colnum))
Try(entry.colExtract <-tkentry(ttcolExtract,width="4",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.colExtract,bg="white"))
Try(tkgrid(tklabel(ttcolExtract,text=paste("Please enter the number associated to the columnof interest\n", mycol,collapse=" "),font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.colExtract))
onOK <- function()
{
Try(colnum <- as.numeric(tclvalue(Local.colExtract)))
Try(assign("colnum", as.numeric(tclvalue(Local.colExtract)),affylmGUIenvironment))
Try(tkgrab.release(ttcolExtract));Try(tkdestroy(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttcolExtract,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttcolExtract,text=" ")))
Try(tkfocus(entry.colExtract))
Try(tkbind(entry.colExtract, "<Return>",onOK))
Try(tkbind(ttcolExtract, "<Destroy>", function(){Try(tkgrab.release(ttcolExtract));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttcolExtract))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(colnum <- get("colnum", affylmGUIenvironment))
if(colnum > length(names(mySel))){
Try(tkmessageBox(title="Column extraction",message="You have selected a non existing column!"))
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
Try(tempFileName <- as.vector(unlist(strsplit(tempFileName, "/"))))
Try(if(length(tempFileName) > 1) tempFileName <- tempFileName[length(tempFileName)])
Try(saving.file <- paste("col.",colnum,".from.",tempFileName,".txt",sep=""))
Try(tkmessageBox(title="Column extraction",message="Saving the extracted column."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(FileName <- tclvalue(tkgetSaveFile(initialfile=saving.file, filetypes="{{Tab-Delimited Text Files} {.txt .xls}} {{All files} *}")))
Try(if(!nchar(FileName))
return())
Try(myout <- as.character(as.vector(mySel[,colnum])))
Try(zz <- file(FileName, "w"))
Try(writeLines(myout, con = zz, sep = "\n"))
Try(close(zz))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
#save affy libraries in allylibs dir as new dir in oneChannelPath
"geneExonLibs" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Gene Exon 1.0 ST libraries",message="This routine installs, in a user defined folder,\nall library files needed for analysis of Gene/Exon Affymetrix arrays."))
Try(myWD <- getwd())
#Try(SetWD())
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(libDirLocation <- myinfo[which(myinfo[,1]=="libDirLocation"),2])
Try(if(is.na(libDirLocation)) libDirLocation <- "")
if(libDirLocation != ""){
Try(assign("libDirLocation", libDirLocation, affylmGUIenvironment))
Try(mbVal <- tkmessageBox(title="Gene Exon 1.0 ST libraries",
message="There already a folder defined for Affymetrix libraries.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
} else{
Try(.downloadLibs())
Try(setwd(myWD))
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
Try(.downloadLibs())
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
}
".downloadLibs" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(libDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/affylibs", sep=""))
Try(dir.create(libDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(libDirLocation))
Try(assign("libDirLocation", libDirLocation, affylmGUIenvironment))#directory where affy library files are located
Try(cat("\nBegin downloads of library files.....\n"))
Try(cat("Be patient!\n"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/HuEx.zip", "HuEx.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/HuGene.zip","HuGene.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/MoEx.zip", "MoEx.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/MoGene.zip","MoGene.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/RaEx.zip","RaEx.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/RaGene.zip","RaGene.zip", mode="wb"))
Try(download.file("http://www.bioinformatica.unito.it/downloads/HTA_2.0.zip","HTA_2.0.zip", mode="wb"))
#in file exondata.zip are located transcripts annotation and variant exons
#generated with the function buildingLocalAnnotation()
#and with the function variantExons()
#are zipped and loaded on www.bioinformatica.unito.it to be downloaded in oneChannelGUI affylibs dir
#the first time an exon array is loaded (to be made)
Try(download.file("http://www.bioinformatica.unito.it/downloads/exondata.zip","exondata.zip", mode="wb"))
Try(cat("\nEnd downloads of 7 library files.....\n"))
Try(cat("\nBegin unzip library files.....\n"))
if(.Platform$OS.type=="windows"){
Try(unzip("exondata.zip"))
Try(unzip("HuGene.zip"))
Try(unzip("HuEx.zip"))
Try(unzip("MoEx.zip"))
Try(unzip("MoGene.zip"))
Try(unzip("RaEx.zip"))
Try(unzip("RaGene.zip"))
Try(unzip("HTA_2.0.zip"))
} else{
Try(system(paste("unzip exondata.zip", sep="")))
Try(system(paste("unzip HuGene.zip", sep="")))
Try(system(paste("unzip HuEx.zip")))
Try(system(paste("unzip MoEx.zip")))
Try(system(paste("unzip MoGene.zip")))
Try(system(paste("unzip RaEx.zip")))
Try(system(paste("unzip RaGene.zip")))
Try(system(paste("unzip HTA_2.0.zip")))
}
Try(cat("\nEnd unzip library files.....\n"))
Try(cat("\nLibrary files are ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="libDirLocation"),2] <- libDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
#######################################################################################################
#define the folder where apt tools are locate
"aptFolder" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="APT tools folder",message="Please select the folder where APT tools are located."))
Try(myWD <- getwd())
#Try(SetWD())
Try(aptDir <- get("aptDir",envir=affylmGUIenvironment))
if(is.na(aptDir)){aptDir <- ""}
if(aptDir == ""){
Try(SetED())
Try(aptDir <- getwd())
if(length(grep("apt-probeset-summarize", dir(paste(aptDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="APT tools dir ",message="You have not correctly defined the main folder where APT tools are located!",icon="error"))
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="aptDir"),2] <- aptDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
} else{
Try(mbVal <- tkmessageBox(title="APT tools folder",
message="There already a folder defined for APT tools.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
if(tclvalue(mbVal)=="yes"){
Try(SetED())
Try(aptDir <- getwd())
if(length(grep("apt-probeset-summarize", dir(paste(aptDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="APT tools dir ",message="You have not correctly defined the main folder where APT tools are located!",icon="error"))
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="aptDir"),2] <- aptDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
}
}
# Try(mbVal <- tkmessageBox(title="RefSeq Fasta",
# message="Do you wish to download reference sequence for exon-level analysis?\nIf you answer NO oneChannelGUI you can also do it later. Be patient!",
# icon="question",type="yesno",default="no"
# )#end of tkmessageBox
# )#end of Try(mbVal..
# if(tclvalue(mbVal)=="yes"){
# Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(refseqDownload())
# Try(tkmessageBox(title="APT tools folder",message="Please install the BLAST executable in the apt/blast dir.\nDownload the BAST from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"))
# }
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
###########################################################################################
#define the folder where apt tools are locate
"javaFolder" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="JAVA folder",message="Please select the folder where JAVA is located."))
Try(myWD <- getwd())
#Try(SetWD())
Try(javaDir <- get("javaDir",envir=affylmGUIenvironment))
if(is.na(javaDir)){javaDir <- ""}
if(javaDir == ""){
Try(SetED())
Try(javaDir <- getwd())
#javaDir <- paste('"',javaDir,"/bin/",'"', sep="")
#javabin <- paste(javaDir, "/java -version", sep="")
if(length(grep("java", dir(paste(javaDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="Java dir ",message="You have not correctly defined the main folder where java binary is located!\nIn windows should be C:/somewhere/Java/jre6",icon="error"))
assign("javaDir.Available",FALSE,affylmGUIenvironment)
assign("javaDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="javaDir"),2] <- javaDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("javaDir.Available",TRUE,affylmGUIenvironment)
assign("javaDir", javaDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
} else{
Try(mbVal <- tkmessageBox(title="Java folder",
message="There already a folder defined for Java.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
if(tclvalue(mbVal)=="yes"){
Try(SetED())
Try(javaDir <- getwd())
if(length(grep("java", dir(paste(javaDir, "/bin", sep="")))) == 0){
Try(tkmessageBox(title="Java dir ",message="You have not correctly defined the main folder where java binary is located!\nIn windows should be C:/somewhere/Java/jre6",icon="error"))
assign("javaDir.Available",FALSE,affylmGUIenvironment)
assign("javaDir", "" ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
} else {
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="javaDir"),2] <- javaDir)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
assign("javaDir.Available",TRUE,affylmGUIenvironment)
assign("javaDir", javaDir ,affylmGUIenvironment)
Try(setwd(myWD))
#Try(return())
}
}
}
# Try(mbVal <- tkmessageBox(title="RefSeq Fasta",
# message="Do you wish to download reference sequence for exon-level analysis?\nIf you answer NO oneChannelGUI you can also do it later. Be patient!",
# icon="question",type="yesno",default="no"
# )#end of tkmessageBox
# )#end of Try(mbVal..
# if(tclvalue(mbVal)=="yes"){
# Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(refseqDownload())
# Try(tkmessageBox(title="APT tools folder",message="Please install the BLAST executable in the apt/blast dir.\nDownload the BAST from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"))
# }
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
###########################################################################################
"deleteLocalData" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(mbVal <- tkmessageBox(title="Local setting",
message="Do you want to the delete the local setting for Gene Exon arrays analysis?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
} else{
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="libDirLocation"),2] <- "")
Try(myinfo[which(myinfo[,1]=="aptDir"),2] <- "")
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names= F, quote=F))
Try(tkmessageBox(title="Local settings",message="Local setting were reset."))
return()
}
}
################################################################################
#building gene and exon annotation for oneChannelGUI
"buildingLocalAnnotation" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(libDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/affylibs/", sep = ""))
#gathering affy libs and apt tools folders
Try(netaffxUpdates <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/netaffxUpdates.txt", sep=""))
Try(cat(readLines(netaffxUpdates), sep="\n"))
#username
Try(ttGetUserName<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetUserName))
Try(tkgrab.set(ttGetUserName))
Try(tkfocus(ttGetUserName))
Try(tkwm.title(ttGetUserName,"NetAffx User Name"))
Try(tkgrid(tklabel(ttGetUserName,text=" ")))
Try(UserNameText <- "")
Try(Local.UserName <- tclVar(init=UserNameText))
Try(entry.UserName <-tkentry(ttGetUserName,width="30",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.UserName,bg="white"))
Try(tkgrid(tklabel(ttGetUserName,text="Please enter your NetAffx User Name.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.UserName))
onOK <- function()
{
Try(UserNameText <- tclvalue(Local.UserName))
if(nchar(UserNameText)==0)
UserNameText <- "Unselected"
Try(assign("UserNameText",UserNameText,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$UserNameTcl) <- UserNameText)
Try(tkgrab.release(ttGetUserName));Try(tkdestroy(ttGetUserName));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetUserName,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetUserName,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetUserName,text=" ")))
Try(tkfocus(entry.UserName))
Try(tkbind(entry.UserName, "<Return>",onOK))
Try(tkbind(ttGetUserName, "<Destroy>", function(){Try(tkgrab.release(ttGetUserName));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetUserName))
Try(tkfocus(.affylmGUIglobals$ttMain))
#########################
#password
Try(ttGetUserPw<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetUserPw))
Try(tkgrab.set(ttGetUserPw))
Try(tkfocus(ttGetUserPw))
Try(tkwm.title(ttGetUserPw,"NetAffx User Password"))
Try(tkgrid(tklabel(ttGetUserPw,text=" ")))
Try(UserPwText <- "")
Try(Local.UserPw <- tclVar(init=UserPwText))
Try(entry.UserPw <-tkentry(ttGetUserPw,width="20",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.UserPw,bg="white"))
Try(tkgrid(tklabel(ttGetUserPw,text="Please enter your NetAffx User Password.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.UserPw))
onOK <- function()
{
Try(UserPwText <- tclvalue(Local.UserPw))
if(nchar(UserPwText)==0)
UserPwText <- "Unselected"
Try(assign("UserPwText",UserPwText,affylmGUIenvironment))
Try(tclvalue(.affylmGUIglobals$UserPwTcl) <- UserPwText)
Try(tkgrab.release(ttGetUserPw));Try(tkdestroy(ttGetUserPw));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttGetUserPw,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetUserPw,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttGetUserPw,text=" ")))
Try(tkfocus(entry.UserPw))
Try(tkbind(entry.UserPw, "<Return>",onOK))
Try(tkbind(ttGetUserPw, "<Destroy>", function(){Try(tkgrab.release(ttGetUserPw));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttGetUserPw))
Try(tkfocus(.affylmGUIglobals$ttMain))
#########################
Try(username.tmp <- get("UserNameText", env=affylmGUIenvironment))
Try(userpw.tmp <- get("UserPwText", env=affylmGUIenvironment))
if(username.tmp != "Unselected" & userpw.tmp != "Unselected"){
Try(rsrc <- NetAffxResource(user = username.tmp, password = userpw.tmp, affxLicence = "BIOCON0808"))
Try(rsrc)
#selecting the annotation to be updated
Try(ttIfDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttIfDialog))
Try(tkgrab.set(ttIfDialog))
Try(tkfocus(ttIfDialog))
Try(tkwm.title(ttIfDialog,"Defining the Gene level annotation file to be updated"))
Try(tkgrid(tklabel(ttIfDialog,text=" ")))
Try(frame1 <- tkframe(ttIfDialog,relief="groove",borderwidth=2))
Try(HowManyQuestion1 <- tklabel(frame1,text="Select the genechip of interest",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(HowManyQuestion1))
Try(tkgrid.configure(HowManyQuestion1,columnspan=2,sticky="w"))
Try(netaffxTcl <- tclVar("none"))
Try(I1.but <- tkradiobutton(frame1,text="Human exon genechip: HuEx",variable=netaffxTcl,value="HuEx",font=.affylmGUIglobals$affylmGUIfont2))
# Try(I2.but <- tkradiobutton(frame1,text="Human gene genechip: HuGene",variable=netaffxTcl,value="HuGene-",font=.affylmGUIglobals$affylmGUIfont2))
Try(I3.but <- tkradiobutton(frame1,text="Mouse exon genechip: MoEx",variable=netaffxTcl,value="MoEx",font=.affylmGUIglobals$affylmGUIfont2))
# Try(I4.but <- tkradiobutton(frame1,text="Mouse gene genechip: MoGene",variable=netaffxTcl,value="MoGene-",font=.affylmGUIglobals$affylmGUIfont2))
Try(I5.but <- tkradiobutton(frame1,text="Rat exon genechip: RaEx",variable=netaffxTcl,value="RaEx",font=.affylmGUIglobals$affylmGUIfont2))
# Try(I6.but <- tkradiobutton(frame1,text="Rat gene genechip: RaGene",variable=netaffxTcl,value="RaGene-",font=.affylmGUIglobals$affylmGUIfont2))
Try(I7.but <- tkradiobutton(frame1,text="None",variable=netaffxTcl,value="none",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(I1.but,sticky="w"))
# Try(tkgrid(I2.but,sticky="w"))
Try(tkgrid(I3.but,sticky="w"))
# Try(tkgrid(I4.but,sticky="w"))
Try(tkgrid(I5.but,sticky="w"))
# Try(tkgrid(I6.but,sticky="w"))
Try(tkgrid(I7.but,sticky="w"))
Try(tkgrid.configure(HowManyQuestion1,I1.but,I3.but,I5.but,I7.but,sticky="w"))
Try(onOK <- function()
{
Try(ReturnNetaffx <<- as.character(tclvalue(netaffxTcl)))
Try(tkgrab.release(ttIfDialog))
Try(tkdestroy(ttIfDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
})
Try(frame3 <- tkframe(ttIfDialog,borderwidth=2))
Try(onCancel <- function() {
Try(tkgrab.release(ttIfDialog))
Try(tkdestroy(ttIfDialog))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
})
Try(OK.but <-tkbutton(frame3,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <-tkbutton(frame3,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(frame3,text=" "),OK.but,Cancel.but,tklabel(frame3,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" "),frame1,tklabel(ttIfDialog,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" "),frame3,tklabel(ttIfDialog,text=" ")))
Try(tkgrid(tklabel(ttIfDialog,text=" ")))
Try(tkgrid.configure(frame1,frame3,sticky="w"))
Try(tkfocus(ttIfDialog))
Try(tkbind(ttIfDialog, "<Destroy>", function() {Try(tkgrab.release(ttIfDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttIfDialog))
if(ReturnNetaffx == "none"){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
if(ReturnNetaffx != "none"){
Try(annos <- rsrc[[grep(ReturnNetaffx, names(rsrc))]])
#gene level
Try(anno <- affxAnnotation(annos)[[grep("Transcript Cluster Annotations, CSV", affxDescription(rsrc[[grep(ReturnNetaffx, names(rsrc))]]))]]) #"transcript clusters Annotation, CSV Format"
Try(df <- readAnnotation(rsrc, annotation = anno, content=FALSE))
Try(df1 <- as.character(unlist(strsplit(df, ".zip"))))
Try(df1 <- as.character(unlist(strsplit(df1,'/'))))
Try(df1 <- df1[length(df1)])
Try(conn <- unz(df, df1))
Try(tmp <- readLines(conn, n=500))
Try(myskip <- grep("transcript_cluster_id", tmp))
Try(df.ann <- read.csv(conn, skip= (myskip - 1), header=T, as.is=T))
Try(df.ann <- df.ann[,which(names(df.ann)%in%c("probeset_id", "gene_assignment"))])
#IMPORTANT to build the GENE level oneChannelGUI annotation file I use only the first assignment mapped on the gen_assignment field in the annotation files
geneAnnExtraction <- function(x){
mx <- strsplit(x, '//')
mx <- as.vector(unlist(mx))
if(length(mx) >= 4){
mx <- mx[1:4]
mxtmp <- gsub(" ", "", mx[c(1:2,4)])
mx <- c(mxtmp[1:2], mx[3], mxtmp[3])
return(mx)
} else{
mx <- rep(NA, 4)
return(mx)
}
}
myann <- sapply(df.ann[,2], geneAnnExtraction)
myann <- t(myann)
rownames(myann) <- df.ann[,1]
df.ann <- cbind(df.ann[,1], myann)
df.ann <- as.data.frame(df.ann)
names(df.ann) <- c("PROBESETID","ACC","SYMBOL","DESCRIPTION","CYTOBAND")
#exon level
if(length(grep("Probeset Annotations, CSV Format", affxDescription(rsrc[[grep(ReturnNetaffx, names(rsrc))]]))) > 0){
Try(annops <- affxAnnotation(annos)[[grep("Probeset Annotations, CSV Format", affxDescription(rsrc[[grep(ReturnNetaffx, names(rsrc))]]))]]) #"exon probe set level Annotation, CSV Format"
Try(dfps <- readAnnotation(rsrc, annotation = annops, content=FALSE))
Try(df1ps <- as.character(unlist(strsplit(dfps, ".zip"))))
Try(df1ps <- as.character(unlist(strsplit(df1ps,'/'))))
Try(df1ps <- df1ps[length(df1ps)])
Try(connps <- unz(dfps, df1ps))
Try(tmpps <- readLines(connps, n=500))
Try(myskipps <- grep("probeset_id", tmpps))
Try(df.annps <- read.csv(connps, skip= (myskipps - 1), header=T, as.is=T))
Try(df.annps <- df.annps[,which(names(df.annps)%in%c("probeset_id", "seqname", "strand", "start", "stop", "transcript_cluster_id","level"))])
Try(names(df.annps) <- c("EPROBESETID", "CHR", "STRAND", "START", "STOP", "GPROBESETID","ANNLEVEL"))
}
####
if(ReturnNetaffx == "HuEx"){
huex.annotation <- df.ann
save(huex.annotation, file="huex.annotation.rda", ascii=T)
#hs exon-level probesets
cat("\nCreating annotation for Hs exon-level probesets. \nBased on USCS golden path data from hg19 genome release\n")
download.file("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/affyAllExonProbes.txt.gz", "affyAllExonProbes.txt.gz", mode="wb")
cat(".")
zz <- gzfile("affyAllExonProbes.txt.gz","r")
cat(".")
tmp <- readLines(con=zz)
cat(".")
close(zz)
tmp <- strsplit(tmp, "\t")
cat(".")
tmp <- as.data.frame(do.call(rbind, tmp), stringsAsFactors=F)
cat(".")
names(tmp) <- c("X", "CHR", "START", "STOP", "NAME", "SCORE", "STRAND")
tmp1 <- tmp$NAME
tmp1 <- strsplit(as.character(tmp1), "\\|")
cat(".")
eid <- sapply(tmp1, function(x)x[1])
cat(".")
eann <- sapply(tmp1, function(x)x[2])
cat(".")
crosshybhuex.annotation <- data.frame(eid, as.character(tmp[,2]), as.character(tmp[,3]), as.character(tmp[,4]), as.character(tmp[,7]), eann, as.character(tmp[,6]), stringsAsFactors=F)
names(crosshybhuex.annotation) <- c("EPROBESETID", "CHR", "START", "STOP", "STRAND", "ANNLEVEL", "SCORE")
cat(".")
df.annps <- df.annps[which(df.annps$EPROBESETID %in% crosshybhuex.annotation$EPROBESETID),]
crosshybhuex.annotation <- crosshybhuex.annotation[which(crosshybhuex.annotation$EPROBESETID %in% df.annps$EPROBESETID),]
df.annps <- df.annps[order(df.annps$EPROBESETID),]
crosshybhuex.annotation <- crosshybhuex.annotation[order(crosshybhuex.annotation$EPROBESETID),]
if(identical(as.character(df.annps$EPROBESETID), crosshybhuex.annotation$EPROBESETID)){
crosshybhuex.annotation <- cbind(crosshybhuex.annotation$EPROBESETID, as.character(df.annps$GPROBESETID), crosshybhuex.annotation[,2:dim(crosshybhuex.annotation)[2]])
names(crosshybhuex.annotation)[1] <- "EPROBESETID"
names(crosshybhuex.annotation)[2] <- "GPROBESETID"
save(crosshybhuex.annotation, file="crosshybhuex.annotation.rda")
} else{
cat("\nInternal error in buildingLocalAnnotation function. \nPlease report to oneChannelGUI maintainer raffaele.calogero@unito.it\n")
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
if(ReturnNetaffx == "HuGene-"){
hugene.annotation <- df.ann
save(hugene.annotation, file="hugene.annotation.rda", ascii=T)
}
if(ReturnNetaffx == "MoEx"){
moex.annotation <- df.ann
save(moex.annotation, file="moex.annotation.rda", ascii=T)
#mm exon-level probesets
cat("\nCreating annotation for Mm exon-level probesets. \nBased on USCS golden path data from mm9 genome release\n")
download.file("ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/affyAllExonProbes.txt.gz", "affyAllExonProbes.txt.gz", mode="wb")
cat(".")
zz <- gzfile("affyAllExonProbes.txt.gz","r")
cat(".")
tmp <- readLines(con=zz)
cat(".")
close(zz)
tmp <- strsplit(tmp, "\t")
cat(".")
tmp <- as.data.frame(do.call(rbind, tmp), stringsAsFactors=F)
cat(".")
names(tmp) <- c("X", "CHR", "START", "STOP", "NAME", "SCORE", "STRAND")
tmp1 <- tmp$NAME
tmp1 <- strsplit(as.character(tmp1), "\\|")
cat(".")
eid <- sapply(tmp1, function(x)x[1])
cat(".")
eann <- sapply(tmp1, function(x)x[2])
cat(".")
crosshybmoex.annotation <- data.frame(eid, as.character(tmp[,2]), as.character(tmp[,3]), as.character(tmp[,4]), as.character(tmp[,7]), eann, as.character(tmp[,6]), stringsAsFactors=F)
names(crosshybmoex.annotation) <- c("EPROBESETID", "CHR", "START", "STOP", "STRAND", "ANNLEVEL", "SCORE")
cat(".")
df.annps <- df.annps[which(df.annps$EPROBESETID %in% crosshybmoex.annotation$EPROBESETID),]
crosshybmoex.annotation <- crosshybmoex.annotation[which(crosshybmoex.annotation$EPROBESETID %in% df.annps$EPROBESETID),]
df.annps <- df.annps[order(df.annps$EPROBESETID),]
crosshybmoex.annotation <- crosshybmoex.annotation[order(crosshybmoex.annotation$EPROBESETID),]
if(identical(as.character(df.annps$EPROBESETID), crosshybmoex.annotation$EPROBESETID)){
crosshybmoex.annotation <- cbind(crosshybmoex.annotation$EPROBESETID, as.character(df.annps$GPROBESETID), crosshybmoex.annotation[,2:dim(crosshybmoex.annotation)[2]])
names(crosshybmoex.annotation)[1] <- "EPROBESETID"
names(crosshybmoex.annotation)[2] <- "GPROBESETID"
save(crosshybmoex.annotation, file="crosshybmoex.annotation.rda")
} else{
cat("\nInternal error in buildingLocalAnnotation function. \nPlease report to oneChannelGUI maintainer raffaele.calogero@unito.it\n")
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
if(ReturnNetaffx == "MoGene-"){
mogene.annotation <- df.ann
save(mogene.annotation, file="mogene.annotation.rda", ascii=T)
}
if(ReturnNetaffx == "RaEx"){
raex.annotation <- df.ann
save(raex.annotation, file="raex.annotation.rda", ascii=T)
#rm exon-level probesets
cat("\nCreating annotation for Rn exon-level probesets. \nBased on USCS golden path data from rn4 genome release\n")
download.file("ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/affyAllExonProbes.txt.gz", "affyAllExonProbes.txt.gz", mode="wb")
cat(".")
zz <- gzfile("affyAllExonProbes.txt.gz","r")
cat(".")
tmp <- readLines(con=zz)
cat(".")
close(zz)
tmp <- strsplit(tmp, "\t")
cat(".")
tmp <- as.data.frame(do.call(rbind, tmp), stringsAsFactors=F)
cat(".")
names(tmp) <- c("X", "CHR", "START", "STOP", "NAME", "SCORE", "STRAND")
tmp1 <- tmp$NAME
tmp1 <- strsplit(as.character(tmp1), "\\|")
cat(".")
eid <- sapply(tmp1, function(x)x[1])
cat(".")
eann <- sapply(tmp1, function(x)x[2])
cat(".")
crosshybraex.annotation <- data.frame(eid, as.character(tmp[,2]), as.character(tmp[,3]), as.character(tmp[,4]), as.character(tmp[,7]), eann, as.character(tmp[,6]), stringsAsFactors=F)
names(crosshybraex.annotation) <- c("EPROBESETID", "CHR", "START", "STOP", "STRAND", "ANNLEVEL", "SCORE")
cat(".")
df.annps <- df.annps[which(df.annps$EPROBESETID %in% crosshybraex.annotation$EPROBESETID),]
crosshybraex.annotation <- crosshybraex.annotation[which(crosshybraex.annotation$EPROBESETID %in% df.annps$EPROBESETID),]
df.annps <- df.annps[order(df.annps$EPROBESETID),]
crosshybraex.annotation <- crosshybraex.annotation[order(crosshybraex.annotation$EPROBESETID),]
if(identical(as.character(df.annps$EPROBESETID), crosshybraex.annotation$EPROBESETID)){
crosshybraex.annotation <- cbind(crosshybraex.annotation$EPROBESETID, as.character(df.annps$GPROBESETID), crosshybraex.annotation[,2:dim(crosshybraex.annotation)[2]])
names(crosshybraex.annotation)[1] <- "EPROBESETID"
names(crosshybraex.annotation)[2] <- "GPROBESETID"
save(crosshybraex.annotation, file="crosshybraex.annotation.rda")
} else{
cat("\nInternal error in buildingLocalAnnotation function. \nPlease report to oneChannelGUI maintainer raffaele.calogero@unito.it\n")
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
}
if(ReturnNetaffx == "RaGene-"){
ragene.annotation <- df.ann
save(ragene.annotation, file="ragene.annotation.rda", ascii=T)
}
Try(tkmessageBox(title="Annotation data update",message=paste("\n", ReturnNetaffx, "annotation file was correctly updated in oneChannelGUI\n"),type="ok",icon="info"))
Try(zz <- file(netaffxUpdates, "a")) # open an output file connection
Try(writeLines(paste(ReturnNetaffx, "annotation file was updated on", as.character(Sys.Date())), zz))
Try(close(zz))
}
} else {
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkmessageBox(title="Annotation update",message="User or password for netaffx was not inserted!",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
################################################################################
"refseqDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(aptDir <- get("aptDir",envir=affylmGUIenvironment))
Try(home <- getwd())
Try(blastDir <- paste(aptDir, "/blast/", sep=""))
Try(setwd(blastDir))
Try(cat("\nBegin downloads of fasta files.....\n"))
Try(cat("Be patient!\n"))
#require(Biostrings) || stop("library Biostrings could not be found !")
Try(download.file("ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz", "human.rna.fna.gz", mode="wb"))
#Try(refseq <- read.DNAStringSet(zz, "fasta"))
#Try(write.XStringSet(refseq, file="hs.fa", format="fasta"))
Try(download.file("ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.rna.fna.gz", "mouse.rna.fna.gz", mode="wb"))
Try(download.file("ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.rna.fna.gz", "rat.rna.fna.gz", mode="wb"))
Try(cat("\nEnd downloads of 3 RefSeq fasta files.....\n"))
Try(mbVal <- tkmessageBox(title="RefSeq Fasta",
message=paste("Do you wish to unpack manually the gz files in ", getwd(), "\n If you answer NO oneChannelGUI will handle unpacking,\nbut the procedure can be quite long. Be patient!"),
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="yes"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(cat("\nRefSeq fasta gz files are located in ", getwd(),"\n"))
Try(setwd(home))
return()
}
Try(zz <- gzfile("human.rna.fna.gz", "r"))
Try(refseq <- readFASTA(zz, strip.desc=TRUE))
Try(writeFASTA(refseq, file="human.rna.fna", width=80))
Try(zz <- gzfile("mouse.rna.fna.gz", "r"))
Try(refseq <- readFASTA(zz, strip.desc=TRUE))
Try(writeFASTA(refseq, file="mouse.rna.fna", width=80))
Try(zz <- gzfile("rat.rna.fna.gz", "r"))
Try(refseq <- readFASTA(zz, strip.desc=TRUE))
Try(writeFASTA(refseq, file="rat.rna.fna", width=80))
Try(cat("\nRefSeq fasta files are ready to be used in ", getwd(),"\n"))
Try(setwd(home))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
#"madscrosshybDownload" <- function(){
# Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
# Try(home <- getwd())
# Try(libDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/affylibs/", sep = ""))
# Try(setwd(libDirLocation))
#gathering affy libs and apt tools folders
# Try(cat("\nBegin downloads of MADS CrossHyb data.....\n"))
# Try(cat("Be patient!\n"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Human_CrossHyb.txt", "Human_CrossHyb.txt", mode="w"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Mouse_CrossHyb.txt", "Mouse_CrossHyb.txt", mode="w"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Human_CrossHyb_core.txt", "Human_CrossHyb_core.txt", mode="w"))
# Try(download.file("http://biogibbs.stanford.edu/~yxing/MADS/Mouse_CrossHyb_core.txt", "Mouse_CrossHyb_core.txt", mode="w"))
# Try(cat("\nEnd downloads of Human and Mouse MADS crosshyb files.....\n"))
# hs <- read.table("Human_CrossHyb_core.txt", sep="\t", header=T, as.is=T)
#building a mps without crosshyb exon probe sets, selecting bad probes on the basis of MADS approach
# mm <- read.table("Mouse_CrossHyb_core.txt", sep="\t", header=T, as.is=T)
# crossRefs <- which(mm$MaxCorrCrossHybRefseqEvidence > 0)
#hist(MaxCorrWithCrossHybTranscript[crossRefs])
# mm.cross <- mm[crossRefs,]
# mm.cross <- mm.cross[which(mm.cross$MaxCorrWithCrossHybTranscript >= 0.2),]
# mps <- mps[grep("core", mps)]
# mps <- mps[grep("mps$", mps)]
# mps.df <- read.table(mps, sep="\t", header=T, as.is=T)
# for(i in 1:dim(mm.cross)[1]){
# tmp <- mps.df[which(mps.df[,2] == mm.cross$TranscriptClusterId[1]),]
# tmp.p <- as.character(unlist(strsplit(as.character(tmp[3])," ")))
# tmp.p <- tmp.p[which(tmp.p != as.character(mm.cross$ProbesetId[1]))]
# tmp.p <- paste(tmp.p, collapse=" ")
# mps.df[which(mps.df[,2] == mm.cross$TranscriptClusterId[1]),3] <- tmp.p
#write.table.....
# }
# Try(setwd(home))
#}
################################################################################
"updateLibs" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(mbVal <- tkmessageBox(title="Updating Bioconductor Libraries",
message="You are updating all Bioconductor libraries files. \nThe process might take some time!", icon="question",type="yesno",default="yes"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
################################################################################
#inernal function used in variantExons
".outvsp" <- function(ov, affyR, vspR, chr, genome){
# myout <- list("affyname"=names(affyR)[ov[2]],"affystart"=start(affyR)[ov[2]],
# "affyend"=end(affyR)[ov[2]], "affywidth"=width(affyR)[ov[2]],
# "vspname"=names(vspR)[ov[1]],"vspstart"=start(vspR)[ov[1]],
# "vspend"=end(vspR)[ov[1]], "vspwidth"=width(vspR)[ov[1]])
affyname <- strsplit(names(affyR)[ov[2]],"\\.")[[1]][1]
affystrand <- strsplit(names(affyR)[ov[2]],"\\.")[[1]][2]
vspname <- strsplit(names(vspR)[ov[1]],"\\.")[[1]][1]
vspstrand <- strsplit(names(vspR)[ov[1]],"\\.")[[1]][2]
myout <- c(affyname,start(affyR)[ov[2]],end(affyR)[ov[2]], width(affyR)[ov[2]], affystrand,
vspname, start(vspR)[ov[1]], end(vspR)[ov[1]], width(vspR)[ov[1]], vspstrand,as.character(sub("chr","", chr)), genome)
}
"variantExons" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#require(IRanges) || stop("\nMissing IRanges library\n")
#loading exon level annotation
for(j in c("huex","moex","raex")){
out.all <- NULL
if(j=="huex"){
genome <- "organism=Human&version=hg19"
data(HuExExonProbesetLocation)
subject<- get("HuExExonProbesetLocation",envir=.GlobalEnv)
}
if(j=="moex"){
genome <- "organism=Mouse&version=mm9"
data(MoExExonProbesetLocation)
subject<- get("MoExExonProbesetLocation",envir=.GlobalEnv)
}
if(j=="raex"){
genome <- "organism=Rattus&version=rn4"
data(RaExExonProbesetLocation)
subject<- get("RaExExonProbesetLocation",envir=.GlobalEnv)
}
#retrieving variant exon file
vsp.file <- paste("http://www6.unito.it/RRE/Query/ensembleQuery.php?", genome, sep="")
tmpfile <- tempfile(tmpdir = getwd())
download.file(vsp.file, tmpfile, mode="w")
query <- read.table(tmpfile, header=T, as.is=T, sep="\t")
chr <- unique(query$chromosome)
chr <- chr[setdiff(seq(1,length(chr)),grep("_", chr))]
exoncore <- subject[which(subject$ANNLEVEL == "core"),]
for(i in chr){
vsp.tmp <- query[which(query$chromosome==i),]
vspRanges <- IRanges(start=vsp.tmp$start, end=vsp.tmp$end, names=paste(vsp.tmp$"transcript_id", vsp.tmp$"strand", sep="."))
#retrieving exon level annotation
exonchr <- subject[which(subject$CHR == i),]
affyRanges <- IRanges(start=as.numeric(exonchr$START), end=as.numeric(exonchr$STOP), names=paste(as.character(exonchr$EPROBESETID),exonchr$STRAND,sep="."))
ov <- findOverlaps(affyRanges, query=vspRanges)
ov <- matchMatrix(ov)
out <- apply(ov, 1,.outvsp, affyR=affyRanges, vspR=vspRanges, chr=i, genome=genome)
out <- t(out)
out <- out[which(out[,5] == out[,10]),]
out.all <- rbind(out.all, out)
}
dimnames(out.all)[[2]] <- c("affyname", "affystart", "affyend", "affywidth", "affystrand","vspname", "vspstart", "vspend", "vspwidth","vspstrand","chr","genome")
if(j == "huex"){
huex.variantexons <- out.all
save(huex.variantexons, file="huex.variantexons.rda", ascii=T)
cat("\n huex.variantexons.rda variant exons dataset is now ready to be now copied in oneChannelGUI data dir\n")
}
if(j == "moex"){
moex.variantexons <- out.all
save(moex.variantexons, file="moex.variantexons.rda", ascii=T)
cat("\n moex.variantexons.rda variant exons dataset is now ready to be now copied in oneChannelGUI data dir\n")
}
if(j == "raex"){
raex.variantexons <- out.all
save(raex.variantexons, file="raex.variantexons.rda", ascii=T)
cat("\n raex.variantexons.rda variant exons dataset is now ready to be now copied in oneChannelGUI data dir\n")
}
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
"exportFASTA" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#require(Biostrings) || stop("\nMissing Biostrings library\n")
#which organism
Try(ttGetOrganism <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetOrganism))
Try(tkgrab.set(ttGetOrganism))
Try(tkfocus(ttGetOrganism))
Try(tkwm.title(ttGetOrganism,"Which organism"))
Try(tkgrid(tklabel(ttGetOrganism,text=" ")))
Try(ttGetOrganismTcl <- tclVar("hs"))
Try(rbIQR.5 <- tkradiobutton(ttGetOrganism,text="H. sapiens",variable=ttGetOrganismTcl,value="hs",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.25<-tkradiobutton(ttGetOrganism,text="M. musculus",variable=ttGetOrganismTcl,value="mm",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.1<-tkradiobutton(ttGetOrganism,text="R. norvegicus",variable=ttGetOrganismTcl,value="rn",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.15<-tkradiobutton(ttGetOrganism,text="B. taurus",variable=ttGetOrganismTcl,value="bo",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.5))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.25))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.1))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),rbIQR.15))
Try(tkgrid.configure(rbIQR.5,rbIQR.25,rbIQR.1, rbIQR.15,columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),tklabel(ttGetOrganism,text=" ")))
Try(ReturnVal <- "")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetOrganism));Try(tkdestroy(ttGetOrganism));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetOrganismTcl));Try(tkgrab.release(ttGetOrganism));Try(tkdestroy(ttGetOrganism));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetOrganism,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetOrganism,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetOrganism,text=" "),OK.but,Cancel.but, tklabel(ttGetOrganism,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetOrganism,text=" ")))
Try(tkbind(ttGetOrganism,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetOrganism));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetOrganism))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
#miRbase19
Try(load(paste(find.package(package="oneChannelGUI"),"/data/hairpin.rda",sep="")))
if(ReturnVal == ""){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else if (ReturnVal == "hs"){
#hsa precursor
Try(hsfa <- hairpin[grep("^hsa-",names(hairpin))])
Try(writeXStringSet(hsfa, file="ncHs.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncHs.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
} else if (ReturnVal == "mm"){
#mmu precursor
Try(mmfa <- hairpin[grep("^hsa-",names(hairpin))])
Try(writeXStringSet(mmfa, file="ncMm.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncMm.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
} else if (ReturnVal == "rn"){
#rno precursor
Try(rnfa <- hairpin[grep("^rno-",names(hairpin))])
Try(writeXStringSet(rnfa, file="ncRn.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncRn.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
else if (ReturnVal == "bo"){
#bta precursor
Try(bofa <- hairpin[grep("^bta-",names(hairpin))])
Try(writeXStringSet(bofa, file="ncBo.fa"))
Try(tkmessageBox(title="FASTA reference file",message="The fasta reference file for non-coding RNA quantification is saved in ncBo.fa\n Use it for mapping NGS reads",type="ok", icon="info"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
}
################################################################################
"ngsperlDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="NGS perl scripts",message="This routine creates a folder for the perl scripts used to reformat NGS primary mapping output."))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(myWD <- getwd())
#Try(SetWD())
Try(perlDirLocation <- get("perlDirLocation",envir=affylmGUIenvironment))
if(perlDirLocation != ""){
Try(mbVal <- tkmessageBox(title="NGS perl scripts",
message="There already a folder defined for NGS perl scripts.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
}
Try(perlDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/ngsperl", sep=""))
Try(dir.create(perlDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(perlDirLocation))
Try(assign("perlDirLocation", perlDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(cat("\nBegin downloads of NGS scripts.....\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/ngsperl.zip/download", "ngsperl.zip", mode="wb"))
if(.Platform$OS.type=="windows"){
Try(unzip("ngsperl.zip"))
# Try(setwd("ngsperl"))
# Try(system('XCOPY /S *.* ..'))
# Try(setwd(".."))
} else{
Try(system(paste("unzip ngsperl.zip", sep="")))
# Try(setwd("ngsperl"))
# Try(system("mv * .."))
# Try(setwd(".."))
}
Try(cat("\nEnd unzip NGS scripts.....\n"))
Try(cat("\nNGS scripts are ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="perlDirLocation"),2] <- perlDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("perlDirLocation", perlDirLocation, affylmGUIenvironment))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
}
################################################################################
"meVDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="meV software",message="This routine creates a folder to install the meV software."))
Try(myWD <- getwd())
#Try(SetWD())
Try(meVDirLocation.Available <- get("meVDirLocation.Available",envir=affylmGUIenvironment))
if(meVDirLocation.Available){
Try(mbVal <- tkmessageBox(title="meV software",
message="There already a folder defined for meV software.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
return()
}
}
Try(meVDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/meV", sep=""))
Try(dir.create(meVDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(meVDirLocation))
Try(assign("meVDirLocation", meVDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(cat("\nBegin downloads of meV.....\n"))
#defining which program to be downloaded
Try(ttGetMev <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetMev))
Try(tkgrab.set(ttGetMev))
Try(tkfocus(ttGetMev))
Try(tkwm.title(ttGetMev,"Which OS are you using?"))
Try(tkgrid(tklabel(ttGetMev,text=" ")))
Try(ttGetMevTcl <- tclVar("win"))
Try(rbIQR.win <- tkradiobutton(ttGetMev,text="windows ",variable=ttGetMevTcl,value="win",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mac<-tkradiobutton(ttGetMev,text="mac ",variable=ttGetMevTcl,value="mac",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.linux<-tkradiobutton(ttGetMev,text="linux ",variable=ttGetMevTcl,value="linux",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetMev,text=" "),rbIQR.win))
Try(tkgrid(tklabel(ttGetMev,text=" "),rbIQR.mac))
Try(tkgrid(tklabel(ttGetMev,text=" "),rbIQR.linux))
Try(tkgrid.configure(rbIQR.win,rbIQR.mac,rbIQR.linux, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetMev,text=" "),tklabel(ttGetMev,text=" ")))
Try(ReturnVal <- "win")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetMev));Try(tkdestroy(ttGetMev));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetMevTcl));Try(tkgrab.release(ttGetMev));Try(tkdestroy(ttGetMev));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetMev,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetMev,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetMev,text=" "),OK.but,Cancel.but, tklabel(ttGetMev,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetMev,text=" ")))
Try(tkbind(ttGetMev,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetMev));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetMev))
if(ReturnVal=="win"){
Try(download.file("http://sourceforge.net/projects/mev-tm4/files/mev-tm4/MeV%204.8/MeV_4_8_0_r2721_win.zip/download", "mev.zip", mode="wb"))
Try(unzip("mev.zip"))
Try(setwd("MeV_4_8_0"))
Try(system('XCOPY /S *.* ..'))
Try(setwd(".."))
Try(cat("\nThe MeV downloaded version is MeV_4_8_0\n"))
} else if (ReturnVal=="mac"){
Try(download.file("http://sourceforge.net/projects/mev-tm4/files/mev-tm4/MeV%204.8/MeV_4_8_0_r2721_mac.tgz/download", "mev.tgz", mode="wb"))
Try(system(paste("gzip -d ","mev.tgz", sep="")))
Try(system(paste("tar xvf ","mev.tar", sep="")))
Try(cat("\nThe MeV downloaded version is MeV_4_8_0\n"))
Try(setwd("MeV_4_8_0"))
Try(system("cp -fR * .."))
Try(setwd(".."))
Try(system("rm -fR MeV_4_8_0"))
} else if (ReturnVal=="linux"){
Try(download.file("http://sourceforge.net/projects/mev-tm4/files/mev-tm4/MeV%204.8/MeV_4_8_0_r2721_linux.tar.gz/download", "mev.tar.gz", mode="wb"))
Try(system(paste("gzip -d ","mev.tar.gz", sep="")))
Try(system(paste("tar xvf ","mev.tar", sep="")))
Try(cat("\nThe MeV downloaded version is MeV_4_8_0\n"))
Try(setwd("MeV_4_8_0"))
Try(system("cp -fR * .."))
Try(setwd(".."))
}
Try(cat("\nEnd unzip meV files.....\n"))
Try(cat("\nMeV software is ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="meVDirLocation"),2] <- meVDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("meVDirLocation", meVDirLocation, affylmGUIenvironment))
assign("meVDirLocation.Available",TRUE,affylmGUIenvironment)
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
}
################################################################################
#external package info
"extPckInfo" <- function(){
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(tmp <- system("perl -v 2>&1", intern = T))
Try(if(length(tmp) > 0) perl.version <- tmp[2])
# Try(tmp <- system("python -V 2>&1", intern = T))
# Try(if(length(tmp) > 0) python.version <- tmp)
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(perlDirLocation <- get("perlDirLocation",envir=affylmGUIenvironment))
# Try(pythonDirLocation <- get("pythonDirLocation",envir=affylmGUIenvironment))
Try(bowtieRefs <- get("bowtieRefs",envir=affylmGUIenvironment))
Try(installed <- names(bowtieRefs)[which(bowtieRefs=="Y")])
Try(tkmessageBox(title="External Packages associated to oneChannelGUI",message=paste("Affymetrix libraries: ", myinfo[1,2],
"\nAPT tools: ",myinfo[2,2],
"\nmeV clustering tool: ",myinfo[3,2],
"\nBowtie short reads aligner: ",myinfo[4,2],
"\nJava: ",myinfo[5,2],
"\nBowtie genomes: ", paste(installed, collapse=", "),
"\nPerl software: ", perl.version,
"\nPerl scripts: ", perlDirLocation,
"\n",sep="")))
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
"combining2eSet" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="combining two datasets",message="This routine combines two matrices having the same number of row and the same row identifiers."))
Try(tempFileName1 <- tclvalue(tkgetOpenFile(filetypes = "{{Text Files} {.txt}} {{All files} *}")))
if (!nchar(tempFileName1)) {
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(mySel1 <- read.table(tempFileName1, sep = "\t", header = T, as.is = TRUE, row.names=1))
Try(tempFileName2 <- tclvalue(tkgetOpenFile(filetypes = "{{Text Files} {.txt}} {{All files} *}")))
if (!nchar(tempFileName2)) {
tkfocus(.affylmGUIglobals$ttMain)
return()
}
Try(mySel2 <- read.table(tempFileName2, sep = "\t", header = T, as.is = TRUE, row.names=1))
Try(mySel1 <- mySel1[order(rownames(mySel1)),])
Try(mySel2 <- mySel2[order(rownames(mySel2)),])
if(identical(rownames(mySel1), rownames(mySel2))){
tempFileName1 <- unlist(strsplit(tempFileName1, "/"))
tempFileName1 <- tempFileName1[length(tempFileName1)]
tempFileName1 <- sub(".txt$", "", tempFileName1)
tempFileName2 <- unlist(strsplit(tempFileName2, "/"))
tempFileName2 <- tempFileName2[length(tempFileName2)]
tempFileName2 <- sub(".txt$", "", tempFileName2)
tempFileName <- paste(tempFileName1, "_", tempFileName2,".txt",sep="")
Try(mySel <- cbind(mySel1, mySel2))
Try(write.table(mySel, file = tempFileName, sep = "\t", quote = FALSE, col.names = NA))
Try(tkmessageBox(title="Combining two datasets",message=paste("The combined dataset is available in",getwd(),"as",tempFileName,sep="\n")))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
} else{
Try(tkmessageBox(title="Combining datasets",message="The two datasets do not have the same row identifiers.\nThey cannot be combined!",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
#using bowtieDownload I can also call the function to download or build the ref genomes for bowtie
#alos downloading tophat and cufflinks
"bowtieDownload" <- function(){
Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(require(Biostrings) || stop("library Biostrings could not be found !"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(myWD <- getwd())
Try(tkmessageBox(title="Bowtie primary mapping of short reads",message="This routine creates a folder to install the bowtie software and \nPicard tools to handle SAM files."))
# Try(libDirLocation <- get("libDirLocation",envir=affylmGUIenvironment))
# if(libDirLocation == ""){
# Try(.downloadLibs())
# Try(setwd(myWD))
# Try(tkfocus(.affylmGUIglobals$ttMain))
# }
Try(binDir.Available <- get("binDir.Available",envir=affylmGUIenvironment))
if(!binDir.Available){
Try(setBinDir())
}
#download fastQC
Try(cat("\nDownloading the fastQC java tool for qc analysis of fastq files\n"))
Try(fastqcDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/FastQC", sep=""))
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(setwd(path.package("oneChannelGUI", quiet = FALSE)))
Try(download.file("http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip", "fastqc.zip", mode="wb"))
Try(unzip("fastqc.zip"))
Try(cat("\nThe fastQC downloaded version is fastqc_v0.11.2\n"))
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",TRUE,affylmGUIenvironment))
#download bowtie
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(bowtieDirLocation.Available){
Try(mbVal <- tkmessageBox(title="Bowtie software",
message="There already a folder defined for bowtie software.\nDo you want to change it?",
icon="question",type="yesno",default="no"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="no"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
Try(setwd(bowtieDirLocation))
Try(.bowtieGenomes())
Try(setwd(myWD))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
}
Try(bowtieDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/bowtie", sep=""))
Try(dir.create(bowtieDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(bowtieDirLocation))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))#directory where NGS perl scripts are located
Try(cat("\nBegin downloads of bowtie.....\n"))
#defining which program to be downloaded
Try(ttGetBowtie <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetBowtie))
Try(tkgrab.set(ttGetBowtie))
Try(tkfocus(ttGetBowtie))
Try(tkwm.title(ttGetBowtie,"Which OS are you using?"))
Try(tkgrid(tklabel(ttGetBowtie,text=" ")))
Try(ttGetBowtieTcl <- tclVar("win32"))
Try(rbIQR.win32 <- tkradiobutton(ttGetBowtie,text="windows ",variable=ttGetBowtieTcl,value="win32",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mac32<-tkradiobutton(ttGetBowtie,text="mac 32 bits ",variable=ttGetBowtieTcl,value="mac32",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mac64<-tkradiobutton(ttGetBowtie,text="mac 64 bits ",variable=ttGetBowtieTcl,value="mac64",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.linux32<-tkradiobutton(ttGetBowtie,text="linux 32 bits ",variable=ttGetBowtieTcl,value="linux32",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.linux64<-tkradiobutton(ttGetBowtie,text="linux 64 bits ",variable=ttGetBowtieTcl,value="linux64",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.win32))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.mac32))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.mac64))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.linux32))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),rbIQR.linux64))
Try(tkgrid.configure(rbIQR.win32,rbIQR.mac32,rbIQR.mac64,rbIQR.linux32,rbIQR.linux64, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),tklabel(ttGetBowtie,text=" ")))
Try(ReturnVal <- "win32")
Try(onCancel <- function() {Try(ReturnVal <<- "");Try(tkgrab.release(ttGetBowtie));Try(tkdestroy(ttGetBowtie));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal <<- tclvalue(ttGetBowtieTcl));Try(tkgrab.release(ttGetBowtie));Try(tkdestroy(ttGetBowtie));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetBowtie,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetBowtie,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetBowtie,text=" "),OK.but,Cancel.but, tklabel(ttGetBowtie,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetBowtie,text=" ")))
Try(tkbind(ttGetBowtie,"<Destroy>",function() {ReturnVal <- "";Try(tkgrab.release(ttGetBowtie));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetBowtie))
#down-loading gene leve scaffolds
Try(cat("\nDownloading the gene-level scaffolds for human mouse and rat.\nThose scaffolds are used to build gne-oriented eSets containing RNA-seq mapped data\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/gene-level_USCS.GRanges/rn4_gene-level.scaffold.Rda/download", "rn4_gene-level.scaffold.Rda", mode="wb"))
Try(cat("\nThe The gene-level scaffolds for Rat genome were correctly downloaded\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/gene-level_USCS.GRanges/mm9_gene-level.scaffold.Rda/download", "mm9_gene-level.scaffold.Rda", mode="wb"))
Try(cat("\nThe The gene-level scaffolds for Mouse genome were correctly downloaded\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/gene-level_USCS.GRanges/hg19_gene-level.scaffold.Rda/download", "hg19_gene-level.scaffold.Rda", mode="wb"))
Try(cat("\nThe The gene-level scaffolds for Human genome were correctly downloaded\n"))
#download mirbase latest
Try(download.file("ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.zip", "hairpin.fa.zip", mode="wb"))
#Try(system("gzip -d hairpin.fa.gz"))
Try(unzip("hairpin.fa.zip"))
Try(cat("\nLatest miRbase was correctly downloaded\n"))
Try(hairpin <- readRNAStringSet("hairpin.fa"))
Try(hairpin <- DNAStringSet(hairpin))
Try(save(hairpin,file=paste(find.package(package="oneChannelGUI"),"/data/hairpin.rda",sep="")))
if(ReturnVal=="win32"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-mingw-x86_64.zip/download", "bowtie.zip", mode="wb"))
Try(unzip("bowtie.zip"))
Try(cat("\nThe Bowtie downloaded version is bowtie_1_1_1\n"))
Try(setwd("bowtie-1.1.1"))
Try(system('XCOPY /S *.* ..'))
Try(setwd(".."))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
} else if (ReturnVal=="mac32"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-macos-10.5-i386.zip/download", "bowtie.zip", mode="wb"))
Try(unzip("bowtie.zip"))
Try(cat("\nThe Bowtie downloaded version is bowtie_0_12_7\n"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(system("cp -fR ./bowtie-0.12.7/* ."))
Try(system("rm -fR ./bowtie-0.12.7/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
} else if (ReturnVal=="mac64"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-macos-x86_64.zip/download", "bowtie.zip", mode="wb"))
Try(unzip("bowtie.zip"))
Try(cat("\nThe Bowtie downloaded version is bowtie_1_1_1\n"))
Try(system("cp -fR ./bowtie-1.1.1/* ."))
Try(system("rm -fR ./bowtie-1.1.1/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
#tophat
Try(tophatDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/tophat", sep=""))
Try(dir.create(tophatDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(tophatDirLocation))
Try(cat("\nBegin downloads of tophat.....\n"))
Try(download.file("http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.OSX_x86_64.tar.gz", "tophat.tar.gz", mode="wb"))
Try(system("gzip -d tophat.tar.gz"))
Try(system("tar xvf tophat.tar"))
Try(cat("\nThe TopHat downloaded version is tophat-2.0.411.OSX_x86_64\n"))
Try(system("cp -fR ./tophat-2.0.13.OSX_x86_64/* ."))
Try(system("rm -fR ./tophat-2.0.13.OSX_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="tophatDirLocation"),2] <- tophatDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment))
#cufflinks
Try(cuffDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/cufflinks", sep=""))
Try(dir.create(cuffDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(cuffDirLocation))
Try(cat("\nBegin downloads of cufflinks.....\n"))
Try(download.file("http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz", "cufflinks.tar.gz", mode="wb"))
Try(system("gzip -d cufflinks.tar.gz"))
Try(system("tar xvf cufflinks.tar"))
Try(cat("\nThe Cufflinks downloaded version is cufflinks-2.1.1.OSX_x86_64\n"))
Try(system("cp -fR ./cufflinks-2.2.1.OSX_x86_64/* ."))
Try(system("rm -fR ./cufflinks-2.2.1.OSX_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="cuffDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment))
#samtools
Try(samtoolsDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/samtools", sep=""))
Try(dir.create(samtoolsDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(samtoolsDirLocation))
Try(cat("\nBegin downloads of samtools.....\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/tools/samtools_mac64.tar.gz/download", "samtools.tar.gz", mode="wb"))
Try(system("gzip -d samtools.tar.gz"))
Try(system("tar xvf samtools.tar"))
Try(cat("\nThe Samtools downloaded version is samtools-0.1.18\n"))
Try(system("cp -fR ./samtools-0.1.18/* ."))
Try(system("rm -fR ./samtools-0.1.18/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment))
Try(tuxedoSetup())
} else if (ReturnVal=="linux32"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-i386.zip/download", "bowtie.zip", mode="wb"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(cat("\nThe Bowtie downloaded version is bowtie_0_12_7\n"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(system("cp -fR ./bowtie-0.12.7/* ."))
Try(system("rm -fR ./bowtie-0.12.7/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
} else if (ReturnVal=="linux64"){
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-linux-x86_64.zip/download", "bowtie.zip", mode="wb"))
Try(cat("\nThe Bowtie downloaded version is bowtie_1_1_1\n"))
Try(system(paste("unzip bowtie.zip", sep="")))
Try(system("cp -fR ./bowtie-1.1.1/* ."))
Try(system("rm -fR ./bowtie-1.1.1/"))
Try(assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment))
#tophat
Try(tophatDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/tophat", sep=""))
Try(dir.create(tophatDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(tophatDirLocation))
Try(cat("\nBegin downloads of tophat.....\n"))
Try(download.file("http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz", "tophat.tar.gz", mode="wb"))
Try(system("gzip -d tophat.tar.gz"))
Try(system("tar xvf tophat.tar"))
Try(cat("\nThe TopHat downloaded version is tophat-2.0.11.Linux_x86_64\n"))
Try(system("cp -fR ./tophat-2.0.13.Linux_x86_64/* ."))
Try(system("rm -fR ./tophat-2.0.13.Linux_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="tophatDirLocation"),2] <- tophatDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment))
Try(cat("\nEnd unzip tophat files.....\n"))
#cufflinks
Try(cuffDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/cufflinks", sep=""))
Try(dir.create(cuffDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(cuffDirLocation))
Try(cat("\nBegin downloads of cufflinks.....\n"))
Try(download.file("http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz", "cufflinks.tar.gz", mode="wb"))
Try(system("gzip -d cufflinks.tar.gz"))
Try(system("tar xvf cufflinks.tar"))
Try(cat("\nThe TopHat downloaded version is cufflinks-2.2.1.Linux_x86_64\n"))
Try(system("cp -fR ./cufflinks-2.2.1.Linux_x86_64/* ."))
Try(system("rm -fR ./ccufflinks-2.2.1.Linux_x86_64/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="cuffDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment))
Try(cat("\nEnd unzip cufflinks files.....\n"))
#samtools
Try(samtoolsDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/samtools", sep=""))
Try(dir.create(samtoolsDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(setwd(samtoolsDirLocation))
Try(cat("\nBegin downloads of samtools.....\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/tools/samtools_linux64.tar.gz/download", "samtools.tar.gz", mode="wb"))
Try(system("gzip -d samtools.tar.gz"))
Try(system("tar xvf samtools.tar"))
Try(cat("\nThe Samtools downloaded version is samtools-0.1.18\n"))
Try(system("cp -fR ./samtools-0.1.18/* ."))
Try(system("rm -fR ./samtools-0.1.18/"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2] <- cuffDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment))
Try(tuxedoSetup())
}
Try(cat("\nEnd unzip Bowtie files.....\n"))
Try(cat("\nStart download of Picard tools for sam to bam conversion.....\n"))
#non ti dimenticare di aggiustare tuttui i nuovi nomi se modifichi la versione di picard
Try(setwd(bowtieDirLocation))
Try(download.file("http://sourceforge.net/projects/picard/files/picard-tools/1.119/picard-tools-1.119.zip/download", "picard.zip", mode="wb"))
Try(cat("\nThe Picard downloaded version is picard-tools-1.115\n"))
if(ReturnVal=="win32"){
Try(unzip("picard.zip"))
Try(setwd("picard-tools-1.119"))
Try(system('XCOPY /S *.* ..'))
Try(setwd(".."))
} else{
Try(system(paste("unzip picard.zip", sep="")))
Try(system("cp -fR ./picard-tools-1.119/* ."))
Try(system("rm -fR ./picard-tools-1.119/"))
Try(system("chmod -fR +x *"))
}
Try(cat("\nBowtie and Picard tools are ready to be used in ", getwd(),"\n"))
#save the info to be recovered in a new session
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myinfo[which(myinfo[,1]=="bowtieDirLocation"),2] <- bowtieDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(cat("\nInstalling bowtie reference sequences for miRNA analysis....\n"))
Try(cat("\nStart building Hs...\n"))
Try(hsfa <- hairpin[grep("^hsa-",names(hairpin))])
Try(writeXStringSet(hsfa, file="ncHs.fa"))
if(.Platform$OS.type=="windows"){
Try(system("bowtie-build.exe -f ncHs.fa hs_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncHs.fa hs_nc", sep="")))
}
Try(cat("\nThe fasta reference file for Hs miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(cat("\nStart building Mm...\n"))
Try(mmfa <- hairpin[grep("^mmu-",names(hairpin))])
Try(writeXStringSet(mmfa, file="ncMm.fa"))
if(.Platform$OS.type=="windows" ){
Try(system("bowtie-build.exe -f ncMm.fa mm_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncMm.fa mm_nc", sep="")))
}
Try(cat("\nThe fasta reference file for Mm miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(cat("\nStart building Rn...\n"))
Try(rnfa <- hairpin[grep("^rno-",names(hairpin))])
Try(writeXStringSet(rnfa, file="ncRn.fa"))
if(.Platform$OS.type=="windows" ){
Try(system("bowtie-build.exe -f ncRn.fa rn_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncRn.fa rn_nc",sep="")))
}
Try(cat("\nThe fasta reference file for Rn miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(cat("\nStart building Bo...\n"))
Try(bofa <- hairpin[grep("^bta-",names(hairpin))])
Try(writeXStringSet(bofa, file="ncBo.fa"))
if(.Platform$OS.type=="windows" ){
Try(system("bowtie-build.exe -f ncBo.fa bo_nc"))
} else if(.Platform$OS.type!="windows" ){
Try(system(paste(bowtieDirLocation,"/bowtie-build -f ncBo.fa bo_nc", sep="")))
}
Try(cat("\nThe fasta reference file for Bovine miRNA has been indexed for Illumina data mapping with bowtie\n"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkmessageBox(title="Bowtie primary mapping of short reads",message="Bowtie is installed with the miRNA precursors sets\nIf you wish to install other reference genomes, please use the function:\nDownload and build hs, mm, rn bowtie reference sets."))
Try(setwd(myWD))
#test if java path is defined
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
Try(javaDir <- myinfo[which(myinfo[,1]== "javaDir"),2])
if(is.na(javaDir)){javaDir <- ""}
if(javaDir == ""){
Try(tmp.java <- NULL)
Try(tmp.java <- system("java -version 2>&1", intern=T))
if(length(grep("Java", tmp.java)) == 0){
Try(tkmessageBox(title="Bowtie primary mapping of short reads",message="It seems that java dir is not defined in the system path.\nPlease provide the path for java.\nIn windows should be C:/somewhere/Java/jre6.", icon="error"))
Try(javaFolder())
}
}
Try(tkfocus(.affylmGUIglobals$ttMain))
}
################################################################################
################################################################################
"bowtieGenomes" <- function(){
Try(ptm <- proc.time())
# Try(require(R.utils) || stop("\nMissing R.utils library!\n"))
Try(tkfocus(.affylmGUIglobals$ttMain))
#Try(require(Biostrings) || stop("library Biostrings could not be found !"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
if(is.na(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2])){
Try(tkmessageBox(title="Bowtie",message="Bowtie cannot be found please go to the General tool menu and use the function:\nInstall Bowtie and Picard tools\nto install Bowtie.",icon="error",type="ok"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(setwd(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2]))
#which ref
Try(ttGetGenomes <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetGenomes))
Try(tkgrab.set(ttGetGenomes))
Try(tkfocus(ttGetGenomes))
Try(tkwm.title(ttGetGenomes,"Which genome do you want to use as reference?"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(ttGetGenomesTcl <- tclVar("hg19e"))
Try(rbIQR.hs <- tkradiobutton(ttGetGenomes,text="Human hg19 genome ",variable=ttGetGenomesTcl,value="hg19",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mm<-tkradiobutton(ttGetGenomes,text="Mouse mm9 genome ",variable=ttGetGenomesTcl,value="mm9",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.rn<-tkradiobutton(ttGetGenomes,text="Rat rn4 genome ",variable=ttGetGenomesTcl,value="rn4",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.hs))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.mm))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.rn))
Try(tkgrid.configure(rbIQR.hs,rbIQR.mm,rbIQR.rn, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),tklabel(ttGetGenomes,text=" ")))
Try(ReturnVal1 <- "")
Try(onCancel <- function() {Try(ReturnVal1 <<- "");Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal1 <<- tclvalue(ttGetGenomesTcl));Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetGenomes,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetGenomes,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),OK.but,Cancel.but, tklabel(ttGetGenomes,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(tkbind(ttGetGenomes,"<Destroy>",function() {ReturnVal1 <- "";Try(tkgrab.release(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetGenomes))
Try(cat("\nStart Downloading and building chromosome references for bowtie primary mapping.\n"))
Try(cat("\nBe patient! Download and installation will take a while...\n"))
Try(bowtieRefs <- get("bowtieRefs",envir=affylmGUIenvironment))
#creating the gene-level scaffold to upload the reads
Try(gene.scaffold <- makeGeneScaffold(whichRef = ReturnVal1))
#Please not that if bowtie annotation is available the corresponding gene-level scaffold is also present
#therefore for each bowtieRefs == Y there is also the gene-level scaffold
if(.Platform$OS.type=="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading Chr22\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_22/hs_ref_GRCh37.p2_chr22.fa.gz", "chr22.fa.gz", mode="wb"))
Try(gunzip("chr22.fa.gz"))
Try(system("bowtie-build.exe -f chr22.fa hs_chr22"))
Try(file.remove("chr22.fa"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_21/hs_ref_GRCh37.p2_chr21.fa.gz", "chr21.fa.gz", mode="wb"))
Try(gunzip("chr21.fa.gz"))
Try(system("bowtie-build.exe -f chr21.fa hs_chr21"))
Try(file.remove("chr21.fa"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_20/hs_ref_GRCh37.p2_chr20.fa.gz", "chr20.fa.gz", mode="wb"))
Try(gunzip("chr20.fa.gz"))
Try(system("bowtie-build.exe -f chr20.fa hs_chr20"))
Try(file.remove("chr20.fa"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/hs_ref_GRCh37.p2_chr19.fa.gz", "chr19.fa.gz", mode="wb"))
Try(gunzip("chr19.fa.gz"))
Try(system("bowtie-build.exe -f chr19.fa hs_chr19"))
Try(file.remove("chr19.fa"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_18/hs_ref_GRCh37.p2_chr18.fa.gz", "chr18.fa.gz", mode="wb"))
Try(gunzip("chr18.fa.gz"))
Try(system("bowtie-build.exe -f chr18.fa hs_chr18"))
Try(file.remove("chr18.fa"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_17/hs_ref_GRCh37.p2_chr17.fa.gz", "chr17.fa.gz", mode="wb"))
Try(gunzip("chr17.fa.gz"))
Try(system("bowtie-build.exe -f chr17.fa hs_chr17"))
Try(file.remove("chr17.fa"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_16/hs_ref_GRCh37.p2_chr16.fa.gz", "chr16.fa.gz", mode="wb"))
Try(gunzip("chr16.fa.gz"))
Try(system("bowtie-build.exe -f chr16.fa hs_chr16"))
Try(file.remove("chr16.fa"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_15/hs_ref_GRCh37.p2_chr15.fa.gz", "chr15.fa.gz", mode="wb"))
Try(gunzip("chr15.fa.gz"))
Try(system("bowtie-build.exe -f chr15.fa hs_chr15"))
Try(file.remove("chr15.fa"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_14/hs_ref_GRCh37.p2_chr14.fa.gz", "chr14.fa.gz", mode="wb"))
Try(gunzip("chr14.fa.gz"))
Try(system("bowtie-build.exe -f chr14.fa hs_chr14"))
Try(file.remove("chr14.fa"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_13/hs_ref_GRCh37.p2_chr13.fa.gz", "chr13.fa.gz", mode="wb"))
Try(gunzip("chr13.fa.gz"))
Try(system("bowtie-build.exe -f chr13.fa hs_chr13"))
Try(file.remove("chr13.fa"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_12/hs_ref_GRCh37.p2_chr12.fa.gz", "chr12.fa.gz", mode="wb"))
Try(gunzip("chr12.fa.gz"))
Try(system("bowtie-build.exe -f chr12.fa hs_chr12"))
Try(file.remove("chr12.fa"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_11/hs_ref_GRCh37.p2_chr11.fa.gz", "chr11.fa.gz", mode="wb"))
Try(gunzip("chr11.fa.gz"))
Try(system("bowtie-build.exe -f chr11.fa hs_chr11"))
Try(file.remove("chr11.fa"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_10/hs_ref_GRCh37.p2_chr10.fa.gz", "chr10.fa.gz", mode="wb"))
Try(gunzip("chr10.fa.gz"))
Try(system("bowtie-build.exe -f chr10.fa hs_chr10"))
Try(file.remove("chr10.fa"))
Try(cat("\nDownloading Chr9\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_09/hs_ref_GRCh37.p2_chr9.fa.gz", "chr09.fa.gz", mode="wb"))
Try(gunzip("chr09.fa.gz"))
Try(system("bowtie-build.exe -f chr09.fa hs_chr09"))
Try(file.remove("chr09.fa"))
Try(cat("\nDownloading Chr8\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_08/hs_ref_GRCh37.p2_chr8.fa.gz", "chr08.fa.gz", mode="wb"))
Try(gunzip("chr08.fa.gz"))
Try(system("bowtie-build.exe -f chr08.fa hs_chr08"))
Try(file.remove("chr08.fa"))
Try(cat("\nDownloading Chr7\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_07/hs_ref_GRCh37.p2_chr7.fa.gz", "chr07.fa.gz", mode="wb"))
Try(gunzip("chr07.fa.gz"))
Try(system("bowtie-build.exe -f chr07.fa hs_chr07"))
Try(file.remove("chr07.fa"))
Try(cat("\nDownloading Chr6\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_06/hs_ref_GRCh37.p2_chr6.fa.gz", "chr06.fa.gz", mode="wb"))
Try(gunzip("chr06.fa.gz"))
Try(system("bowtie-build.exe -f chr06.fa hs_chr06"))
Try(file.remove("chr06.fa"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_05/hs_ref_GRCh37.p2_chr5.fa.gz", "chr05.fa.gz", mode="wb"))
Try(gunzip("chr05.fa.gz"))
Try(system("bowtie-build.exe -f chr05.fa hs_chr05"))
Try(file.remove("chr05.fa"))
Try(cat("\nDownloading Chr4\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_04/hs_ref_GRCh37.p2_chr4.fa.gz", "chr04.fa.gz", mode="wb"))
Try(gunzip("chr04.fa.gz"))
Try(system("bowtie-build.exe -f chr04.fa hs_chr04"))
Try(file.remove("chr04.fa"))
Try(cat("\nDownloading Ch3\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_03/hs_ref_GRCh37.p2_chr3.fa.gz", "chr03.fa.gz", mode="wb"))
Try(gunzip("chr03.fa.gz"))
Try(system("bowtie-build.exe -f chr03.fa hs_chr03"))
Try(file.remove("chr03.fa"))
Try(cat("\nDownloading Ch2\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_02/hs_ref_GRCh37.p2_chr2.fa.gz", "chr02.fa.gz", mode="wb"))
Try(gunzip("chr02.fa.gz"))
Try(system("bowtie-build.exe -f chr02.fa hs_chr02"))
Try(file.remove("chr02.fa"))
Try(cat("\nDownloading Ch1\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_GRCh37.p2_chr1.fa.gz", "chr01.fa.gz", mode="wb"))
Try(gunzip("chr01.fa.gz"))
Try(system("bowtie-build.exe -f chr01.fa hs_chr01"))
Try(file.remove("chr01.fa"))
Try(cat("\nDownloading ChX\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_X/hs_ref_GRCh37.p2_chrX.fa.gz", "chrX.fa.gz", mode="wb"))
Try(gunzip("chrX.fa.gz"))
Try(system("bowtie-build.exe -f chrX.fa hs_chrX"))
Try(file.remove("chrX.fa"))
Try(cat("\nDownloading ChY\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_Y/hs_ref_GRCh37.p2_chrY.fa.gz", "chrY.fa.gz", mode="wb"))
Try(gunzip("chrY.fa.gz"))
Try(system("bowtie-build.exe -f chrY.fa hs_chrY"))
Try(file.remove("chrY.fa"))
Try(cat("\nDownloading ChMT\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_MT/hs_ref_GRCh37.p2_chrMT.fa.gz", "chrMT.fa.gz", mode="wb"))
Try(gunzip("chrMT.fa.gz"))
Try(system("bowtie-build.exe -f chrMT.fa hs_chrMT"))
Try(file.remove("chrMT.fa"))
Try(bowtieRefs[1] <- "Y")
} else if(.Platform$OS.type!="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading Chr22\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_22/hs_ref_GRCh37.p2_chr22.fa.gz", "chr22.fa.gz", mode="wb"))
Try(gunzip("chr22.fa.gz"))
Try(system("bowtie-build -f chr22.fa hs_chr22"))
Try(file.remove("chr22.fa"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_21/hs_ref_GRCh37.p2_chr21.fa.gz", "chr21.fa.gz", mode="wb"))
Try(gunzip("chr21.fa.gz"))
Try(system("bowtie-build -f chr21.fa hs_chr21"))
Try(file.remove("chr21.fa"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_20/hs_ref_GRCh37.p2_chr20.fa.gz", "chr20.fa.gz", mode="wb"))
Try(gunzip("chr20.fa.gz"))
Try(system("bowtie-build -f chr20.fa hs_chr20"))
Try(file.remove("chr20.fa"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_19/hs_ref_GRCh37.p2_chr19.fa.gz", "chr19.fa.gz", mode="wb"))
Try(gunzip("chr19.fa.gz"))
Try(system("bowtie-build -f chr19.fa hs_chr19"))
Try(file.remove("chr19.fa"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_18/hs_ref_GRCh37.p2_chr18.fa.gz", "chr18.fa.gz", mode="wb"))
Try(gunzip("chr18.fa.gz"))
Try(system("bowtie-build -f chr18.fa hs_chr18"))
Try(file.remove("chr18.fa"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_17/hs_ref_GRCh37.p2_chr17.fa.gz", "chr17.fa.gz", mode="wb"))
Try(gunzip("chr17.fa.gz"))
Try(system("bowtie-build -f chr17.fa hs_chr17"))
Try(file.remove("chr17.fa"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_16/hs_ref_GRCh37.p2_chr16.fa.gz", "chr16.fa.gz", mode="wb"))
Try(gunzip("chr16.fa.gz"))
Try(system("bowtie-build -f chr16.fa hs_chr16"))
Try(file.remove("chr16.fa"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_15/hs_ref_GRCh37.p2_chr15.fa.gz", "chr15.fa.gz", mode="wb"))
Try(gunzip("chr15.fa.gz"))
Try(system("bowtie-build -f chr15.fa hs_chr15"))
Try(file.remove("chr15.fa"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_14/hs_ref_GRCh37.p2_chr14.fa.gz", "chr14.fa.gz", mode="wb"))
Try(gunzip("chr14.fa.gz"))
Try(system("bowtie-build -f chr14.fa hs_chr14"))
Try(file.remove("chr14.fa"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_13/hs_ref_GRCh37.p2_chr13.fa.gz", "chr13.fa.gz", mode="wb"))
Try(gunzip("chr13.fa.gz"))
Try(system("bowtie-build -f chr13.fa hs_chr13"))
Try(file.remove("chr13.fa"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_12/hs_ref_GRCh37.p2_chr12.fa.gz", "chr12.fa.gz", mode="wb"))
Try(gunzip("chr12.fa.gz"))
Try(system("bowtie-build -f chr12.fa hs_chr12"))
Try(file.remove("chr12.fa"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_11/hs_ref_GRCh37.p2_chr11.fa.gz", "chr11.fa.gz", mode="wb"))
Try(gunzip("chr11.fa.gz"))
Try(system("bowtie-build -f chr11.fa hs_chr11"))
Try(file.remove("chr11.fa"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_10/hs_ref_GRCh37.p2_chr10.fa.gz", "chr10.fa.gz", mode="wb"))
Try(gunzip("chr10.fa.gz"))
Try(system("bowtie-build -f chr10.fa hs_chr10"))
Try(file.remove("chr10.fa"))
Try(cat("\nDownloading Chr09\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_09/hs_ref_GRCh37.p2_chr9.fa.gz", "chr09.fa.gz", mode="wb"))
Try(gunzip("chr09.fa.gz"))
Try(system("bowtie-build -f chr09.fa hs_chr09"))
Try(file.remove("chr09.fa"))
Try(cat("\nDownloading Chr08\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_08/hs_ref_GRCh37.p2_chr8.fa.gz", "chr08.fa.gz", mode="wb"))
Try(gunzip("chr08.fa.gz"))
Try(system("bowtie-build -f chr08.fa hs_chr08"))
Try(file.remove("chr08.fa"))
Try(cat("\nDownloading Chr07\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_07/hs_ref_GRCh37.p2_chr7.fa.gz", "chr07.fa.gz", mode="wb"))
Try(gunzip("chr07.fa.gz"))
Try(system("bowtie-build -f chr07.fa hs_chr7"))
Try(file.remove("chr07.fa"))
Try(cat("\nDownloading Chr06\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_06/hs_ref_GRCh37.p2_chr6.fa.gz", "chr06.fa.gz", mode="wb"))
Try(gunzip("chr06.fa.gz"))
Try(system("bowtie-build -f chr06.fa hs_chr6"))
Try(file.remove("chr06.fa"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_05/hs_ref_GRCh37.p2_chr5.fa.gz", "chr05.fa.gz", mode="wb"))
Try(gunzip("chr05.fa.gz"))
Try(system("bowtie-build -f chr05.fa hs_chr05"))
Try(file.remove("chr05.fa"))
Try(cat("\nDownloading Chr04\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_04/hs_ref_GRCh37.p2_chr4.fa.gz", "chr04.fa.gz", mode="wb"))
Try(gunzip("chr04.fa.gz"))
Try(system("bowtie-build -f chr04.fa hs_chr04"))
Try(file.remove("chr04.fa"))
Try(cat("\nDownloading Ch03\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_03/hs_ref_GRCh37.p2_chr3.fa.gz", "chr03.fa.gz", mode="wb"))
Try(gunzip("chr03.fa.gz"))
Try(system("bowtie-build -f chr03.fa hs_chr3"))
Try(file.remove("chr03.fa"))
Try(cat("\nDownloading Ch02\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_02/hs_ref_GRCh37.p2_chr2.fa.gz", "chr02.fa.gz", mode="wb"))
Try(gunzip("chr02.fa.gz"))
Try(system("bowtie-build -f chr02.fa hs_chr02"))
Try(file.remove("chr02.fa"))
Try(cat("\nDownloading Ch01\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_GRCh37.p2_chr1.fa.gz", "chr01.fa.gz", mode="wb"))
Try(gunzip("chr01.fa.gz"))
Try(system("bowtie-build -f chr01.fa hs_chr01"))
Try(file.remove("chr01.fa"))
Try(cat("\nDownloading ChX\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_X/hs_ref_GRCh37.p2_chrX.fa.gz", "chrX.fa.gz", mode="wb"))
Try(gunzip("chrX.fa.gz"))
Try(system("bowtie-build -f chrX.fa hs_chrX"))
Try(file.remove("chrX.fa"))
Try(cat("\nDownloading ChY\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_Y/hs_ref_GRCh37.p2_chrY.fa.gz", "chrY.fa.gz", mode="wb"))
Try(gunzip("chrY.fa.gz"))
Try(system("bowtie-build -f chrY.fa hs_chrY"))
Try(file.remove("chrY.fa"))
Try(cat("\nDownloading ChMT\n"))
Try(download.file("ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_MT/hs_ref_GRCh37.p2_chrMT.fa.gz", "chrMT.fa.gz", mode="wb"))
Try(gunzip("chrMT.fa.gz"))
Try(system("bowtie-build -f chrMT.fa hs_chrMT"))
Try(file.remove("chrMT.fa"))
Try(bowtieRefs[1] <- "Y")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
}
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
Try(bowtieRefs <- paste(bowtieRefs, collapse=","))
Try(myinfo[which(myinfo[,1]=="bowtieRefs"),2] <- bowtieRefs)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
Try(usedtime <- proc.time() - ptm)
Try(cat("\nUsed CPU time (min) ",usedtime[3]/60,"\n"))
Try(cat("\nEnd downloading and building chromosome references for bowtie primary mapping.\n"))
Try(return())
}
###############################################################################
"wrapNGS" <- function(){
Try(mbVal <- tkmessageBox(title="Installing external software for RNA-seq",
message="Do you wish to install all external software needed for RNA-seq?",
icon="question",type="yesno",default="yes"
)#end of tkmessageBox
)#end of Try(mbVal..
if(tclvalue(mbVal)=="yes"){
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(myWD <-getwd())
#gathering affy libs and apt tools folders
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(bowtieDirLocation <- myinfo[which(myinfo[,1]=="bowtieDirLocation"),2]) #loacation of bowtie
if(bowtieDirLocation==""){
Try(bowtieDirLocation <- paste(path.package("oneChannelGUI", quiet = FALSE), "/bowtie", sep=""))
Try(dir.create(bowtieDirLocation, showWarnings = TRUE, recursive = FALSE))
Try(myinfo[which(myinfo[,1]=="bowtieDirLocation"),2] <- bowtieDirLocation)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(setwd(myWD))
Try(bowtieDownload())
# ngsperlDownload()
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
} else{
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(return())
}
}
################################################################################
"bowtieBuilt" <- function(){
# Try(require(R.utils) || stop("\nMissing R.utils library!\n"))
Try(tkfocus(.affylmGUIglobals$ttMain))
# Try(require(Biostrings) || stop("library Biostrings could not be found !"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
if(is.na(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2])){
Try(tkmessageBox(title="Bowtie",message="Bowtie cannot be found please go to the General tool menu and use the function:\nInstall Bowtie and Picard tools\nto install Bowtie.",icon="error",type="ok"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
Try(setwd(myinfo[which(myinfo[,1]== "bowtieDirLocation"),2]))
#which ref
Try(ttGetGenomes <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttGetGenomes))
Try(tkgrab.set(ttGetGenomes))
Try(tkfocus(ttGetGenomes))
Try(tkwm.title(ttGetGenomes,"Which genome do you want to use as reference?"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(ttGetGenomesTcl <- tclVar("hg19"))
Try(rbIQR.hs <- tkradiobutton(ttGetGenomes,text="Human hg19 genome ",variable=ttGetGenomesTcl,value="hg19",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.mm<-tkradiobutton(ttGetGenomes,text="Mouse mm9 genome ",variable=ttGetGenomesTcl,value="mm9",font=.affylmGUIglobals$affylmGUIfont2))
Try(rbIQR.rn<-tkradiobutton(ttGetGenomes,text="Rat rn4 genome ",variable=ttGetGenomesTcl,value="rn4",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.hs))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.mm))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),rbIQR.rn))
Try(tkgrid.configure(rbIQR.hs,rbIQR.mm,rbIQR.rn, columnspan=2,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),tklabel(ttGetGenomes,text=" ")))
Try(ReturnVal1 <- "")
Try(onCancel <- function() {Try(ReturnVal1 <<- "");Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(onOK <- function() {Try(ReturnVal1 <<- tclvalue(ttGetGenomesTcl));Try(tkgrab.release(ttGetGenomes));Try(tkdestroy(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain))})
Try(OK.but <- tkbutton(ttGetGenomes,text="OK",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttGetGenomes,text="Cancel",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttGetGenomes,text=" "),OK.but,Cancel.but, tklabel(ttGetGenomes,text=" ")))
Try(tkgrid.configure(OK.but,sticky="e"))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttGetGenomes,text=" ")))
Try(tkbind(ttGetGenomes,"<Destroy>",function() {ReturnVal1 <- "";Try(tkgrab.release(ttGetGenomes));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkbind(OK.but, "<Return>",onOK))
Try(tkbind(Cancel.but, "<Return>",onCancel))
Try(tkwait.window(ttGetGenomes))
Try(cat("\nStart Downloading and building chromosome references for bowte primary mapping.\n"))
Try(cat("\nBe patient! Download and installation will take a while...\n"))
Try(bowtieRefs <- get("bowtieRefs",envir=affylmGUIenvironment))
#Please not that if bowtie annotation is available the corresponding gene-level scaffold is also present
#therefore for each bowtieRefs == Y there is also the gene-level scaffold
if(.Platform$OS.type=="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading ChrX and ChrY\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chrXY.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr22\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr22.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr21.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr20.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr19.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr18.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr17.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr16.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr15.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr14.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr13.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr12.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr11.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr10.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr9\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr9.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr8\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr8.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr7\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr7.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr6\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr6.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr5.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr4\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr4.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr3\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr3.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr2\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr2.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr1\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr1.zip/download", "chr.zip", mode="wb"))
Try(unzip("chr.zip"))
Try(file.remove("chr.zip"))
Try(bowtieRefs[1] <- "Y")
} else if(.Platform$OS.type!="windows" && ReturnVal1=="hg19"){
Try(cat("\nDownloading ChrX and ChrY\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chrXY.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr22\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr22.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr21\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr21.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr20\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr20.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr19\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr19.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr18\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr18.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr17\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr17.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr16\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr16.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr15\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr15.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr14\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr14.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr13\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr13.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr12\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr12.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr11\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr11.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr10\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr10.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr9\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr9.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr8\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr8.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr7\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr7.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr6\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr6.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr5\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr5.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr4\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr4.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr3\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr3.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr2\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr2.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(cat("\nDownloading Chr1\n"))
Try(download.file("http://sourceforge.net/projects/ochguiextras/files/bowtie_hs/hs_chr1.zip/download", "chr.zip", mode="wb"))
Try(system(paste("unzip chr.zip", sep="")))
Try(file.remove("chr.zip"))
Try(bowtieRefs[1] <- "Y")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="mm9"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[2] <- "N")
}
if(.Platform$OS.type=="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
} else if (.Platform$OS.type!="windows" && ReturnVal1=="rn4"){
cat("\nNot implemented, yet\n")
Try(bowtieRefs[3] <- "N")
}
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
Try(bowtieRefs <- paste(bowtieRefs, collapse=","))
Try(myinfo[which(myinfo[,1]=="bowtieRefs"),2] <- bowtieRefs)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(setwd(myWD))
Try(cat("\nEnd downloading built chromosome references for bowtie primary mapping.\n"))
Try(return())
}
#####################################################################################
genomeStudioReformat <- function(){
#loading the tab delimited file
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkmessageBox(title="Reformat a GenomeStudio export file",message="Open the Genome Studio exported file."))
Try(tempFileName <- tclvalue(tkgetOpenFile(filetypes="{{Text Files} {.txt}} {{All files} *}")))
if(!nchar(tempFileName))
{
tkfocus(.affylmGUIglobals$ttMain)
return()
}
##start grabbing the first 8 lines
Try(con <- file(tempFileName, "r", blocking = FALSE))
Try(gsInfo <- readLines(con, n=8))
Try(close(con))
Try(gsInfo <- gsub("\t","",gsInfo))
Try(mysel <- read.table(tempFileName, sep="\t", header=T, skip=8, fill=T))
Try(refined.df <- mysel[,grep("AVG_Signal",names(mysel))])
Try(refined.df <- refined.df[setdiff(seq(1,dim(mysel)[1]),which(duplicated(as.character(mysel$PROBE_ID)))),])
Try(rnames <- mysel$PROBE_ID[setdiff(seq(1,dim(mysel)[1]),which(duplicated(as.character(mysel$PROBE_ID))))])
Try(refined.df <- cbind(rnames,refined.df))
Try(tmp.df <- matrix(rep(" ", dim(refined.df)[2]*8), nrow=8))
Try(tmp.df[,1]<- gsInfo)
Try(tmp.df <- rbind(tmp.df, gsub("X","",names(refined.df))))
Try(tmp.df[9,1] <- "PROBE_ID")
Try(write.table(tmp.df, file = paste(tempFileName,"_reformatted.txt",sep=""), sep="\t", col.names=F,row.names=F, quote=F))
#Try(dimnames(tmp.df)[[2]] <- names(refined.df))
#Try(tmp.df <- rbind(tmp.df,refined.df))
Try(write.table(refined.df, file = paste(tempFileName,"_reformatted.txt",sep=""), sep="\t", col.names=F,row.names=F, append=T, quote=F))
Try(tkmessageBox(title="Reformat GenomeStudio output files",message=paste("The reformated file iis saved in your working directory as: ", paste(tempFileName,"_reformatted.txt",sep=""),"\nis made of ",dim(refined.df)[1]," rows and ",dim(refined.df)[2]," columns",sep=""),icon="info",type="ok"))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(return())
}
###############
setBinDir <- function(){
Try(wd <- tclVar(getwd()))
Try(
if(.Platform$OS.type=="windows"){
Try(tkmessageBox(title="Select user bin folder",message="Not implemented in windows",icon="info",type="ok"))
Try(return())
}
)
Try(ttChooseDir <- tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.title(ttChooseDir,"Choose Output directory"))
Try(tkwm.deiconify(ttChooseDir))
Try(tkgrab.set(ttChooseDir))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
Try(label1 <- tklabel(ttChooseDir,text="Choose user bin directory:",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttChooseDir,text=" "),label1,sticky="w"))
Try(tkgrid.configure(label1,columnspan=3))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
#
#
Try(
onBrowse <- function(){
Try(if(file.exists(gsub("\\\\","/",tclvalue(wd)))) initialdir<-gsub("\\\\","/",tclvalue(wd)) else initialdir<-getwd())
Try(dir1 <- tclvalue(tkchooseDirectory(title="Please choose the user bin dir",initialdir=initialdir)))
Try(if(nchar(dir1)>0) tclvalue(wd) <- dir1)
Try(
if(.Platform$OS.type=="windows"){
Try(tclvalue(wd) <- gsub("/","\\\\",tclvalue(wd)))
}
)
} #end of onBrowse <- function()
)# end of Try
#
#
Try(ReturnVal <- "")
#
#
Try(
onOK <- function(){
Try(DirChosen <- tclvalue(wd))
Try(tkgrab.release(ttChooseDir))
Try(tkdestroy(ttChooseDir))
Try(DirChosen <- gsub("\\\\","/",DirChosen))
Try(ReturnVal <<- DirChosen)
} #end of onOK <- function()
)
#
#
Try(
onCancel <- function(){
Try(tkgrab.release(ttChooseDir));
Try(tkdestroy(ttChooseDir))
} #end of onCancel <- function()
) #end of try
#
#
Try(Browse.but <- tkbutton(ttChooseDir,text="Browse",command=onBrowse,font=.affylmGUIglobals$affylmGUIfont2))
Try(OK.but <- tkbutton(ttChooseDir,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(Cancel.but <- tkbutton(ttChooseDir,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2))
#
Try(entry1 <- tkentry(ttChooseDir,textvariable=wd,width=40,font=.affylmGUIglobals$affylmGUIfont2))
#
Try(tkgrid(tklabel(ttChooseDir,text=" "),entry1))
Try(tkgrid.configure(entry1,columnspan=3))
Try(tkgrid(tklabel(ttChooseDir,text=" "),row=3,column=4))
Try(tkgrid(Browse.but,row=3,column=5))
Try(tkgrid(tklabel(ttChooseDir,text=" "),row=3,column=6))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
Try(tkgrid(tklabel(ttChooseDir,text=" "),tklabel(ttChooseDir,text=" "),OK.but,Cancel.but))
Try(tkgrid.configure(Cancel.but,sticky="w"))
Try(tkgrid(tklabel(ttChooseDir,text=" ")))
#
Try(tkfocus(entry1))
Try(tkbind(ttChooseDir,"<Destroy>",function()tkgrab.release(ttChooseDir)))
Try(tkbind(entry1,"<Return>",onOK))
Try(tkwait.window(ttChooseDir))
Try(tkfocus(.affylmGUIglobals$ttMain))
#
Try(assign("binDir", ReturnVal, affylmGUIenvironment))#bin dir
Try(assign("binDir.Available",TRUE,affylmGUIenvironment))
Try(etcDir <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc", sep=""))
Try(localdata <- paste(etcDir, "/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(myWD <- getwd())
Try(myinfo[which(myinfo[,1]=="binDir"),2] <- ReturnVal)
Try(write.table(myinfo, localdata, sep="\t", row.names=F, col.names=F, quote=F))
}
#################
tuxedoSetup<- function(){
Try(binDir.available <- get("binDir.Available",envir=affylmGUIenvironment))
if(!binDir.available){
setBinDir()
}
Try(binDir <- get("binDir",envir=affylmGUIenvironment))
#####bowtie
#already available in bowtieDirLocation
Try(bowtieDirLocation.Available <- get("bowtieDirLocation.Available",envir=affylmGUIenvironment))
if(!bowtieDirLocation.Available){
bowtieDownload()
}
Try(bowtieDirLocation <- get("bowtieDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",bowtieDirLocation, "/bowtie", sep="")))
Try(system(paste("ln -fs ",bowtieDirLocation,"/bowtie ", binDir, "/bowtie", sep="")))
Try(system(paste("chmod +x ",bowtieDirLocation, "/bowtie-build", sep="")))
Try(system(paste("ln -fs ",bowtieDirLocation,"/bowtie-build ", binDir, "/bowtie-build", sep="")))
Try(system(paste("chmod +x ",bowtieDirLocation, "/bowtie-inspect", sep="")))
Try(system(paste("ln -fs ",bowtieDirLocation,"/bowtie-inspect ", binDir, "/bowtie-inspect", sep="")))
#samtools dir
Try(samtoolsDirLocation.Available <- get("samtoolsDirLocation.Available",envir=affylmGUIenvironment))
if(!samtoolsDirLocation.Available){
bowtieDownload()
}
Try(samtoolsDirLocation <- get("samtoolsDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",samtoolsDirLocation, "/samtools", sep="")))
Try(system(paste("ln -fs ",samtoolsDirLocation,"/samtools ", binDir, "/samtools", sep="")))
#fastqc
Try(fastqcDirLocation.Available <- get("fastqcDirLocation.Available",envir=affylmGUIenvironment))
if(!fastqcDirLocation.Available){
bowtieDownload()
}
Try(fastqcDirLocation <- get("fastqcDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",fastqcDirLocation, "/fastqc", sep="")))
Try(system(paste("ln -fs ",fastqcDirLocation,"/fastqc ", binDir, "/fastqc", sep="")))
##tophat
Try(tophatDirLocation.Available <- get("tophatDirLocation.Available",envir=affylmGUIenvironment))
if(!tophatDirLocation.Available){
bowtieDownload()
}
Try(tophatDir <- get("tophatDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",tophatDir, "/bam2fastx", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/bam2fastx ", binDir, "/bam2fastx", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/bam_merge", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/bam_merge ", binDir, "/bam_merge", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/bed_to_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/bed_to_juncs ", binDir, "/bed_to_juncs", sep="")))
# Try(system(paste("chmod +x ",tophatDir, "/closure_juncs", sep="")))
# Try(system(paste("ln -fs ",tophatDir,"/closure_juncs ", binDir, "/closure_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/contig_to_chr_coords", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/contig_to_chr_coords ", binDir, "/contig_to_chr_coords", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/fix_map_ordering", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/fix_map_ordering ", binDir, "/fix_map_ordering", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/gtf_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/gtf_juncs ", binDir, "/gtf_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/gtf_to_fasta", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/gtf_to_fasta ", binDir, "/gtf_to_fasta", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/juncs_db", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/juncs_db ", binDir, "/juncs_db", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/long_spanning_reads", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/long_spanning_reads ", binDir, "/long_spanning_reads", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/map2gtf", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/map2gtf ", binDir, "/map2gtf", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/prep_reads", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/prep_reads ", binDir, "/prep_reads", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/sam_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/sam_juncs ", binDir, "/sam_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/segment_juncs", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/segment_juncs ", binDir, "/segment_juncs", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/sra_to_solid", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/sra_to_solid ", binDir, "/sra_to_solid", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat ", binDir, "/tophat", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat-fusion-post", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat-fusion-post ", binDir, "/tophat-fusion-post", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat2", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat2 ", binDir, "/tophat", sep="")))
Try(system(paste("chmod +x ",tophatDir, "/tophat2", sep="")))
Try(system(paste("ln -fs ",tophatDir,"/tophat2 ", binDir, "/tophat", sep="")))
#cufflinks
Try(cuffDirLocation.available <- get("cuffDirLocation.Available",envir=affylmGUIenvironment))
if(!cuffDirLocation.available){
bowtieDownload()
}
Try(cuffDir <- get("cuffDirLocation",envir=affylmGUIenvironment))
Try(system(paste("chmod +x ",cuffDir, "/cuffcompare", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cuffcompare ", binDir, "/cuffcompare", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/cuffdiff", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cuffdiff ", binDir, "/cuffdiff", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/cufflinks", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cufflinks ", binDir, "/cufflinks", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/cuffmerge", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/cuffmerge ", binDir, "/cuffmerge", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/gffread", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/gffread ", binDir, "/gffread", sep="")))
Try(system(paste("chmod +x ",cuffDir, "/gtf_to_sam", sep="")))
Try(system(paste("ln -fs ",cuffDir,"/gtf_to_sam ", binDir, "/gtf_to_sam", sep="")))
}
##############
openPdf <- function(){
while(as.numeric(dev.cur())> 1){
Try(dev.off())
}
#selecting a pdf file to save results
Try(ttpdf<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttpdf))
Try(tkgrab.set(ttpdf))
Try(tkfocus(ttpdf))
Try(tkwm.title(ttpdf,"Opening pdf output"))
Try(tkgrid(tklabel(ttpdf,text=" ")))
Try(pdfName<- "")
Try(Local.pdf <- tclVar(init=pdfName))
Try(entry.pdf <-tkentry(ttpdf,width="20",font=.affylmGUIglobals$affylmGUIfont2,textvariable=Local.pdf,bg="white"))
Try(tkgrid(tklabel(ttpdf,text="Please enter the name of the pdf file to be created.",font=.affylmGUIglobals$affylmGUIfont2)))
Try(tkgrid(entry.pdf))
onOK <- function()
{
Try(pdfName <<- as.character(tclvalue(Local.pdf)))
Try(tkgrab.release(ttpdf));Try(tkdestroy(ttpdf));Try(tkfocus(.affylmGUIglobals$ttMain))
}
Try(OK.but <-tkbutton(ttpdf,text=" OK ",command=onOK,font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttpdf,text=" ")))
Try(tkgrid(OK.but))
Try(tkgrid.configure(OK.but))
Try(tkgrid(tklabel(ttpdf,text=" ")))
Try(tkfocus(entry.pdf))
Try(tkbind(entry.pdf, "<Return>",onOK))
Try(tkbind(ttpdf, "<Destroy>", function(){Try(tkgrab.release(ttpdf));Try(tkfocus(.affylmGUIglobals$ttMain));return(0)}))
Try(tkwait.window(ttpdf))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(pdf(pdfName))
Try(return())
}
##############################################################################
closePdf <- function(){
while(as.numeric(dev.cur())> 1){
Try(dev.off())
}
Try(tkmessageBox(title="Closing pdf outputs",message="pdf files are closed",type="ok",icon="info"))
Try(return())
}
##############################################################################
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