R/zinbagui.R
In sivarajankumar/zinba: ZINBA: Zero-Inflation Negative Binomial Algorithm
run=function(util){
###################################################################
###################################################################
if(util=="Generate Alignability"){
genalign <- aDialog(items=list(
mapdir=fileItem(attr=c(type="selectdir"), tooltip="Path to unpacked mappability directory", label="Mappability\nDirectory"),
outdir=fileItem(attr=c(type="selectdir"), tooltip="Path to alignability directory where output files will be placed",label="Output\nDirectory"),
athresh=numericItem(1, tooltip="Alignability threshold used to filter mapped reads, 1 corresponding that reads only mapping to one place in genome were used", label="Alignability\nThreshold"),
extension=numericItem(200, tooltip="Average length in fragment library used in preparing sample/input reads for sequencing", label="Extension"),
twoBitFile=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file for analysis", label=".2bit file")
), title="Generate Alignability Directory")
view_genalign <- aContainer("mapdir", "outdir", "athresh", "extension", "twoBitFile")
genalign$make_gui(gui_layout=view_genalign, visible=FALSE)
genalign$OK_handler <- function(.) {
genalignvar=.$to_R()
do.call("generateAlignability",list(mapdir=genalignvar$mapdir, outdir=genalignvar$outdir, athresh=genalignvar$athresh, extension=genalignvar$extension, twoBitFile=genalignvar$twoBitFile))
.$close_gui()
}
genalign$visible(TRUE)
}
if(util=="Generate SBC file (basecount)"){
basecount <- aDialog(items=list(
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
basecountdir=fileItem(attr=c(type="selectdir"), tooltip="Directory where basecountfile will be placed", label="Output\nDirectory"),
filename=stringItem("name of SBC (basecount) file to be created", tooltip="Name of SBC (basecount) file, for example ctcf.basecount", label="SBC file"),
twoBitFile=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file for analysis", label=".2bit file"),
extension=numericItem(200, tooltip="Average length in fragment library used in preparing sample/input reads for sequencing", label="Extension"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of mapped sample read file", label="File Type")
), title="Generate SBC (basecount) File")
view_basecount <- aContainer("seq","filetype","basecountdir","filename","twoBitFile","extension")
basecount$make_gui(gui_layout=view_basecount, visible=FALSE)
basecount$OK_handler <- function(.) {
basecountvar=.$to_R()
do.call("basealigncount",list(inputfile=basecountvar$seq,outputfile=paste(basecountvar$basecount, "/",basecountvar$filename,sep="") ,twoBitFile=basecountvar$twoBitFile,extension=basecountvar$extension,filetype=basecountvar$filetype))
.$close_gui()
}
basecount$visible(TRUE)
}
if(util=="twobittofa"){
twobittofa <- aDialog(items=list(
twoBitFile=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file for Conversion to fasta format",label=".2bit file"),
chrm=stringItem("all", tooltip="Name of chromosome where sequence will be converted from, or all if convering an entire directory of fasta files", label="chromosome"),
outdir=fileItem(attr=c(type="selectdir"), tooltip="Path to directory where converted fasta files will be placed",label="Output\nDirectory"),
start=numericItem(0, tooltip="Base Start Position (if chromosome != all) of sequence to be extracted to fasta format",label="Sequence Start"),
end=numericItem(0, tooltip="Base Stop Position (if chromosome != all) of sequence to be extracted to fasta format",label="Sequence End"),
gcSeq=stringItem("path to output file", tooltip="Path to file where extracted fasta sequence will be placed", label="chromosome")
), title="Convert .2bit to fasta format")
view_twobittofa <- aContainer("twoBitFile","chrm","outdir",
aContext("start", context=twobittofa,
enabled_when=function(.) {
val <- .$to_R()$chrm
val !="all"}),
aContext("end", context=twobittofa,
enabled_when=function(.) {
val <- .$to_R()$chrm
val !="all"
}),
aContext("gcSeq", context=twobittofa,
enabled_when=function(.) {
val <- .$to_R()$chrm
val !="all"
})
)
twobittofa$make_gui(gui_layout=view_twobittofa, visible=FALSE)
twobittofa$OK_handler <- function(.) {
twobittofavar=.$to_R()
do.call("twobittofa",list(twoBitFile=twobittofavar$twoBitFile,chrm=twobittofavar$chrm,outdir=twobittofavar$outdir, start=twobittofavar$start,end=twobittofavar$end,gcSeq=twobittofavar$gcSeq))
.$close_gui()
}
twobittofa$visible(TRUE)
}
if(util=="fatotwobit"){
fatotwobit <- aDialog(items=list(
outFile=stringItem("/home/data/genome.2bit", tooltip="if a directory is not selected, path to file where resulting .2bit file will be outputted", label="Path to\nOutput File"),
fadir=fileItem(" ",attr=c(type="selectdir"), tooltip="Path to directory where fasta files to be converted are stored", label="fasta directory"),
faFile=stringItem(" ", tooltip="path to specific fasta file if not specifying a directory", label="chromosome")
), title="Convert fasta file to to .2bit format")
view_fatotwobit <- aContainer("fadir",
aContext("faFile", context=fatotwobit,
enabled_when=function(.) {
val <- .$to_R()$fadir
val ==" "}),
"outFile")
fatotwobit$make_gui(gui_layout=view_fatotwobit, visible=FALSE)
fatotwobit$OK_handler <- function(.) {
fatotwobitvar=.$to_R()
do.call("fatotwobit",list(fadir=fatotwobitvar$fadir,faFile=fatotwobitvar$faFile,outFile=fatotwobitvar$outFile))
.$close_gui()
}
fatotwobit$visible(TRUE)
}
if(util=="getwindowcounts"){
getwindowcounts <- aDialog(items=list(
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of sample and input mapped read file",label="File Type"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
winSize=integerItem(500, tooltip="Window Size for data, smaller is better for low signal to noise, high background data", label="Window Size"),
offset=integerItem(0, tooltip="BP offset to shift windows, window size must be a multiple of this number. Yields better sensitivity", label="Window Offset"),
extension=integerItem(200, tooltip="average fragment length in sample library used for sequencing reads, usually 150bp-200bp", label="Extension")
),title="Get Window Read Counts for data")
view_getwindowcounts <- aContainer("seq","filetype","twoBit","winSize","offset", "extension")
getwindowcounts$make_gui(gui_layout=view_getwindowcounts, visible=FALSE)
getwindowcounts$OK_handler <- function(.) {
getwindowcountsvar=.$to_R()
do.call("getwindowcounts",list(seq=getwindowcountsvar$seq,filetype=getwindowcountsvar$filetype,twoBit=getwindowcountsvar$twoBit,winSize=getwindowcountsvar$winSize, offset=getwindowcountsvar$offset, extension=getwindowcountsvar$extension))
.$close_gui()
}
getwindowcounts$visible(TRUE)
}
if(util=="Signal to Noise Analysis"){
signalnoise <- aDialog(items=list(
inputfile=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"basecount" = list(patterns=c("*.basecount")),
"All files" = list(patterns=c("*"))
)),tooltip="Select basecount file for analysis", label="SBC (basecount) File"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
winSize=integerItem(100000, tooltip="Window Size for analysis, larger, 100kb suggested", label="Window Size")), title="Signal to Noise Analysis")
view_signalnoise <- aContainer("inputfile","twoBit","winSize")
signalnoise$make_gui(gui_layout=view_signalnoise, visible=FALSE)
signalnoise$OK_handler <- function(.) {
signalnoisevar=.$to_R()
do.call("signalnoise",list(inputfile=signalnoisevar$inputfile,twoBit=signalnoisevar$twoBit,winSize=signalnoisevar$winSize))
.$close_gui()
}
signalnoise$visible(TRUE)
}
###################################################################
###################################################################
if(util=="Run Zinba"){
dlg <- aDialog(items=list(
RunChoice=choiceItem("", values=c("Build Windows?","Run Window Analysis?", "Refine Merged Significant Regions?"), tooltip="The Zinba steps you want to run, either together or alone", editor_type="gcheckboxgroup", , label=" Run Options"),
printFullOut=choiceItem(as.integer(1), values=c(as.integer(1), as.integer(0)),tooltip="If 0, only prints out window coordinates, filter status, and window enrichment probability columns for .wins files from window analysis, rather than whole dataset",editor_type="gcombobox", label=" Print Option"),
method=choiceItem("mixture", values=c("mixture", "pscl"), tooltip="analysis method to use, either mixture regression model or pscl method (FAIRE)",editor_type="gcombobox", label="Analysis Method"),
outfile=stringItem("prefix for output files", tooltip="path and prefix to where .wins and .peaks are placed if analysis and refinement selected together, for example '/home/data/analysis_1'"),
numProc=integerItem(1, tooltip="How many processing cores to allocate, more processors means faster execution but more memory needed", label="Num Processors"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
input=fileItem("none", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped input control reads file (if available) for analysis",label="Input Reads"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of sample and input mapped read file",label="File Type"),
align=fileItem(attr=c(type="selectdir", text="Path To Align Directory"), label="Align Directory"),
createfilelist=stringItem("Path To filelist", tooltip="Path to filelist that will be created, holds locations of build datasets"),
winSize=integerItem(500, tooltip="Window Size for data, smaller is better for low signal to noise, high background data", label="Window Size"),
offset=integerItem(125, tooltip="BP offset to shift windows, window size must be a multiple of this number. Yields better sensitivity", label="Window Offset"),
extension=integerItem(200, tooltip="average fragment length in sample library used for sequencing reads, usually 150bp-200bp", label="Extension"),
filelist=fileItem("Path existing file list", attr=list(
filter=list(
"file list" = list(patterns=c("*.list")),
"All files" = list(patterns=c("*"))
)), label="Select Filelist"),
formula=stringItem("", tooltip="formula for modeling background: some combination of gcPerc, align_perc, exp_cnvwin_log, and input_count", label=" BG Formula"),
formulaE=stringItem("exp_count~1", tooltip="formula for modeling enriched region: some combination of, gcPerc, align_perc, exp_cnvwin_log, and input_count", label=" Enrich Formula"),
threshold=numericItem(.01, tooltip="FDR threshold for the pscl method only, lower is more stringent", label="PSCL Thresh"),
peakconfidence=numericItem(.8, tooltip="Posterior window encrichment probability threshold for mixture method only, higher is more stringent", label="Mixture Thresh"),
basecountfile=fileItem("", attr=list(
filter=list(
"basecount" = list(patterns=c("*.basecount")),
"All files" = list(patterns=c("*"))
)), tooltip="Path to SBC (basecountfile) generated from Generate SBC (Basecount) File()"),
winlist=fileItem("Path to.winlist from previous window analysis", attr=list(
filter=list(
"winlist" = list(patterns=c("*.winlist")),
"All files" = list(patterns=c("*"))
)), label=" winlist"),
peaksfilename=stringItem("Path To file for refined peaks", tooltip="Path To file for refined peaks"),
pWinSize=integerItem(200, tooltip='sliding window size to detect local maximums, smaller values are more sensitive but may yield insignificant peaks'),
pquant=numericItem(1, tooltip='quantile threshold for basecounts, 1 means taking only the max of the entire merged region'),
cnvWinSize=integerItem(100000, tooltip="Window size for estimating cnv activity"),
cnvOffset=integerItem(2500, tooltip="BP offset to shift CNV windows, CNV window size must be a multiple of this number"),
tol=numericItem(.00001, tooltip='mixture regression convergence relative tolerance level'),
initmethod=choiceItem("count", values=c("count","quantile", "pscl"),editor_type="gcombobox") ,
cleanup=trueFalseItem(FALSE, tooltip=paste("If true, then intermediate files are deleted once zinba is complete"))
),
title="Zinba Custom GUI",
help_string="Select a file, then adjust parameters.")
view <- aNotebook(
aNotebookPage( aFrame(
aFrame(aContainer("RunChoice" ,"printFullOut","method",aContext("threshold", context=dlg, enabled_when=function(.) {
val <- .$to_R()$method
val =="pscl"
}),aContext("peakconfidence", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$method
val =="mixture"
}),"outfile","numProc","twoBit", "cleanup"),label='General Options'
),
aFrame(aContainer("seq","input","filetype","align","createfilelist","winSize","offset", "extension"),label='Build Window Data',
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val=="Build Windows?")==1
}
)
,label='', horizontal=TRUE
),
aFrame(
aFrame(aContainer(
aContext("filelist", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val =="Build Windows?")==0
})
,"formula",
aContext("formulaE", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$method
val =="mixture"
}), "cnvWinSize", "cnvOffset","tol", "initmethod"),
label='Window Analysis Options',
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val=="Run Window Analysis?")==1
}
),
aFrame(aContainer("basecountfile",
aContext("winlist", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val =="Build Windows?")==0 & sum(val=="Run Window Analysis?")==0
}),
aContext("peaksfilename", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val =="Build Windows?")==0 & sum(val=="Run Window Analysis?")==0
})
,"pWinSize","pquant"),label='Peak Refinement Options',
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val=="Refine Merged Significant Regions?")==1
}
),
label='', horizontal=TRUE
),
label="Run Zinba"
)
)
dlg$OK_handler <- function(.) {
var=.$to_R()
#set up exectution options
if(sum(var$RunChoice=="Build Windows?")==1){
listvar=var$createfilelist
build=1
}else{
listvar=var$filelist
build=0
}
if(sum(var$RunChoice=="Run Window Analysis?")==1){
analysis=1
}else{
analysis=0
}
if(sum(var$RunChoice=="Refine Merged Significant Regions?")==1){
refine=1
}else{
refine=0
}
#run conditional execution
if(build==1 & analysis==0 & refine==0){
do.call("buildwindowdata",list(seq=var$seq,align=var$align,input=var$input,twoBit=var$twoBit,winSize=var$winSize,offset=var$offset,cnvWinSize=var$cnvWinSize,cnvOffset=var $cnvOffset,filelist=listvar,filetype=var$filetype,extension=var$extension))
}else if(build==0 & analysis==0 & refine==1){
do.call("getrefinedpeaks",list(winlist=var$winlist,basecountfile=var$basecountfile,bpout=paste(var$outfile,'.temp', sep=''),peakout=var$peaksfilename,twoBit=var$twoBit,winSize=500,pWinSize=var$pWinSize,pquant=var$pquant,printFullOut=var$printFullOut,peakconfidence=var$peakconfidence,threshold=var$threshold,method=var$method))
}else{
do.call("run.zinba",list(filelist=listvar,formula=as.formula(var$formula),formulaE=as.formula(var$formulaE), outfile=var$outfile, seq=var$seq,align=var$align,input=var$input,twoBit=var$twoBit,winSize=var$winSize,offset=var$offset,cnvWinSize=var$cnvWinSize,cnvOffset=var$cnvOffset, basecountfile=var$basecountfile, threshold=var$threshold,peakconfidence=var$peakconfidence,tol=var$tol,numProc=var$numProc, buildwin=build, pWinSize=var$pWinSize,pquant=var$pquant,refinepeaks=refine, printFullOut=var$printFullOut,method=var$method,initmethod=var$initmethod, diff=0, filetype=var$filetype,extension=var$extension, cleanup=var$cleanup ))
}
}
dlg$make_gui(gui_layout=view)
}
###################################################################
###################################################################
if(util=="Run Zinba Preset"){
dlg <- aDialog(items=list(
preset=choiceItem("High Signal-to-Noise", values=c("High Signal-to-Noise","Moderate STN/Broad-Sharp Mix","Low STN/Broad"), tooltip="Examples:High STN = CTCF ChIP-seq; Moderate STN/Broad-Sharp Mix = PolII ChIP-seq; Low STN = FAIRE-seq/Histone-seq", editor_type="gcombobox", , label=" Data Type"),
method=choiceItem("mixture", values=c("mixture", "pscl"), tooltip="analysis method to use, either mixture regression model or pscl method (FAIRE)",editor_type="gcombobox", label="Analysis Method"),
outfile=stringItem("prefix for output files", tooltip="path and prefix to where .wins and .peaks are placed if analysis and refinement selected together, for example '/home/data/analysis_1'"),
numProc=integerItem(1, tooltip="How many processing cores to allocate, more processors means faster execution but more memory needed", label="Num Processors"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
input=fileItem("none", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped input control reads file (if available) for analysis",label="Input Reads"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of sample and input mapped read file",label="File Type"),
align=fileItem(attr=c(type="selectdir", text="Path To Align Directory"), label="Align Directory"),
extension=integerItem(200, tooltip="average fragment length in sample library used for sequencing reads, usually 150bp-200bp", label="Extension"),
basecountfile=fileItem("", attr=list(
filter=list(
"basecount" = list(patterns=c("*.basecount")),
"All files" = list(patterns=c("*"))
)), tooltip="Path to SBC (basecountfile) generated from Generate SBC (Basecount) File()"),
cleanup=trueFalseItem(FALSE, tooltip=paste("If true, then intermediate files are deleted once zinba is complete"))
),
title="Run Zinba Pipeline With Data Presets",
help_string="Select a file, then adjust parameters.")
view <- aFrame(aContainer("preset" ,"method","outfile","numProc","twoBit","seq",aContext("input",context=dlg,
enabled_when=function(.) {
val <- .$to_R()$preset
sum(val ==c("High Signal-to-Noise","Moderate STN/Broad-Sharp Mix"))>0
}),
"filetype","align","extension","basecountfile", "cleanup"),
label='', horizontal=TRUE)
dlg$OK_handler <- function(.) {
var=.$to_R()
if(var$preset=="High Signal-to-Noise"){
printFullOut=1;
winSize=500;
offset=125;
formula="exp_count~input_count";
formulaE="exp_count~1";
threshold=.01;
peakconfidence=.99;
pWinSize=200;
pquant=1;
cnvWinSize=100000;
cnvOffset=2500;
tol=.00001;
initmethod="count"
}else if(var$preset=="Moderate STN/Broad-Sharp Mix"){
printFullOut=1;
winSize=1000;
offset=250;
formula="exp_count~input_count";
formulaE="exp_count~1";
threshold=.01;
peakconfidence=.99;
pWinSize=200;
pquant=1;
cnvWinSize=100000;
cnvOffset=2500;
tol=.00001;
initmethod="count"
}else if(var$preset=="Low STN/Broad"){
printFullOut=1;
winSize=250;
offset=125;
formula="exp_count~gcPerc+align_perc+exp_cnvwin_log";
formulaE="exp_count~1";
threshold=.01;
peakconfidence=.8;
pWinSize=200;
pquant=1;
cnvWinSize=100000;
cnvOffset=2500;
tol=.00001;
initmethod="count"
}
finalrunlist=list(filelist=NULL,formula=as.formula(formula),formulaE=as.formula(formulaE), outfile=var$outfile, seq=var$seq,align=var$align,input=var$input,twoBit=var$twoBit,winSize=winSize,offset=offset,cnvWinSize=cnvWinSize,cnvOffset=cnvOffset, basecountfile=var$basecountfile, threshold=threshold,peakconfidence=peakconfidence,tol=tol,numProc=var$numProc, buildwin=1, pWinSize=pWinSize,pquant=pquant,refinepeaks=1, printFullOut=printFullOut,method=var$method,initmethod=initmethod, diff=0, filetype=var$filetype,extension=var$extension, cleanup=var$cleanup)
print(finalrunlist)
do.call("run.zinba",finalrunlist)
}
dlg$make_gui(gui_layout=view)
}
}
zinbagui=function(){
require(traitr)
require(gWidgets)
require(zinba)
options(guiToolkit="RGtk2")
eval(parse(text="statusold=c('Select a utility','Yes','Yes', '?')"), envir=.GlobalEnv)
dlg <- aDialog(items=list(
util=choiceItem("Select a utility", values=c("Select a utility","Generate Alignability Directory", "Generate SBC (Basecount) File", "Convert .2bit to .fa","Convert .fa to .2bit", "Get Window Counts","Signal to Noise Analysis"), tooltip="Various utilities to compute files needed for ZINBA",editor_type="gcombobox", label="Utilities"),
align=choiceItem("Yes", values=c("Yes", "No"), tooltip="If no, then will open a dialog to generate your alignability directory for you",editor_type="gcombobox", label="Have you generated your alignability directory?"),
basecount=choiceItem("Yes", values=c("Yes", "No"), tooltip="If no, then will open a dialog to generate your SBC (basecount) file",editor_type="gcombobox",label="Have you generated your SBC (basecount) track?"),
runzinba=choiceItem("?", values=c("?","Run Zinba Data Preset","Run Zinba Custom Parameters"), tooltip="Open Zinba Dialog Window",editor_type="gcombobox", label="Zinba Options")
),
title=" Zinba GUI ",
model_value_changed=function(.) {
l <- .$to_R()
if(l$util=="Convert .2bit to .fa" & l$util!=statusold[1]){
do.call("run", list("twobittofa"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Generate Alignability Directory" & l$util!=statusold[1]){
do.call("run", list("Generate Alignability"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Generate SBC (Basecount) File" & l$util!=statusold[1]){
do.call("run", list("Generate SBC file (basecount)"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Convert .fa to .2bit" & l$util!=statusold[1]){
do.call("run", list("fatotwobit"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Get Window Counts" & l$util!=statusold[1]){
do.call("run", list("getwindowcounts"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Signal to Noise Analysis" & l$util!=statusold[1]){
do.call("run", list("Signal to Noise Analysis"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Select a utility" & l$util!=statusold[1]){
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}
if(l$align=="No" & l$align!=statusold[2]){
do.call("run", list("Generate Alignability"))
eval(parse(text=paste("statusold[2]='",l$align,"'", sep="")), envir=.GlobalEnv)
}
if(l$basecount=="No" & l$basecount!=statusold[3]){
do.call("run", list("Generate SBC file (basecount)"))
eval(parse(text=paste("statusold[3]='",l$basecount,"'", sep="")), envir=.GlobalEnv)
}
if(l$runzinba =="Run Zinba Custom Parameters" & l$runzinba!=statusold[4]){
do.call("run", list("Run Zinba"))
eval(parse(text=paste("statusold[4]='",l$runzinba,"'", sep="")), envir=.GlobalEnv)
}else if(l$runzinba =="Run Zinba Data Preset"& l$runzinba!=statusold[4])
do.call("run", list("Run Zinba Preset"))
eval(parse(text=paste("statusold[4]='",l$runzinba,"'", sep="")), envir=.GlobalEnv)
}
)
view <- aContainer(aFrame("util", label="Zinba Utilities"),aFrame("align", label="File Check"), aFrame("basecount", label="File Check"), aFrame("runzinba", label="Choose How to Run Zinba"))
dlg$make_gui(gui_layout=view)
}
sivarajankumar/zinba documentation built on May 29, 2019, 10:11 p.m.
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run=function(util){
###################################################################
###################################################################
if(util=="Generate Alignability"){
genalign <- aDialog(items=list(
mapdir=fileItem(attr=c(type="selectdir"), tooltip="Path to unpacked mappability directory", label="Mappability\nDirectory"),
outdir=fileItem(attr=c(type="selectdir"), tooltip="Path to alignability directory where output files will be placed",label="Output\nDirectory"),
athresh=numericItem(1, tooltip="Alignability threshold used to filter mapped reads, 1 corresponding that reads only mapping to one place in genome were used", label="Alignability\nThreshold"),
extension=numericItem(200, tooltip="Average length in fragment library used in preparing sample/input reads for sequencing", label="Extension"),
twoBitFile=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file for analysis", label=".2bit file")
), title="Generate Alignability Directory")
view_genalign <- aContainer("mapdir", "outdir", "athresh", "extension", "twoBitFile")
genalign$make_gui(gui_layout=view_genalign, visible=FALSE)
genalign$OK_handler <- function(.) {
genalignvar=.$to_R()
do.call("generateAlignability",list(mapdir=genalignvar$mapdir, outdir=genalignvar$outdir, athresh=genalignvar$athresh, extension=genalignvar$extension, twoBitFile=genalignvar$twoBitFile))
.$close_gui()
}
genalign$visible(TRUE)
}
if(util=="Generate SBC file (basecount)"){
basecount <- aDialog(items=list(
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
basecountdir=fileItem(attr=c(type="selectdir"), tooltip="Directory where basecountfile will be placed", label="Output\nDirectory"),
filename=stringItem("name of SBC (basecount) file to be created", tooltip="Name of SBC (basecount) file, for example ctcf.basecount", label="SBC file"),
twoBitFile=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file for analysis", label=".2bit file"),
extension=numericItem(200, tooltip="Average length in fragment library used in preparing sample/input reads for sequencing", label="Extension"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of mapped sample read file", label="File Type")
), title="Generate SBC (basecount) File")
view_basecount <- aContainer("seq","filetype","basecountdir","filename","twoBitFile","extension")
basecount$make_gui(gui_layout=view_basecount, visible=FALSE)
basecount$OK_handler <- function(.) {
basecountvar=.$to_R()
do.call("basealigncount",list(inputfile=basecountvar$seq,outputfile=paste(basecountvar$basecount, "/",basecountvar$filename,sep="") ,twoBitFile=basecountvar$twoBitFile,extension=basecountvar$extension,filetype=basecountvar$filetype))
.$close_gui()
}
basecount$visible(TRUE)
}
if(util=="twobittofa"){
twobittofa <- aDialog(items=list(
twoBitFile=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file for Conversion to fasta format",label=".2bit file"),
chrm=stringItem("all", tooltip="Name of chromosome where sequence will be converted from, or all if convering an entire directory of fasta files", label="chromosome"),
outdir=fileItem(attr=c(type="selectdir"), tooltip="Path to directory where converted fasta files will be placed",label="Output\nDirectory"),
start=numericItem(0, tooltip="Base Start Position (if chromosome != all) of sequence to be extracted to fasta format",label="Sequence Start"),
end=numericItem(0, tooltip="Base Stop Position (if chromosome != all) of sequence to be extracted to fasta format",label="Sequence End"),
gcSeq=stringItem("path to output file", tooltip="Path to file where extracted fasta sequence will be placed", label="chromosome")
), title="Convert .2bit to fasta format")
view_twobittofa <- aContainer("twoBitFile","chrm","outdir",
aContext("start", context=twobittofa,
enabled_when=function(.) {
val <- .$to_R()$chrm
val !="all"}),
aContext("end", context=twobittofa,
enabled_when=function(.) {
val <- .$to_R()$chrm
val !="all"
}),
aContext("gcSeq", context=twobittofa,
enabled_when=function(.) {
val <- .$to_R()$chrm
val !="all"
})
)
twobittofa$make_gui(gui_layout=view_twobittofa, visible=FALSE)
twobittofa$OK_handler <- function(.) {
twobittofavar=.$to_R()
do.call("twobittofa",list(twoBitFile=twobittofavar$twoBitFile,chrm=twobittofavar$chrm,outdir=twobittofavar$outdir, start=twobittofavar$start,end=twobittofavar$end,gcSeq=twobittofavar$gcSeq))
.$close_gui()
}
twobittofa$visible(TRUE)
}
if(util=="fatotwobit"){
fatotwobit <- aDialog(items=list(
outFile=stringItem("/home/data/genome.2bit", tooltip="if a directory is not selected, path to file where resulting .2bit file will be outputted", label="Path to\nOutput File"),
fadir=fileItem(" ",attr=c(type="selectdir"), tooltip="Path to directory where fasta files to be converted are stored", label="fasta directory"),
faFile=stringItem(" ", tooltip="path to specific fasta file if not specifying a directory", label="chromosome")
), title="Convert fasta file to to .2bit format")
view_fatotwobit <- aContainer("fadir",
aContext("faFile", context=fatotwobit,
enabled_when=function(.) {
val <- .$to_R()$fadir
val ==" "}),
"outFile")
fatotwobit$make_gui(gui_layout=view_fatotwobit, visible=FALSE)
fatotwobit$OK_handler <- function(.) {
fatotwobitvar=.$to_R()
do.call("fatotwobit",list(fadir=fatotwobitvar$fadir,faFile=fatotwobitvar$faFile,outFile=fatotwobitvar$outFile))
.$close_gui()
}
fatotwobit$visible(TRUE)
}
if(util=="getwindowcounts"){
getwindowcounts <- aDialog(items=list(
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of sample and input mapped read file",label="File Type"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
winSize=integerItem(500, tooltip="Window Size for data, smaller is better for low signal to noise, high background data", label="Window Size"),
offset=integerItem(0, tooltip="BP offset to shift windows, window size must be a multiple of this number. Yields better sensitivity", label="Window Offset"),
extension=integerItem(200, tooltip="average fragment length in sample library used for sequencing reads, usually 150bp-200bp", label="Extension")
),title="Get Window Read Counts for data")
view_getwindowcounts <- aContainer("seq","filetype","twoBit","winSize","offset", "extension")
getwindowcounts$make_gui(gui_layout=view_getwindowcounts, visible=FALSE)
getwindowcounts$OK_handler <- function(.) {
getwindowcountsvar=.$to_R()
do.call("getwindowcounts",list(seq=getwindowcountsvar$seq,filetype=getwindowcountsvar$filetype,twoBit=getwindowcountsvar$twoBit,winSize=getwindowcountsvar$winSize, offset=getwindowcountsvar$offset, extension=getwindowcountsvar$extension))
.$close_gui()
}
getwindowcounts$visible(TRUE)
}
if(util=="Signal to Noise Analysis"){
signalnoise <- aDialog(items=list(
inputfile=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"basecount" = list(patterns=c("*.basecount")),
"All files" = list(patterns=c("*"))
)),tooltip="Select basecount file for analysis", label="SBC (basecount) File"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
winSize=integerItem(100000, tooltip="Window Size for analysis, larger, 100kb suggested", label="Window Size")), title="Signal to Noise Analysis")
view_signalnoise <- aContainer("inputfile","twoBit","winSize")
signalnoise$make_gui(gui_layout=view_signalnoise, visible=FALSE)
signalnoise$OK_handler <- function(.) {
signalnoisevar=.$to_R()
do.call("signalnoise",list(inputfile=signalnoisevar$inputfile,twoBit=signalnoisevar$twoBit,winSize=signalnoisevar$winSize))
.$close_gui()
}
signalnoise$visible(TRUE)
}
###################################################################
###################################################################
if(util=="Run Zinba"){
dlg <- aDialog(items=list(
RunChoice=choiceItem("", values=c("Build Windows?","Run Window Analysis?", "Refine Merged Significant Regions?"), tooltip="The Zinba steps you want to run, either together or alone", editor_type="gcheckboxgroup", , label=" Run Options"),
printFullOut=choiceItem(as.integer(1), values=c(as.integer(1), as.integer(0)),tooltip="If 0, only prints out window coordinates, filter status, and window enrichment probability columns for .wins files from window analysis, rather than whole dataset",editor_type="gcombobox", label=" Print Option"),
method=choiceItem("mixture", values=c("mixture", "pscl"), tooltip="analysis method to use, either mixture regression model or pscl method (FAIRE)",editor_type="gcombobox", label="Analysis Method"),
outfile=stringItem("prefix for output files", tooltip="path and prefix to where .wins and .peaks are placed if analysis and refinement selected together, for example '/home/data/analysis_1'"),
numProc=integerItem(1, tooltip="How many processing cores to allocate, more processors means faster execution but more memory needed", label="Num Processors"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
input=fileItem("none", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped input control reads file (if available) for analysis",label="Input Reads"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of sample and input mapped read file",label="File Type"),
align=fileItem(attr=c(type="selectdir", text="Path To Align Directory"), label="Align Directory"),
createfilelist=stringItem("Path To filelist", tooltip="Path to filelist that will be created, holds locations of build datasets"),
winSize=integerItem(500, tooltip="Window Size for data, smaller is better for low signal to noise, high background data", label="Window Size"),
offset=integerItem(125, tooltip="BP offset to shift windows, window size must be a multiple of this number. Yields better sensitivity", label="Window Offset"),
extension=integerItem(200, tooltip="average fragment length in sample library used for sequencing reads, usually 150bp-200bp", label="Extension"),
filelist=fileItem("Path existing file list", attr=list(
filter=list(
"file list" = list(patterns=c("*.list")),
"All files" = list(patterns=c("*"))
)), label="Select Filelist"),
formula=stringItem("", tooltip="formula for modeling background: some combination of gcPerc, align_perc, exp_cnvwin_log, and input_count", label=" BG Formula"),
formulaE=stringItem("exp_count~1", tooltip="formula for modeling enriched region: some combination of, gcPerc, align_perc, exp_cnvwin_log, and input_count", label=" Enrich Formula"),
threshold=numericItem(.01, tooltip="FDR threshold for the pscl method only, lower is more stringent", label="PSCL Thresh"),
peakconfidence=numericItem(.8, tooltip="Posterior window encrichment probability threshold for mixture method only, higher is more stringent", label="Mixture Thresh"),
basecountfile=fileItem("", attr=list(
filter=list(
"basecount" = list(patterns=c("*.basecount")),
"All files" = list(patterns=c("*"))
)), tooltip="Path to SBC (basecountfile) generated from Generate SBC (Basecount) File()"),
winlist=fileItem("Path to.winlist from previous window analysis", attr=list(
filter=list(
"winlist" = list(patterns=c("*.winlist")),
"All files" = list(patterns=c("*"))
)), label=" winlist"),
peaksfilename=stringItem("Path To file for refined peaks", tooltip="Path To file for refined peaks"),
pWinSize=integerItem(200, tooltip='sliding window size to detect local maximums, smaller values are more sensitive but may yield insignificant peaks'),
pquant=numericItem(1, tooltip='quantile threshold for basecounts, 1 means taking only the max of the entire merged region'),
cnvWinSize=integerItem(100000, tooltip="Window size for estimating cnv activity"),
cnvOffset=integerItem(2500, tooltip="BP offset to shift CNV windows, CNV window size must be a multiple of this number"),
tol=numericItem(.00001, tooltip='mixture regression convergence relative tolerance level'),
initmethod=choiceItem("count", values=c("count","quantile", "pscl"),editor_type="gcombobox") ,
cleanup=trueFalseItem(FALSE, tooltip=paste("If true, then intermediate files are deleted once zinba is complete"))
),
title="Zinba Custom GUI",
help_string="Select a file, then adjust parameters.")
view <- aNotebook(
aNotebookPage( aFrame(
aFrame(aContainer("RunChoice" ,"printFullOut","method",aContext("threshold", context=dlg, enabled_when=function(.) {
val <- .$to_R()$method
val =="pscl"
}),aContext("peakconfidence", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$method
val =="mixture"
}),"outfile","numProc","twoBit", "cleanup"),label='General Options'
),
aFrame(aContainer("seq","input","filetype","align","createfilelist","winSize","offset", "extension"),label='Build Window Data',
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val=="Build Windows?")==1
}
)
,label='', horizontal=TRUE
),
aFrame(
aFrame(aContainer(
aContext("filelist", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val =="Build Windows?")==0
})
,"formula",
aContext("formulaE", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$method
val =="mixture"
}), "cnvWinSize", "cnvOffset","tol", "initmethod"),
label='Window Analysis Options',
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val=="Run Window Analysis?")==1
}
),
aFrame(aContainer("basecountfile",
aContext("winlist", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val =="Build Windows?")==0 & sum(val=="Run Window Analysis?")==0
}),
aContext("peaksfilename", context=dlg,
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val =="Build Windows?")==0 & sum(val=="Run Window Analysis?")==0
})
,"pWinSize","pquant"),label='Peak Refinement Options',
enabled_when=function(.) {
val <- .$to_R()$RunChoice
sum(val=="Refine Merged Significant Regions?")==1
}
),
label='', horizontal=TRUE
),
label="Run Zinba"
)
)
dlg$OK_handler <- function(.) {
var=.$to_R()
#set up exectution options
if(sum(var$RunChoice=="Build Windows?")==1){
listvar=var$createfilelist
build=1
}else{
listvar=var$filelist
build=0
}
if(sum(var$RunChoice=="Run Window Analysis?")==1){
analysis=1
}else{
analysis=0
}
if(sum(var$RunChoice=="Refine Merged Significant Regions?")==1){
refine=1
}else{
refine=0
}
#run conditional execution
if(build==1 & analysis==0 & refine==0){
do.call("buildwindowdata",list(seq=var$seq,align=var$align,input=var$input,twoBit=var$twoBit,winSize=var$winSize,offset=var$offset,cnvWinSize=var$cnvWinSize,cnvOffset=var $cnvOffset,filelist=listvar,filetype=var$filetype,extension=var$extension))
}else if(build==0 & analysis==0 & refine==1){
do.call("getrefinedpeaks",list(winlist=var$winlist,basecountfile=var$basecountfile,bpout=paste(var$outfile,'.temp', sep=''),peakout=var$peaksfilename,twoBit=var$twoBit,winSize=500,pWinSize=var$pWinSize,pquant=var$pquant,printFullOut=var$printFullOut,peakconfidence=var$peakconfidence,threshold=var$threshold,method=var$method))
}else{
do.call("run.zinba",list(filelist=listvar,formula=as.formula(var$formula),formulaE=as.formula(var$formulaE), outfile=var$outfile, seq=var$seq,align=var$align,input=var$input,twoBit=var$twoBit,winSize=var$winSize,offset=var$offset,cnvWinSize=var$cnvWinSize,cnvOffset=var$cnvOffset, basecountfile=var$basecountfile, threshold=var$threshold,peakconfidence=var$peakconfidence,tol=var$tol,numProc=var$numProc, buildwin=build, pWinSize=var$pWinSize,pquant=var$pquant,refinepeaks=refine, printFullOut=var$printFullOut,method=var$method,initmethod=var$initmethod, diff=0, filetype=var$filetype,extension=var$extension, cleanup=var$cleanup ))
}
}
dlg$make_gui(gui_layout=view)
}
###################################################################
###################################################################
if(util=="Run Zinba Preset"){
dlg <- aDialog(items=list(
preset=choiceItem("High Signal-to-Noise", values=c("High Signal-to-Noise","Moderate STN/Broad-Sharp Mix","Low STN/Broad"), tooltip="Examples:High STN = CTCF ChIP-seq; Moderate STN/Broad-Sharp Mix = PolII ChIP-seq; Low STN = FAIRE-seq/Histone-seq", editor_type="gcombobox", , label=" Data Type"),
method=choiceItem("mixture", values=c("mixture", "pscl"), tooltip="analysis method to use, either mixture regression model or pscl method (FAIRE)",editor_type="gcombobox", label="Analysis Method"),
outfile=stringItem("prefix for output files", tooltip="path and prefix to where .wins and .peaks are placed if analysis and refinement selected together, for example '/home/data/analysis_1'"),
numProc=integerItem(1, tooltip="How many processing cores to allocate, more processors means faster execution but more memory needed", label="Num Processors"),
twoBit=fileItem("", attr=list(
filter=list(
"2bit" = list(patterns=c("*.2bit")),
"All files" = list(patterns=c("*"))
)), tooltip="Select .2bit file corresponding on build of genome reads were mapped to",label=".2bit file"),
seq=fileItem("", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped sample reads file for analysis", label="Sample Reads"),
input=fileItem("none", attr=list(
filter=list("Bed"=list(
patterns=c("*.bed")
),
"tagAlign" = list(patterns=c("*.taf","*.tagAlign")),
"All files" = list(patterns=c("*"))
)),tooltip="Select mapped input control reads file (if available) for analysis",label="Input Reads"),
filetype=choiceItem("bed", values=c("bed","tagAlign", "bowtie"), editor_type="gcombobox",tooltip="Select format of sample and input mapped read file",label="File Type"),
align=fileItem(attr=c(type="selectdir", text="Path To Align Directory"), label="Align Directory"),
extension=integerItem(200, tooltip="average fragment length in sample library used for sequencing reads, usually 150bp-200bp", label="Extension"),
basecountfile=fileItem("", attr=list(
filter=list(
"basecount" = list(patterns=c("*.basecount")),
"All files" = list(patterns=c("*"))
)), tooltip="Path to SBC (basecountfile) generated from Generate SBC (Basecount) File()"),
cleanup=trueFalseItem(FALSE, tooltip=paste("If true, then intermediate files are deleted once zinba is complete"))
),
title="Run Zinba Pipeline With Data Presets",
help_string="Select a file, then adjust parameters.")
view <- aFrame(aContainer("preset" ,"method","outfile","numProc","twoBit","seq",aContext("input",context=dlg,
enabled_when=function(.) {
val <- .$to_R()$preset
sum(val ==c("High Signal-to-Noise","Moderate STN/Broad-Sharp Mix"))>0
}),
"filetype","align","extension","basecountfile", "cleanup"),
label='', horizontal=TRUE)
dlg$OK_handler <- function(.) {
var=.$to_R()
if(var$preset=="High Signal-to-Noise"){
printFullOut=1;
winSize=500;
offset=125;
formula="exp_count~input_count";
formulaE="exp_count~1";
threshold=.01;
peakconfidence=.99;
pWinSize=200;
pquant=1;
cnvWinSize=100000;
cnvOffset=2500;
tol=.00001;
initmethod="count"
}else if(var$preset=="Moderate STN/Broad-Sharp Mix"){
printFullOut=1;
winSize=1000;
offset=250;
formula="exp_count~input_count";
formulaE="exp_count~1";
threshold=.01;
peakconfidence=.99;
pWinSize=200;
pquant=1;
cnvWinSize=100000;
cnvOffset=2500;
tol=.00001;
initmethod="count"
}else if(var$preset=="Low STN/Broad"){
printFullOut=1;
winSize=250;
offset=125;
formula="exp_count~gcPerc+align_perc+exp_cnvwin_log";
formulaE="exp_count~1";
threshold=.01;
peakconfidence=.8;
pWinSize=200;
pquant=1;
cnvWinSize=100000;
cnvOffset=2500;
tol=.00001;
initmethod="count"
}
finalrunlist=list(filelist=NULL,formula=as.formula(formula),formulaE=as.formula(formulaE), outfile=var$outfile, seq=var$seq,align=var$align,input=var$input,twoBit=var$twoBit,winSize=winSize,offset=offset,cnvWinSize=cnvWinSize,cnvOffset=cnvOffset, basecountfile=var$basecountfile, threshold=threshold,peakconfidence=peakconfidence,tol=tol,numProc=var$numProc, buildwin=1, pWinSize=pWinSize,pquant=pquant,refinepeaks=1, printFullOut=printFullOut,method=var$method,initmethod=initmethod, diff=0, filetype=var$filetype,extension=var$extension, cleanup=var$cleanup)
print(finalrunlist)
do.call("run.zinba",finalrunlist)
}
dlg$make_gui(gui_layout=view)
}
}
zinbagui=function(){
require(traitr)
require(gWidgets)
require(zinba)
options(guiToolkit="RGtk2")
eval(parse(text="statusold=c('Select a utility','Yes','Yes', '?')"), envir=.GlobalEnv)
dlg <- aDialog(items=list(
util=choiceItem("Select a utility", values=c("Select a utility","Generate Alignability Directory", "Generate SBC (Basecount) File", "Convert .2bit to .fa","Convert .fa to .2bit", "Get Window Counts","Signal to Noise Analysis"), tooltip="Various utilities to compute files needed for ZINBA",editor_type="gcombobox", label="Utilities"),
align=choiceItem("Yes", values=c("Yes", "No"), tooltip="If no, then will open a dialog to generate your alignability directory for you",editor_type="gcombobox", label="Have you generated your alignability directory?"),
basecount=choiceItem("Yes", values=c("Yes", "No"), tooltip="If no, then will open a dialog to generate your SBC (basecount) file",editor_type="gcombobox",label="Have you generated your SBC (basecount) track?"),
runzinba=choiceItem("?", values=c("?","Run Zinba Data Preset","Run Zinba Custom Parameters"), tooltip="Open Zinba Dialog Window",editor_type="gcombobox", label="Zinba Options")
),
title=" Zinba GUI ",
model_value_changed=function(.) {
l <- .$to_R()
if(l$util=="Convert .2bit to .fa" & l$util!=statusold[1]){
do.call("run", list("twobittofa"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Generate Alignability Directory" & l$util!=statusold[1]){
do.call("run", list("Generate Alignability"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Generate SBC (Basecount) File" & l$util!=statusold[1]){
do.call("run", list("Generate SBC file (basecount)"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Convert .fa to .2bit" & l$util!=statusold[1]){
do.call("run", list("fatotwobit"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Get Window Counts" & l$util!=statusold[1]){
do.call("run", list("getwindowcounts"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Signal to Noise Analysis" & l$util!=statusold[1]){
do.call("run", list("Signal to Noise Analysis"))
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}else if(l$util=="Select a utility" & l$util!=statusold[1]){
eval(parse(text=paste("statusold[1]='",l$util,"'", sep="")), envir=.GlobalEnv)
}
if(l$align=="No" & l$align!=statusold[2]){
do.call("run", list("Generate Alignability"))
eval(parse(text=paste("statusold[2]='",l$align,"'", sep="")), envir=.GlobalEnv)
}
if(l$basecount=="No" & l$basecount!=statusold[3]){
do.call("run", list("Generate SBC file (basecount)"))
eval(parse(text=paste("statusold[3]='",l$basecount,"'", sep="")), envir=.GlobalEnv)
}
if(l$runzinba =="Run Zinba Custom Parameters" & l$runzinba!=statusold[4]){
do.call("run", list("Run Zinba"))
eval(parse(text=paste("statusold[4]='",l$runzinba,"'", sep="")), envir=.GlobalEnv)
}else if(l$runzinba =="Run Zinba Data Preset"& l$runzinba!=statusold[4])
do.call("run", list("Run Zinba Preset"))
eval(parse(text=paste("statusold[4]='",l$runzinba,"'", sep="")), envir=.GlobalEnv)
}
)
view <- aContainer(aFrame("util", label="Zinba Utilities"),aFrame("align", label="File Check"), aFrame("basecount", label="File Check"), aFrame("runzinba", label="Choose How to Run Zinba"))
dlg$make_gui(gui_layout=view)
}
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