R/intact_window.R
In melinagallopin/appinetwork: construction and Analysis of Protein-Protein Interactions (PPI) networks for complexes and biological processes
Defines functions
intact_window
format_intact
# intact_othero <- function(organism, organismID, file, pathracine) {
#
# cat("\n\n>FORMATING INTACT DATABASE")
#
# intactFileName <- file
#
# cat("\n>Loading database ... ")
#
# intact <- read.delim(file = intactFileName, header = T, sep = "\t")
#
# if (dim(intact)[2] != 15) {
# cat(paste("\nIncorrect data dimension, read userguide for more informations"))
# stop()
# }
#
# intact <- intact[,-c(3,4,14)]
# intact <- intact[grep("uniprotkb:", intact[,1]),]
# intact <- intact[grep("uniprotkb:", intact[,2]),]
#
# if (organism == "Saccharomyces cerevisiae") {
# organismID <- "559292"
# }
# if (organism == "Homo-sapiens") {
# organismID <- "9606"
# }
# if (organism == "Caenorhabditis elegans") {
# organismID <- "6239"
# }
# if (organism == "Drosophila melanogaster") {
# organismID <- "7227"
# }
# if (organism == "Escherichia coli") {
# organismID <- "562"
# }
# if (organism == "Mus musculus") {
# organismID <- "10090"
# }
# if (organism == "Rattus norvegicus") {
# organismID <- "10116"
# }
#
# rtaxon <- paste("taxid:", organismID, "(", organism, ")", sep = '')
# taxon <- organismID
#
# intact <- intact[grep(taxon, intact[,8]),]
# intact <- intact[grep(taxon, intact[,9]),]
#
# intact[,8] <- rtaxon
# intact[,9] <- rtaxon
#
# if (length(grep("colocalization", intact[,10])) > 0) {
# intact <- intact[-grep("colocalization", intact[,10]),]
# }
# irefindex <- intact
# irefindex[,10] <- rep("physical", dim(irefindex)[1])
# irefindex[,1] <- apply(as.matrix(apply(as.matrix(irefindex[,1]), 1, strsplit, split = ":")), 1, unlist)[2,]
# irefindex[,2] <- apply(as.matrix(apply(as.matrix(irefindex[,2]), 1, strsplit, split = ":")), 1, unlist)[2,]
# if (length(grep("-", irefindex[,1])) > 0) {
# irefindex[grep("-", irefindex[,1]),1] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,1]),1]), 1, strsplit, split = "-")), 1, unlist)[1,]
# }
# if (length(grep("-", irefindex[,2])) > 0) {
# irefindex[grep("-", irefindex[,2]),2] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,2]),2]), 1, strsplit, split = "-")), 1, unlist)[1,]
# }
#
# tmpA1 <- rep("NA", length(irefindex[,3]))
# tmpB1 <- rep("NA", length(irefindex[,3]))
# tmpA2 <- rep("NA", length(irefindex[,3]))
# tmpB2 <- rep("NA", length(irefindex[,3]))
#
# tmpA <- apply(as.matrix(apply(as.matrix(irefindex[,3]), 1, strsplit, split = "\\|")), 1, unlist)
# tmpB <- apply(as.matrix(apply(as.matrix(irefindex[,4]), 1, strsplit, split = "\\|")), 1, unlist)
#
# cat(paste("OK\n>Parsing interactions\n"))
# prsbar <- txtProgressBar(min = 1, max = length(irefindex[,3]), style = 3)
# for (i in 1:length(irefindex[,3])) {
# tmpA1[i] <- tmpA[[i]][1]
# if (length(grep("\\(gene name\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(gene name\\)", tmpA[[i]])]
# }
# else {
# if (length(grep("\\(locus name\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(locus name\\)", tmpA[[i]])]
# }
# else {
# if (length(grep("\\(orf name\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(orf name\\)", tmpA[[i]])]
# }
# else {
# if (length(grep("\\(display_long\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(display_long\\)", tmpA[[i]])]
# }
# }
# }
# }
# tmpB1[i] <- tmpB[[i]][1]
# if (length(grep("\\(gene name\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\(gene name\\)", tmpB[[i]])]
# }
# else {
# if (length(grep("\\(locus name\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\(locus name\\)", tmpB[[i]])]
# }
# else {
# if (length(grep("\\(orf name\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\(orf name\\)", tmpB[[i]])]
# }
# else {
# if (length(grep("\\(display_long\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\((display_long)\\)", tmpB[[i]])]
# }
# }
# }
# }
# setTxtProgressBar(prsbar, i)
# }
#
# GeneNameA <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpA2))
# GeneNameA <- sub("\\(locus name\\)", '', GeneNameA)
# GeneNameA <- sub("\\(orf name\\)", '', GeneNameA)
# GeneNameA <- sub("\\(gene name synonym\\)", '', GeneNameA)
# GeneNameA <- sub("\\(display_long\\)", '', GeneNameA)
# GeneNameA[grep("CELE_", GeneNameA)] <- sub("CELE_", "", GeneNameA[grep("CELE_", GeneNameA)])
# GeneNameA[grep("psi-mi:", GeneNameA)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameA[grep("psi-mi:", GeneNameA)]))
#
# GeneNameB <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpB2))
# GeneNameB <- sub("\\(locus name\\)", '', GeneNameB)
# GeneNameB <- sub("\\(orf name\\)", '', GeneNameB)
# GeneNameB <- sub("\\(gene name synonym\\)", '', GeneNameB)
# GeneNameB <- sub("\\(display_long\\)", '', GeneNameB)
# GeneNameB[grep("CELE_", GeneNameB)] <- sub("CELE_", "", GeneNameB[grep("CELE_", GeneNameB)])
# GeneNameB[grep("psi-mi:", GeneNameB)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameB[grep("psi-mi:", GeneNameB)]))
#
# irefindex[,3] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpA1))
# irefindex[,4] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpB1))
#
# numParticipants <- rep(2, dim(irefindex)[1])
#
# sourcedb <- rep("Intact", dim(irefindex)[1])
# irefindex[,11] <- sourcedb
#
# cat("OK\n>Saving database(s) ... ")
#
# setwd(pathracine)
#
# organism <- gsub(" ", "-", organism)
# organism.path <- paste(pathracine, organism, sep = '/')
# dir.create(organism.path, showWarnings = FALSE)
# database.path <- paste(organism.path, "Databases", sep = '/')
# dir.create(database.path, showWarnings = FALSE)
# setwd(database.path)
#
# irefindex <- irefindex[,c(1:12)]
#
# irefindex <- cbind(irefindex, numParticipants, GeneNameA, GeneNameB)
# colnames(irefindex) <- c("uidA", "uidB", "aliasA", "aliasB", "method", "author", "pmids", "taxa", "taxb", "interactionType", "sourcedb", "confidence", "numParticipants", "GeneNameA", "GeneNameB")
# outputfilename <- paste(organism, "_intact.txt", sep = "")
# write.table(irefindex, fi le = outputfilename, row.names = F, col.names = T, quote = F, sep = "\t")
#
# cat(paste("OK\n\n>Formating intact database is done.\n\nDatabase file is saved in", database.path, sep = " : "))
# cat(paste("\n\n"))
# setwd(pathracine)
#
# visible(mainpanel) <- T
#
# }
format_intact = function(organism, organismID, file, pathracine, other) {
cat("\n\n>FORMATING INTACT DATABASE")
intactFileName <- file
cat("\n>Loading database ... ")
intact <- read.delim(file = intactFileName, header = T, sep = "\t")
intact <- intact[,-c(3,4,14)]
intact <- intact[grep("uniprotkb:", intact[,1]),]
intact <- intact[grep("uniprotkb:", intact[,2]),]
if(other != "Other") {
# Si l'organisme est dans les choix prédéfinis :
list.organism<-cbind(c("Saccharomyces cerevisiae","Homo sapiens","Caenorhabditis elegans","Drosophila melanogaster","Escherichia coli","Mus musculus","Rattus norvegicus","Arabidopsis thaliana"),c("559292","9606","6239","7227","562","10090","10116","3702"))
organismID<-list.organism[list.organism[,1]==organism,2]
}
rtaxon <- paste("taxid:", organismID, "(", organism, ")", sep = '')
taxon <- organismID
intact <- intact[grep(taxon, intact[,8]),]
intact <- intact[grep(taxon, intact[,9]),]
intact[,8] <- rtaxon
intact[,9] <- rtaxon
if (length(grep("colocalization", intact[,10])) > 0) {
intact <- intact[-grep("colocalization", intact[,10]),]
}
irefindex <- intact
irefindex[,10] <- rep("physical", dim(irefindex)[1])
irefindex[,1] <- apply(as.matrix(apply(as.matrix(irefindex[,1]), 1, strsplit, split = ":")), 1, unlist)[2,]
irefindex[,2] <- apply(as.matrix(apply(as.matrix(irefindex[,2]), 1, strsplit, split = ":")), 1, unlist)[2,]
if (length(grep("-", irefindex[,1])) > 0) {
irefindex[grep("-", irefindex[,1]),1] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,1]),1]), 1, strsplit, split = "-")), 1, unlist)[1,]
}
if (length(grep("-", irefindex[,2])) > 0) {
irefindex[grep("-", irefindex[,2]),2] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,2]),2]), 1, strsplit, split = "-")), 1, unlist)[1,]
}
tmpA1 <- rep("NA", length(irefindex[,3]))
tmpB1 <- rep("NA", length(irefindex[,3]))
tmpA2 <- rep("NA", length(irefindex[,3]))
tmpB2 <- rep("NA", length(irefindex[,3]))
tmpA <- apply(as.matrix(apply(as.matrix(irefindex[,3]), 1, strsplit, split = "\\|")), 1, unlist)
tmpB <- apply(as.matrix(apply(as.matrix(irefindex[,4]), 1, strsplit, split = "\\|")), 1, unlist)
cat(paste("OK\n>Parsing interactions\n"))
prsbar <- txtProgressBar(min = 1, max = length(irefindex[,3]), style = 3)
for (i in 1:length(irefindex[,3])) {
tmpA1[i] <- tmpA[[i]][1]
if (length(grep("\\(gene name\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(gene name\\)", tmpA[[i]])]
}
else {
if (length(grep("\\(locus name\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(locus name\\)", tmpA[[i]])]
}
else {
if (length(grep("\\(orf name\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(orf name\\)", tmpA[[i]])]
}
else {
if (length(grep("\\(display_long\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(display_long\\)", tmpA[[i]])]
}
}
}
}
tmpB1[i] <- tmpB[[i]][1]
if (length(grep("\\(gene name\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\(gene name\\)", tmpB[[i]])]
}
else {
if (length(grep("\\(locus name\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\(locus name\\)", tmpB[[i]])]
}
else {
if (length(grep("\\(orf name\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\(orf name\\)", tmpB[[i]])]
}
else {
if (length(grep("\\(display_long\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\((display_long)\\)", tmpB[[i]])]
}
}
}
}
setTxtProgressBar(prsbar, i)
}
GeneNameA <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpA2))
GeneNameA <- sub("\\(locus name\\)", '', GeneNameA)
GeneNameA <- sub("\\(orf name\\)", '', GeneNameA)
GeneNameA <- sub("\\(gene name synonym\\)", '', GeneNameA)
GeneNameA <- sub("\\(display_long\\)", '', GeneNameA)
GeneNameA[grep("CELE_", GeneNameA)] <- sub("CELE_", "", GeneNameA[grep("CELE_", GeneNameA)])
GeneNameA[grep("psi-mi:", GeneNameA)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameA[grep("psi-mi:", GeneNameA)]))
GeneNameB <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpB2))
GeneNameB <- sub("\\(locus name\\)", '', GeneNameB)
GeneNameB <- sub("\\(orf name\\)", '', GeneNameB)
GeneNameB <- sub("\\(gene name synonym\\)", '', GeneNameB)
GeneNameB <- sub("\\(display_long\\)", '', GeneNameB)
GeneNameB[grep("CELE_", GeneNameB)] <- sub("CELE_", "", GeneNameB[grep("CELE_", GeneNameB)])
GeneNameB[grep("psi-mi:", GeneNameB)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameB[grep("psi-mi:", GeneNameB)]))
irefindex[,3] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpA1))
irefindex[,4] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpB1))
numParticipants <- rep(2, dim(irefindex)[1])
sourcedb <- rep("Intact", dim(irefindex)[1])
irefindex[,11] <- sourcedb
cat("Ok\n>Saving database(s) ... ")
setwd(pathracine)
organism <- gsub(" ", "-", organism)
organism.path <- paste(pathracine, organism, sep = '/')
dir.create(organism.path, showWarnings = FALSE)
database.path <- paste(organism.path, "Databases", sep = '/')
dir.create(database.path, showWarnings = FALSE)
setwd(database.path)
irefindex <- irefindex[,c(1:12)]
irefindex <- cbind(irefindex, numParticipants, GeneNameA, GeneNameB)
colnames(irefindex) <- c("uidA", "uidB", "aliasA", "aliasB", "method", "author", "pmids", "taxa", "taxb", "interactionType", "sourcedb", "confidence", "numParticipants", "GeneNameA", "GeneNameB")
outputfilename <- paste(organism, "_intact.txt", sep = "")
write.table(irefindex, file = outputfilename, row.names = F, col.names = T, quote = F, sep = "\t")
cat(paste("OK\n\n>Formating intact database is done.\n\nDatabase file is saved in", database.path, sep = " : "))
cat(paste("\n\n"))
setwd(pathracine)
visible(mainpanel) <<- T
}
intact_window <- function(f_pos, mainpanel, pana, mainpath) {
file <- c()
return.parameter <- c()
panel_para <- gwindow("Intact database file formatting : ", parent = f_pos, visible = T)
pp <- gvbox(container = panel_para)
pp$set_borderwidth(10L)
flyt <- gformlayout(container = pp, expand = TRUE)
# Parametres selection
gcombobox(c('Caenorhabditis elegans', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae','Arabidopsis thaliana', 'Other'), label = "Organism", selected = 7, container = flyt)
# File selection
chdb <- ggroup(container = pp, horizontale = T)
addSpring(chdb)
bouton1 <- gbutton("Intact file", container = chdb, handler = function(...) {
file <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
if (is.null(file) == T) {
gmessage('Selected file is null', icon = 'error')
}
if (is.null(file) == F) {
bouton1$set_value(paste(length(file), 'intact file selected'))
cat(paste('\n>File selected : ', file, sep = ''))
}
})
ppb <- ggroup(container = pp)
addSpring(ppb)
gbutton("Format file", handler = function(h,...) {
return.parameter <<- svalue(flyt)
visible(panel_para) <- F
# selected parametres storage
organism <- as.character(return.parameter[1])
other = organism
# When all paramaters are Ok
if (is.null(file) == F) {
######################################################################################
########################### FORMATING AND PARSING #################################
pathracine <- getwd()
if (organism == "Other") {
panelorganism <- gwindow("Organism description", parent = f_pos, visible = F, expand = T)
pc <- ggroup(container = panelorganism, horizontal = F, use.scrollwindow = T)
pcsb <- ggroup(container = pc, horizontal = F, use.scrollwindow = F)
lg <- gvbox(container = pcsb)
pg <- gvbox(container = pcsb)
fllg <- gformlayout(container = lg)
flpg <- gformlayout(container = pg)
organismName <- gedit(initial.msg = 'Organism Name', label = "NAME", container = fllg)
organismId <- gedit(initial.msg = 'Organism ID', label = "NCBI ID", container = flpg)
visible(panelorganism) <- T
bpc <- ggroup(container = pc); addSpring(bpc)
# 1 : Other organism
bouton1 <- gbutton("OK", handler = function(h,...) {
# Rassemblement des modifications a apporter
org.name <- cbind(names(svalue(fllg)), svalue(fllg))
org.name <- data.frame(org.name, row.names = NULL)
org.id <- cbind(names(svalue(flpg)), svalue(flpg))
org.id <- data.frame(org.id, row.names = NULL)
org <- cbind(org.name, org.id)
colnames(org) <- c('Organism_name', 'Organism_id')
organism <- as.character(org[1,2])
organismID <- as.character(org[1,4])
# intact_othero(organism, organismID, file, pathracine)
format_intact(organism, organismID, file, pathracine, other)
dispose(bpc)
}, container = bpc)
}
else {
format_intact(organism, organismID, file, pathracine, other)
}
dispose(panel_para)
dispose(ppb)
}
# Tests all elements necessary to the function execution
else if (is.null(file) == T) {
gmessage('File selected is null', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
else {
gmessage('Error : Unable to start formatting', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
}, container=ppb)
# Return
gbutton("Return", handler = function(h,...) {
dispose(panel_para)
visible(pana) <<- T
}, container = ppb)
visible(panel_para) <- T
}
melinagallopin/appinetwork documentation built on Nov. 13, 2020, 2:18 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions intact_window format_intact
# intact_othero <- function(organism, organismID, file, pathracine) {
#
# cat("\n\n>FORMATING INTACT DATABASE")
#
# intactFileName <- file
#
# cat("\n>Loading database ... ")
#
# intact <- read.delim(file = intactFileName, header = T, sep = "\t")
#
# if (dim(intact)[2] != 15) {
# cat(paste("\nIncorrect data dimension, read userguide for more informations"))
# stop()
# }
#
# intact <- intact[,-c(3,4,14)]
# intact <- intact[grep("uniprotkb:", intact[,1]),]
# intact <- intact[grep("uniprotkb:", intact[,2]),]
#
# if (organism == "Saccharomyces cerevisiae") {
# organismID <- "559292"
# }
# if (organism == "Homo-sapiens") {
# organismID <- "9606"
# }
# if (organism == "Caenorhabditis elegans") {
# organismID <- "6239"
# }
# if (organism == "Drosophila melanogaster") {
# organismID <- "7227"
# }
# if (organism == "Escherichia coli") {
# organismID <- "562"
# }
# if (organism == "Mus musculus") {
# organismID <- "10090"
# }
# if (organism == "Rattus norvegicus") {
# organismID <- "10116"
# }
#
# rtaxon <- paste("taxid:", organismID, "(", organism, ")", sep = '')
# taxon <- organismID
#
# intact <- intact[grep(taxon, intact[,8]),]
# intact <- intact[grep(taxon, intact[,9]),]
#
# intact[,8] <- rtaxon
# intact[,9] <- rtaxon
#
# if (length(grep("colocalization", intact[,10])) > 0) {
# intact <- intact[-grep("colocalization", intact[,10]),]
# }
# irefindex <- intact
# irefindex[,10] <- rep("physical", dim(irefindex)[1])
# irefindex[,1] <- apply(as.matrix(apply(as.matrix(irefindex[,1]), 1, strsplit, split = ":")), 1, unlist)[2,]
# irefindex[,2] <- apply(as.matrix(apply(as.matrix(irefindex[,2]), 1, strsplit, split = ":")), 1, unlist)[2,]
# if (length(grep("-", irefindex[,1])) > 0) {
# irefindex[grep("-", irefindex[,1]),1] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,1]),1]), 1, strsplit, split = "-")), 1, unlist)[1,]
# }
# if (length(grep("-", irefindex[,2])) > 0) {
# irefindex[grep("-", irefindex[,2]),2] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,2]),2]), 1, strsplit, split = "-")), 1, unlist)[1,]
# }
#
# tmpA1 <- rep("NA", length(irefindex[,3]))
# tmpB1 <- rep("NA", length(irefindex[,3]))
# tmpA2 <- rep("NA", length(irefindex[,3]))
# tmpB2 <- rep("NA", length(irefindex[,3]))
#
# tmpA <- apply(as.matrix(apply(as.matrix(irefindex[,3]), 1, strsplit, split = "\\|")), 1, unlist)
# tmpB <- apply(as.matrix(apply(as.matrix(irefindex[,4]), 1, strsplit, split = "\\|")), 1, unlist)
#
# cat(paste("OK\n>Parsing interactions\n"))
# prsbar <- txtProgressBar(min = 1, max = length(irefindex[,3]), style = 3)
# for (i in 1:length(irefindex[,3])) {
# tmpA1[i] <- tmpA[[i]][1]
# if (length(grep("\\(gene name\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(gene name\\)", tmpA[[i]])]
# }
# else {
# if (length(grep("\\(locus name\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(locus name\\)", tmpA[[i]])]
# }
# else {
# if (length(grep("\\(orf name\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(orf name\\)", tmpA[[i]])]
# }
# else {
# if (length(grep("\\(display_long\\)", tmpA[[i]])) > 0) {
# tmpA2[i] <- tmpA[[i]][grep("\\(display_long\\)", tmpA[[i]])]
# }
# }
# }
# }
# tmpB1[i] <- tmpB[[i]][1]
# if (length(grep("\\(gene name\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\(gene name\\)", tmpB[[i]])]
# }
# else {
# if (length(grep("\\(locus name\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\(locus name\\)", tmpB[[i]])]
# }
# else {
# if (length(grep("\\(orf name\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\(orf name\\)", tmpB[[i]])]
# }
# else {
# if (length(grep("\\(display_long\\)", tmpB[[i]])) > 0) {
# tmpB2[i] <- tmpB[[i]][grep("\\((display_long)\\)", tmpB[[i]])]
# }
# }
# }
# }
# setTxtProgressBar(prsbar, i)
# }
#
# GeneNameA <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpA2))
# GeneNameA <- sub("\\(locus name\\)", '', GeneNameA)
# GeneNameA <- sub("\\(orf name\\)", '', GeneNameA)
# GeneNameA <- sub("\\(gene name synonym\\)", '', GeneNameA)
# GeneNameA <- sub("\\(display_long\\)", '', GeneNameA)
# GeneNameA[grep("CELE_", GeneNameA)] <- sub("CELE_", "", GeneNameA[grep("CELE_", GeneNameA)])
# GeneNameA[grep("psi-mi:", GeneNameA)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameA[grep("psi-mi:", GeneNameA)]))
#
# GeneNameB <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpB2))
# GeneNameB <- sub("\\(locus name\\)", '', GeneNameB)
# GeneNameB <- sub("\\(orf name\\)", '', GeneNameB)
# GeneNameB <- sub("\\(gene name synonym\\)", '', GeneNameB)
# GeneNameB <- sub("\\(display_long\\)", '', GeneNameB)
# GeneNameB[grep("CELE_", GeneNameB)] <- sub("CELE_", "", GeneNameB[grep("CELE_", GeneNameB)])
# GeneNameB[grep("psi-mi:", GeneNameB)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameB[grep("psi-mi:", GeneNameB)]))
#
# irefindex[,3] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpA1))
# irefindex[,4] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpB1))
#
# numParticipants <- rep(2, dim(irefindex)[1])
#
# sourcedb <- rep("Intact", dim(irefindex)[1])
# irefindex[,11] <- sourcedb
#
# cat("OK\n>Saving database(s) ... ")
#
# setwd(pathracine)
#
# organism <- gsub(" ", "-", organism)
# organism.path <- paste(pathracine, organism, sep = '/')
# dir.create(organism.path, showWarnings = FALSE)
# database.path <- paste(organism.path, "Databases", sep = '/')
# dir.create(database.path, showWarnings = FALSE)
# setwd(database.path)
#
# irefindex <- irefindex[,c(1:12)]
#
# irefindex <- cbind(irefindex, numParticipants, GeneNameA, GeneNameB)
# colnames(irefindex) <- c("uidA", "uidB", "aliasA", "aliasB", "method", "author", "pmids", "taxa", "taxb", "interactionType", "sourcedb", "confidence", "numParticipants", "GeneNameA", "GeneNameB")
# outputfilename <- paste(organism, "_intact.txt", sep = "")
# write.table(irefindex, fi le = outputfilename, row.names = F, col.names = T, quote = F, sep = "\t")
#
# cat(paste("OK\n\n>Formating intact database is done.\n\nDatabase file is saved in", database.path, sep = " : "))
# cat(paste("\n\n"))
# setwd(pathracine)
#
# visible(mainpanel) <- T
#
# }
format_intact = function(organism, organismID, file, pathracine, other) {
cat("\n\n>FORMATING INTACT DATABASE")
intactFileName <- file
cat("\n>Loading database ... ")
intact <- read.delim(file = intactFileName, header = T, sep = "\t")
intact <- intact[,-c(3,4,14)]
intact <- intact[grep("uniprotkb:", intact[,1]),]
intact <- intact[grep("uniprotkb:", intact[,2]),]
if(other != "Other") {
# Si l'organisme est dans les choix prédéfinis :
list.organism<-cbind(c("Saccharomyces cerevisiae","Homo sapiens","Caenorhabditis elegans","Drosophila melanogaster","Escherichia coli","Mus musculus","Rattus norvegicus","Arabidopsis thaliana"),c("559292","9606","6239","7227","562","10090","10116","3702"))
organismID<-list.organism[list.organism[,1]==organism,2]
}
rtaxon <- paste("taxid:", organismID, "(", organism, ")", sep = '')
taxon <- organismID
intact <- intact[grep(taxon, intact[,8]),]
intact <- intact[grep(taxon, intact[,9]),]
intact[,8] <- rtaxon
intact[,9] <- rtaxon
if (length(grep("colocalization", intact[,10])) > 0) {
intact <- intact[-grep("colocalization", intact[,10]),]
}
irefindex <- intact
irefindex[,10] <- rep("physical", dim(irefindex)[1])
irefindex[,1] <- apply(as.matrix(apply(as.matrix(irefindex[,1]), 1, strsplit, split = ":")), 1, unlist)[2,]
irefindex[,2] <- apply(as.matrix(apply(as.matrix(irefindex[,2]), 1, strsplit, split = ":")), 1, unlist)[2,]
if (length(grep("-", irefindex[,1])) > 0) {
irefindex[grep("-", irefindex[,1]),1] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,1]),1]), 1, strsplit, split = "-")), 1, unlist)[1,]
}
if (length(grep("-", irefindex[,2])) > 0) {
irefindex[grep("-", irefindex[,2]),2] <- apply(as.matrix(apply(as.matrix(irefindex[grep("-", irefindex[,2]),2]), 1, strsplit, split = "-")), 1, unlist)[1,]
}
tmpA1 <- rep("NA", length(irefindex[,3]))
tmpB1 <- rep("NA", length(irefindex[,3]))
tmpA2 <- rep("NA", length(irefindex[,3]))
tmpB2 <- rep("NA", length(irefindex[,3]))
tmpA <- apply(as.matrix(apply(as.matrix(irefindex[,3]), 1, strsplit, split = "\\|")), 1, unlist)
tmpB <- apply(as.matrix(apply(as.matrix(irefindex[,4]), 1, strsplit, split = "\\|")), 1, unlist)
cat(paste("OK\n>Parsing interactions\n"))
prsbar <- txtProgressBar(min = 1, max = length(irefindex[,3]), style = 3)
for (i in 1:length(irefindex[,3])) {
tmpA1[i] <- tmpA[[i]][1]
if (length(grep("\\(gene name\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(gene name\\)", tmpA[[i]])]
}
else {
if (length(grep("\\(locus name\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(locus name\\)", tmpA[[i]])]
}
else {
if (length(grep("\\(orf name\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(orf name\\)", tmpA[[i]])]
}
else {
if (length(grep("\\(display_long\\)", tmpA[[i]])) > 0) {
tmpA2[i] <- tmpA[[i]][grep("\\(display_long\\)", tmpA[[i]])]
}
}
}
}
tmpB1[i] <- tmpB[[i]][1]
if (length(grep("\\(gene name\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\(gene name\\)", tmpB[[i]])]
}
else {
if (length(grep("\\(locus name\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\(locus name\\)", tmpB[[i]])]
}
else {
if (length(grep("\\(orf name\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\(orf name\\)", tmpB[[i]])]
}
else {
if (length(grep("\\(display_long\\)", tmpB[[i]])) > 0) {
tmpB2[i] <- tmpB[[i]][grep("\\((display_long)\\)", tmpB[[i]])]
}
}
}
}
setTxtProgressBar(prsbar, i)
}
GeneNameA <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpA2))
GeneNameA <- sub("\\(locus name\\)", '', GeneNameA)
GeneNameA <- sub("\\(orf name\\)", '', GeneNameA)
GeneNameA <- sub("\\(gene name synonym\\)", '', GeneNameA)
GeneNameA <- sub("\\(display_long\\)", '', GeneNameA)
GeneNameA[grep("CELE_", GeneNameA)] <- sub("CELE_", "", GeneNameA[grep("CELE_", GeneNameA)])
GeneNameA[grep("psi-mi:", GeneNameA)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameA[grep("psi-mi:", GeneNameA)]))
GeneNameB <- sub("\\(gene name\\)", '', sub("uniprotkb:", '', tmpB2))
GeneNameB <- sub("\\(locus name\\)", '', GeneNameB)
GeneNameB <- sub("\\(orf name\\)", '', GeneNameB)
GeneNameB <- sub("\\(gene name synonym\\)", '', GeneNameB)
GeneNameB <- sub("\\(display_long\\)", '', GeneNameB)
GeneNameB[grep("CELE_", GeneNameB)] <- sub("CELE_", "", GeneNameB[grep("CELE_", GeneNameB)])
GeneNameB[grep("psi-mi:", GeneNameB)] <- sub("_caeel", "", sub("psi-mi:", "", GeneNameB[grep("psi-mi:", GeneNameB)]))
irefindex[,3] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpA1))
irefindex[,4] <- sub("\\(display_long\\)", '', sub("psi-mi:", '', tmpB1))
numParticipants <- rep(2, dim(irefindex)[1])
sourcedb <- rep("Intact", dim(irefindex)[1])
irefindex[,11] <- sourcedb
cat("Ok\n>Saving database(s) ... ")
setwd(pathracine)
organism <- gsub(" ", "-", organism)
organism.path <- paste(pathracine, organism, sep = '/')
dir.create(organism.path, showWarnings = FALSE)
database.path <- paste(organism.path, "Databases", sep = '/')
dir.create(database.path, showWarnings = FALSE)
setwd(database.path)
irefindex <- irefindex[,c(1:12)]
irefindex <- cbind(irefindex, numParticipants, GeneNameA, GeneNameB)
colnames(irefindex) <- c("uidA", "uidB", "aliasA", "aliasB", "method", "author", "pmids", "taxa", "taxb", "interactionType", "sourcedb", "confidence", "numParticipants", "GeneNameA", "GeneNameB")
outputfilename <- paste(organism, "_intact.txt", sep = "")
write.table(irefindex, file = outputfilename, row.names = F, col.names = T, quote = F, sep = "\t")
cat(paste("OK\n\n>Formating intact database is done.\n\nDatabase file is saved in", database.path, sep = " : "))
cat(paste("\n\n"))
setwd(pathracine)
visible(mainpanel) <<- T
}
intact_window <- function(f_pos, mainpanel, pana, mainpath) {
file <- c()
return.parameter <- c()
panel_para <- gwindow("Intact database file formatting : ", parent = f_pos, visible = T)
pp <- gvbox(container = panel_para)
pp$set_borderwidth(10L)
flyt <- gformlayout(container = pp, expand = TRUE)
# Parametres selection
gcombobox(c('Caenorhabditis elegans', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae','Arabidopsis thaliana', 'Other'), label = "Organism", selected = 7, container = flyt)
# File selection
chdb <- ggroup(container = pp, horizontale = T)
addSpring(chdb)
bouton1 <- gbutton("Intact file", container = chdb, handler = function(...) {
file <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
if (is.null(file) == T) {
gmessage('Selected file is null', icon = 'error')
}
if (is.null(file) == F) {
bouton1$set_value(paste(length(file), 'intact file selected'))
cat(paste('\n>File selected : ', file, sep = ''))
}
})
ppb <- ggroup(container = pp)
addSpring(ppb)
gbutton("Format file", handler = function(h,...) {
return.parameter <<- svalue(flyt)
visible(panel_para) <- F
# selected parametres storage
organism <- as.character(return.parameter[1])
other = organism
# When all paramaters are Ok
if (is.null(file) == F) {
######################################################################################
########################### FORMATING AND PARSING #################################
pathracine <- getwd()
if (organism == "Other") {
panelorganism <- gwindow("Organism description", parent = f_pos, visible = F, expand = T)
pc <- ggroup(container = panelorganism, horizontal = F, use.scrollwindow = T)
pcsb <- ggroup(container = pc, horizontal = F, use.scrollwindow = F)
lg <- gvbox(container = pcsb)
pg <- gvbox(container = pcsb)
fllg <- gformlayout(container = lg)
flpg <- gformlayout(container = pg)
organismName <- gedit(initial.msg = 'Organism Name', label = "NAME", container = fllg)
organismId <- gedit(initial.msg = 'Organism ID', label = "NCBI ID", container = flpg)
visible(panelorganism) <- T
bpc <- ggroup(container = pc); addSpring(bpc)
# 1 : Other organism
bouton1 <- gbutton("OK", handler = function(h,...) {
# Rassemblement des modifications a apporter
org.name <- cbind(names(svalue(fllg)), svalue(fllg))
org.name <- data.frame(org.name, row.names = NULL)
org.id <- cbind(names(svalue(flpg)), svalue(flpg))
org.id <- data.frame(org.id, row.names = NULL)
org <- cbind(org.name, org.id)
colnames(org) <- c('Organism_name', 'Organism_id')
organism <- as.character(org[1,2])
organismID <- as.character(org[1,4])
# intact_othero(organism, organismID, file, pathracine)
format_intact(organism, organismID, file, pathracine, other)
dispose(bpc)
}, container = bpc)
}
else {
format_intact(organism, organismID, file, pathracine, other)
}
dispose(panel_para)
dispose(ppb)
}
# Tests all elements necessary to the function execution
else if (is.null(file) == T) {
gmessage('File selected is null', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
else {
gmessage('Error : Unable to start formatting', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
}, container=ppb)
# Return
gbutton("Return", handler = function(h,...) {
dispose(panel_para)
visible(pana) <<- T
}, container = ppb)
visible(panel_para) <- T
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.