R/irefindex_window.R
In melinagallopin/appinetwork: construction and Analysis of Protein-Protein Interactions (PPI) networks for complexes and biological processes
Defines functions
irefindex_window
irefindex_window <- function(f_pos, mainpanel, pana, mainpath) {
file <- c()
return.parameter <- c()
panel_para <- gwindow("iRefIndex database file formatting", parent = f_pos, visible = T)
pp <- gvbox(container = panel_para)
flyt <- gformlayout(container = pp, expand = TRUE)
# Parametres selection
gcombobox(c('Caenorhabditis elegans', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae', 'Other'), label = "Organism", selected = 7, container = flyt)
gcombobox(c(0:20), label = "Maximum number of proteins in a complex", selected = 1, container = flyt)
# File section
chdb <- ggroup(container = pp, horizontale = T)
addSpring(chdb)
bouton1 <- gbutton("iRefIndex 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), 'iRefIndex 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
# Storage of the parameters
organism <- as.character(return.parameter[1])
complex <- as.character(return.parameter[2])
# Parse and format
if (is.null(file) == F) {
mainpath <- getwd()
# Other organism
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)
fllg <- gformlayout(container = lg)
organismName <- gedit(initial.msg = 'Organism Name', label = "NAME", container = fllg)
visible(panelorganism) <- T
bpc <- ggroup(container = pc); addSpring(bpc)
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 <- cbind(org.name)
colnames(org) <- c('Organism_name')
organism <- as.character(org[1,2])
irefindex_othero(organism, complex, file, mainpath)
dispose(bpc)
}, container = bpc)
}
# Organism proposed by the dialog window
else {
cat("\n>FORMATING IREFINDEX DATABASE\n")
if (organism == "Saccharomyces cerevisiae") {
organisme <- "Saccharomyces cerevisiae S288C"
}
else {
organisme <- organism
}
cat(paste("\nOrganism", organisme, sep = " : "))
cat(paste("\niRefIndex file", file, sep = " : "))
cat(paste("\n"))
while (!file.exists(file)) {
cat("\n\t-> incorrect database name ! try again\n")
file <- readline("\t> Type the name of the iRefIndex data set file that you want to parse : ")
}
irefindexfile <- file
setwd(mainpath)
cat("\n>Loading database ... ")
Base <- read.delim(file = irefindexfile, header = T, sep = "\t")
cat("OK")
if (dim(Base)[2] != 54) {
cat(paste("\nIncorrect data dimension, read userguide for more informations"))
stop()
}
colnames(Base)[1] <- "uidA"
## irefindex
## 1 : uidA
## 2 : uidB
## 5 : aliasA
## 6 : aliasB
## 7 : Method
## 8 : author
## 9 : pmids
## 10 : taxa
## 11 : taxb
## 12 : interactionType
## 13 : sourcedb
## 15 : confidence
## 54 : numParticipants
Base.f <- Base[,c(1:2,5:13,15,54)]
Interactions <- Base.f
seuil <- as.integer(complex)
cat("\n>Parsing interactions ... ")
# Add PPIs between proteins of the complexes having less proteins than the chosen Maximum number of proteins in a complex and delete lines containing complexes
lignecomplexe <- c(grep("complex:", Interactions[,1]), grep("complex:", Interactions[,2]))
Interactions.noComplex <- Interactions[-lignecomplexe,]
Interactions.Complex <- Interactions[lignecomplexe,]
Interactions.Complex <- Interactions.Complex[as.integer(Interactions.Complex[,13]) <= seuil,]
nbcomplex <- 0
l <- dim(Interactions.Complex)[1]
i <- 1
while (i < l) {
ListProtofComplex <- unique(Interactions.Complex[Interactions.Complex[,1] == Interactions.Complex[i,1],2])
ListProtofComplex <- as.vector(ListProtofComplex)
ListAliasofComplex <- unique(Interactions.Complex[Interactions.Complex[,1] == Interactions.Complex[i,1],4])
ListAliasofComplex <- as.vector(ListAliasofComplex)
n <- length(ListProtofComplex)
if (n > 1) {
nbcomplex <- nbcomplex + 1
ListPPIofComplex <- as.data.frame(matrix(NA, nrow = (n * (n - 1) / 2), ncol = dim(Interactions.Complex)[2]))
j <- 1
for (k in 1:(n - 1)) {
for (l in (k + 1):n) {
ListPPIofComplex[j,1] <- ListProtofComplex[k]
ListPPIofComplex[j,2] <- ListProtofComplex[l]
ListPPIofComplex[j,3] <- ListAliasofComplex[k]
ListPPIofComplex[j,4] <- ListAliasofComplex[l]
ListPPIofComplex[j,5] <- as.vector(Interactions.Complex[i,5])
ListPPIofComplex[j,6] <- as.vector(Interactions.Complex[i,6])
ListPPIofComplex[j,7] <- as.vector(Interactions.Complex[i,7])
ListPPIofComplex[j,8] <- as.vector(Interactions.Complex[i,8])
ListPPIofComplex[j,9] <- as.vector(Interactions.Complex[i,9])
ListPPIofComplex[j,10] <- as.vector(Interactions.Complex[i,10])
ListPPIofComplex[j,11] <- as.vector(Interactions.Complex[i,11])
ListPPIofComplex[j,12] <- as.vector(Interactions.Complex[i,12])
ListPPIofComplex[j,13] <- n
j <- j + 1
}
}
if (nbcomplex == 1) {
tmp <- ListPPIofComplex
}
if (nbcomplex > 1) {
tmp <- rbind(tmp, ListPPIofComplex)
}
}
Interactions.Complex <- Interactions.Complex[-c(1:dim(Interactions.Complex)[1])[Interactions.Complex[,1] == Interactions.Complex[i,1]],]
l <- dim(Interactions.Complex)[1]
}
colnames(tmp) <- colnames(Interactions)
Interactions <- rbind(Interactions.noComplex, tmp)
cat("OK")
# All lines that don't contain "uniprotkb" and "refseq:NP_" in the columns uidA and uidB are deleted.
cat(paste("\nChecking uniprot-IDs\n"))
prsbar <- txtProgressBar(min = 1, max = dim(Interactions)[1], style = 3)
SUP <- rep(TRUE, dim(Interactions)[1])
for (i in 1:(dim(Interactions)[1])) {
if ((length(grep("uniprotkb", Interactions[i,1], value = FALSE)) != 1) && (length(grep("refseq:NP_", Interactions[i,1], value = FALSE)) != 1)) {
SUP[i] <- FALSE
}
else {
if ((length(grep("uniprotkb", Interactions[i,2], value = FALSE)) != 1) && (length(grep("refseq:NP_", Interactions[i,2], value = FALSE)) != 1)) {
SUP[i] <- FALSE
}
}
setTxtProgressBar(prsbar, i)
}
Interactions <- Interactions[SUP == TRUE,]
# All lines that don't contain the specie's name in the columns taxA and taxB are deleted.
cat(paste("\nChecking taxons\n"))
prsbar <- txtProgressBar(min = 1, max = dim(Interactions)[1], style = 3)
SUP <- rep(FALSE, dim(Interactions)[1])
for (i in 1:(dim(Interactions)[1])) {
if (length(grep(organisme, Interactions[i,8], value = FALSE)) == 1 && length(grep(organisme, Interactions[i,9], value = FALSE)) == 1) {
SUP[i] <- TRUE
}
else if (length(grep(organisme, Interactions[i,8], value = FALSE)) == 1 && length(grep("-", Interactions[i,9], value = FALSE)) == 1) {
SUP[i] <- TRUE
}
else if (length(grep("-", Interactions[i,8], value = FALSE)) == 1 && length(grep(organisme, Interactions[i,9], value = FALSE)) == 1) {
SUP[i] <- TRUE
}
setTxtProgressBar(prsbar, i)
}
Interactions <- Interactions[SUP == TRUE,]
# Interactions<-Interactions[as.character(Interactions[,8])==as.character(Interactions[,9]),]
Interactions <- as.matrix(Interactions)
# Troncate uids
Interactions[,1] <- apply(as.matrix(apply(as.matrix(Interactions[,1]), 1, strsplit, split = ":")), 1, unlist)[2,]
Interactions[,2] <- apply(as.matrix(apply(as.matrix(Interactions[,2]), 1, strsplit, split = ":")), 1, unlist)[2,]
# Give the geneNames
GeneNameA <- Interactions[,1]
GeneNameB <- Interactions[,2]
cat(paste("\nSearching gene name\n"))
prsbar <- txtProgressBar(min = 1, max = dim(Interactions)[1], style = 3)
for (i in 1:(dim(Interactions)[1])) {
listA <- unlist(strsplit(as.character(Interactions[i,3]), "\\|"))
for (j in 1:length(listA)) {
if (length(grep("locuslink:", listA[j])) == 1) {
GeneNameA[i] <- unlist(strsplit(as.character(listA[j]), "locuslink:"))[2]
}
else if (length(grep("hgnc:", listA[j])) == 1) {
GeneNameA[i] <- unlist(strsplit(as.character(listA[j]), "hgnc:"))[2]
}
}
if (GeneNameA[i] == "NA") {
GeneNameA[i] <- Interactions[i,1]
}
listB <- unlist(strsplit(as.character(Interactions[i,4]), "\\|"))
for (j in 1:length(listB)) {
if (length(grep("locuslink:", listB[j])) == 1) {
GeneNameB[i] <- unlist(strsplit(as.character(listB[j]), "locuslink:"))[2]
}
else if (length(grep("hgnc:", listB[j])) == 1) {
GeneNameB[i] <- unlist(strsplit(as.character(listB[j]), "hgnc:"))[2]
}
}
if (GeneNameB[i] == "NA") {
GeneNameB[i] <- Interactions[i,2]
}
Interactions[i,3] <- unlist(strsplit(as.character(Interactions[i,3]), "\\|"))[1]
Interactions[i,3] <- unlist(strsplit(as.character(Interactions[i,3]), ":"))[2]
Interactions[i,4] <- unlist(strsplit(as.character(Interactions[i,4]), "\\|"))[1]
Interactions[i,4] <- unlist(strsplit(as.character(Interactions[i,4]), ":"))[2]
Interactions[i,11] <- unlist(strsplit(as.character(Interactions[i,11]), "\\("))[2]
Interactions[i,11] <- unlist(strsplit(as.character(Interactions[i,11]), "\\)"))[1]
setTxtProgressBar(prsbar, i)
}
Interactions <- cbind(Interactions, GeneNameA, GeneNameB)
Interactions[Interactions[,11] == "grid",11] <- "BioGrid"
# Give the interactions type
Interactions[grep("MI:0254", Interactions[,5], value = FALSE),10] <- "genetic"
Interactions[grep("MI:0001", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0008", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0024", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0045", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0063", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0064", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0363", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0364", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0403", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0686", Interactions[,5], value = FALSE),10] <- "other"
Interactions[(Interactions[,10] != "other") & (Interactions[,10] != "genetic"),10] <- "physical"
cat("\n>Saving database(s) ... ")
List.database <- unlist(unique(Interactions[,11]))
organism <- gsub(" ", "-", organism)
organism.path <- paste(mainpath, organism, sep = '/')
dir.create(organism.path, showWarnings = FALSE)
database.path <- paste(organism.path, "Databases", sep = '/')
dir.create(database.path, showWarnings = FALSE)
setwd(database.path)
for(i in 1:(length(List.database))) {
database.output.name <- paste(organism, "irefindex", List.database[i], "threshold", complex, sep = "_")
database.output <- Interactions[Interactions[,11] == List.database[i],]
write.table(database.output, file = paste(database.output.name, "txt", sep = "."), row.names = F, col.names = T, quote = F, sep = "\t")
}
cat(paste("OK\n>Formating iRefIndex database is done.\n\nDatabase files are saved in", database.path, sep = " : "))
cat(paste("\n\n"))
setwd(mainpath)
visible(mainpanel) <<- T
}
dispose(panel_para)
dispose(ppb)
}
# Test the presence of all the elements necessary to execute the function
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.
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Defines functions irefindex_window
irefindex_window <- function(f_pos, mainpanel, pana, mainpath) {
file <- c()
return.parameter <- c()
panel_para <- gwindow("iRefIndex database file formatting", parent = f_pos, visible = T)
pp <- gvbox(container = panel_para)
flyt <- gformlayout(container = pp, expand = TRUE)
# Parametres selection
gcombobox(c('Caenorhabditis elegans', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae', 'Other'), label = "Organism", selected = 7, container = flyt)
gcombobox(c(0:20), label = "Maximum number of proteins in a complex", selected = 1, container = flyt)
# File section
chdb <- ggroup(container = pp, horizontale = T)
addSpring(chdb)
bouton1 <- gbutton("iRefIndex 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), 'iRefIndex 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
# Storage of the parameters
organism <- as.character(return.parameter[1])
complex <- as.character(return.parameter[2])
# Parse and format
if (is.null(file) == F) {
mainpath <- getwd()
# Other organism
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)
fllg <- gformlayout(container = lg)
organismName <- gedit(initial.msg = 'Organism Name', label = "NAME", container = fllg)
visible(panelorganism) <- T
bpc <- ggroup(container = pc); addSpring(bpc)
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 <- cbind(org.name)
colnames(org) <- c('Organism_name')
organism <- as.character(org[1,2])
irefindex_othero(organism, complex, file, mainpath)
dispose(bpc)
}, container = bpc)
}
# Organism proposed by the dialog window
else {
cat("\n>FORMATING IREFINDEX DATABASE\n")
if (organism == "Saccharomyces cerevisiae") {
organisme <- "Saccharomyces cerevisiae S288C"
}
else {
organisme <- organism
}
cat(paste("\nOrganism", organisme, sep = " : "))
cat(paste("\niRefIndex file", file, sep = " : "))
cat(paste("\n"))
while (!file.exists(file)) {
cat("\n\t-> incorrect database name ! try again\n")
file <- readline("\t> Type the name of the iRefIndex data set file that you want to parse : ")
}
irefindexfile <- file
setwd(mainpath)
cat("\n>Loading database ... ")
Base <- read.delim(file = irefindexfile, header = T, sep = "\t")
cat("OK")
if (dim(Base)[2] != 54) {
cat(paste("\nIncorrect data dimension, read userguide for more informations"))
stop()
}
colnames(Base)[1] <- "uidA"
## irefindex
## 1 : uidA
## 2 : uidB
## 5 : aliasA
## 6 : aliasB
## 7 : Method
## 8 : author
## 9 : pmids
## 10 : taxa
## 11 : taxb
## 12 : interactionType
## 13 : sourcedb
## 15 : confidence
## 54 : numParticipants
Base.f <- Base[,c(1:2,5:13,15,54)]
Interactions <- Base.f
seuil <- as.integer(complex)
cat("\n>Parsing interactions ... ")
# Add PPIs between proteins of the complexes having less proteins than the chosen Maximum number of proteins in a complex and delete lines containing complexes
lignecomplexe <- c(grep("complex:", Interactions[,1]), grep("complex:", Interactions[,2]))
Interactions.noComplex <- Interactions[-lignecomplexe,]
Interactions.Complex <- Interactions[lignecomplexe,]
Interactions.Complex <- Interactions.Complex[as.integer(Interactions.Complex[,13]) <= seuil,]
nbcomplex <- 0
l <- dim(Interactions.Complex)[1]
i <- 1
while (i < l) {
ListProtofComplex <- unique(Interactions.Complex[Interactions.Complex[,1] == Interactions.Complex[i,1],2])
ListProtofComplex <- as.vector(ListProtofComplex)
ListAliasofComplex <- unique(Interactions.Complex[Interactions.Complex[,1] == Interactions.Complex[i,1],4])
ListAliasofComplex <- as.vector(ListAliasofComplex)
n <- length(ListProtofComplex)
if (n > 1) {
nbcomplex <- nbcomplex + 1
ListPPIofComplex <- as.data.frame(matrix(NA, nrow = (n * (n - 1) / 2), ncol = dim(Interactions.Complex)[2]))
j <- 1
for (k in 1:(n - 1)) {
for (l in (k + 1):n) {
ListPPIofComplex[j,1] <- ListProtofComplex[k]
ListPPIofComplex[j,2] <- ListProtofComplex[l]
ListPPIofComplex[j,3] <- ListAliasofComplex[k]
ListPPIofComplex[j,4] <- ListAliasofComplex[l]
ListPPIofComplex[j,5] <- as.vector(Interactions.Complex[i,5])
ListPPIofComplex[j,6] <- as.vector(Interactions.Complex[i,6])
ListPPIofComplex[j,7] <- as.vector(Interactions.Complex[i,7])
ListPPIofComplex[j,8] <- as.vector(Interactions.Complex[i,8])
ListPPIofComplex[j,9] <- as.vector(Interactions.Complex[i,9])
ListPPIofComplex[j,10] <- as.vector(Interactions.Complex[i,10])
ListPPIofComplex[j,11] <- as.vector(Interactions.Complex[i,11])
ListPPIofComplex[j,12] <- as.vector(Interactions.Complex[i,12])
ListPPIofComplex[j,13] <- n
j <- j + 1
}
}
if (nbcomplex == 1) {
tmp <- ListPPIofComplex
}
if (nbcomplex > 1) {
tmp <- rbind(tmp, ListPPIofComplex)
}
}
Interactions.Complex <- Interactions.Complex[-c(1:dim(Interactions.Complex)[1])[Interactions.Complex[,1] == Interactions.Complex[i,1]],]
l <- dim(Interactions.Complex)[1]
}
colnames(tmp) <- colnames(Interactions)
Interactions <- rbind(Interactions.noComplex, tmp)
cat("OK")
# All lines that don't contain "uniprotkb" and "refseq:NP_" in the columns uidA and uidB are deleted.
cat(paste("\nChecking uniprot-IDs\n"))
prsbar <- txtProgressBar(min = 1, max = dim(Interactions)[1], style = 3)
SUP <- rep(TRUE, dim(Interactions)[1])
for (i in 1:(dim(Interactions)[1])) {
if ((length(grep("uniprotkb", Interactions[i,1], value = FALSE)) != 1) && (length(grep("refseq:NP_", Interactions[i,1], value = FALSE)) != 1)) {
SUP[i] <- FALSE
}
else {
if ((length(grep("uniprotkb", Interactions[i,2], value = FALSE)) != 1) && (length(grep("refseq:NP_", Interactions[i,2], value = FALSE)) != 1)) {
SUP[i] <- FALSE
}
}
setTxtProgressBar(prsbar, i)
}
Interactions <- Interactions[SUP == TRUE,]
# All lines that don't contain the specie's name in the columns taxA and taxB are deleted.
cat(paste("\nChecking taxons\n"))
prsbar <- txtProgressBar(min = 1, max = dim(Interactions)[1], style = 3)
SUP <- rep(FALSE, dim(Interactions)[1])
for (i in 1:(dim(Interactions)[1])) {
if (length(grep(organisme, Interactions[i,8], value = FALSE)) == 1 && length(grep(organisme, Interactions[i,9], value = FALSE)) == 1) {
SUP[i] <- TRUE
}
else if (length(grep(organisme, Interactions[i,8], value = FALSE)) == 1 && length(grep("-", Interactions[i,9], value = FALSE)) == 1) {
SUP[i] <- TRUE
}
else if (length(grep("-", Interactions[i,8], value = FALSE)) == 1 && length(grep(organisme, Interactions[i,9], value = FALSE)) == 1) {
SUP[i] <- TRUE
}
setTxtProgressBar(prsbar, i)
}
Interactions <- Interactions[SUP == TRUE,]
# Interactions<-Interactions[as.character(Interactions[,8])==as.character(Interactions[,9]),]
Interactions <- as.matrix(Interactions)
# Troncate uids
Interactions[,1] <- apply(as.matrix(apply(as.matrix(Interactions[,1]), 1, strsplit, split = ":")), 1, unlist)[2,]
Interactions[,2] <- apply(as.matrix(apply(as.matrix(Interactions[,2]), 1, strsplit, split = ":")), 1, unlist)[2,]
# Give the geneNames
GeneNameA <- Interactions[,1]
GeneNameB <- Interactions[,2]
cat(paste("\nSearching gene name\n"))
prsbar <- txtProgressBar(min = 1, max = dim(Interactions)[1], style = 3)
for (i in 1:(dim(Interactions)[1])) {
listA <- unlist(strsplit(as.character(Interactions[i,3]), "\\|"))
for (j in 1:length(listA)) {
if (length(grep("locuslink:", listA[j])) == 1) {
GeneNameA[i] <- unlist(strsplit(as.character(listA[j]), "locuslink:"))[2]
}
else if (length(grep("hgnc:", listA[j])) == 1) {
GeneNameA[i] <- unlist(strsplit(as.character(listA[j]), "hgnc:"))[2]
}
}
if (GeneNameA[i] == "NA") {
GeneNameA[i] <- Interactions[i,1]
}
listB <- unlist(strsplit(as.character(Interactions[i,4]), "\\|"))
for (j in 1:length(listB)) {
if (length(grep("locuslink:", listB[j])) == 1) {
GeneNameB[i] <- unlist(strsplit(as.character(listB[j]), "locuslink:"))[2]
}
else if (length(grep("hgnc:", listB[j])) == 1) {
GeneNameB[i] <- unlist(strsplit(as.character(listB[j]), "hgnc:"))[2]
}
}
if (GeneNameB[i] == "NA") {
GeneNameB[i] <- Interactions[i,2]
}
Interactions[i,3] <- unlist(strsplit(as.character(Interactions[i,3]), "\\|"))[1]
Interactions[i,3] <- unlist(strsplit(as.character(Interactions[i,3]), ":"))[2]
Interactions[i,4] <- unlist(strsplit(as.character(Interactions[i,4]), "\\|"))[1]
Interactions[i,4] <- unlist(strsplit(as.character(Interactions[i,4]), ":"))[2]
Interactions[i,11] <- unlist(strsplit(as.character(Interactions[i,11]), "\\("))[2]
Interactions[i,11] <- unlist(strsplit(as.character(Interactions[i,11]), "\\)"))[1]
setTxtProgressBar(prsbar, i)
}
Interactions <- cbind(Interactions, GeneNameA, GeneNameB)
Interactions[Interactions[,11] == "grid",11] <- "BioGrid"
# Give the interactions type
Interactions[grep("MI:0254", Interactions[,5], value = FALSE),10] <- "genetic"
Interactions[grep("MI:0001", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0008", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0024", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0045", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0063", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0064", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0363", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0364", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0403", Interactions[,5], value = FALSE),10] <- "other"
Interactions[grep("MI:0686", Interactions[,5], value = FALSE),10] <- "other"
Interactions[(Interactions[,10] != "other") & (Interactions[,10] != "genetic"),10] <- "physical"
cat("\n>Saving database(s) ... ")
List.database <- unlist(unique(Interactions[,11]))
organism <- gsub(" ", "-", organism)
organism.path <- paste(mainpath, organism, sep = '/')
dir.create(organism.path, showWarnings = FALSE)
database.path <- paste(organism.path, "Databases", sep = '/')
dir.create(database.path, showWarnings = FALSE)
setwd(database.path)
for(i in 1:(length(List.database))) {
database.output.name <- paste(organism, "irefindex", List.database[i], "threshold", complex, sep = "_")
database.output <- Interactions[Interactions[,11] == List.database[i],]
write.table(database.output, file = paste(database.output.name, "txt", sep = "."), row.names = F, col.names = T, quote = F, sep = "\t")
}
cat(paste("OK\n>Formating iRefIndex database is done.\n\nDatabase files are saved in", database.path, sep = " : "))
cat(paste("\n\n"))
setwd(mainpath)
visible(mainpanel) <<- T
}
dispose(panel_para)
dispose(ppb)
}
# Test the presence of all the elements necessary to execute the function
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
}
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