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Commit 56ad5e08 authored by Gosset Simon's avatar Gosset Simon
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correcting a bug that happened when using path with blank space

parent 669f5b37
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R/thesaurus_window.R
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# thesaurus_othero <- function(organism, uniprot, sequence, mainpath) {
#
# cat(paste("\n\nOrganism", organism, sep = " : "))
# cat(paste("\nUniprot file", uniprot, sep = " : "))
#
# cat("\n\n>THESAURUS CONSTRUCTION ... ")
#
# # Creation du dossier correspondant a l'organisme
# organism <- gsub(" ", "-", organism)
# organisme <- gsub("-", "+", organism)
# organisme <- tolower(organisme)
#
# organism.path <- paste(mainpath, organism, sep = '/')
# dir.create(organism.path, showWarnings = FALSE)
#
# sequences <- paste(sequence, "sequences", sep = '-')
# nomsortie <- paste("Thesaurus", "_", organism, "_", sequences, ".txt", sep = '')
# sortie <- paste(organism.path, nomsortie, sep = '/')
#
# setwd(organism.path)
#
# # Construction du thesaurus
# path <- paste(system.file(package = "appinetwork"), "python/thesaurusPy.py", sep = "/")
# file.copy(path, mainpath)
# path.copy <- paste(mainpath, "thesaurusPy.py", sep = "/")
#
# setwd(mainpath)
# setwd("inst")
# command <- paste("python", "thesaurusPy.py", uniprot, sortie, organisme, sep = " ")
# system(command)
# setwd(mainpath)
#
# file.remove(path.copy)
#
# cat("OK\n>Thesaurus construction is done.")
# cat(paste("\nThesaurus file (output)", sortie, sep = " : "))
# cat(paste("\n\n"))
#
# setwd(mainpath)
#
# visible(mainpanel) <- T
#
# }
construct_id = function(organism, uniprot, sequence, mainpath) {
cat(paste("\n\nOrganism", organism, sep = " : "))
cat(paste("\nUniprot file", uniprot, sep = " : "))
cat("\n\n>BUILDING OF THE ID CORRESPONDENCES FILE ... ")
# Create a directory having the name of the organism
organism <- gsub(" ", "-", organism)
organisme <- gsub("-", "+", organism)
organisme <- tolower(organisme)
organism.path <- paste(mainpath, organism, sep = '/')
dir.create(organism.path, showWarnings = FALSE)
sequences <- paste(sequence, "sequences", sep = '-')
nomsortie <- paste("Thesaurus", "_", organism, "_", sequences, ".txt", sep = '')
sortie <- paste(organism.path, nomsortie, sep = '/')
setwd(organism.path)
# execute thesaurusPy.py (python script) to create the ID correspondences file
path <- paste(system.file(package = "appinetwork"), "thesaurusPy.py", sep = "/")
file.copy(path, mainpath)
path.copy <- paste(mainpath, "thesaurusPy.py", sep = "/")
setwd(mainpath)
cat("\n CAT 1 :",mainpath)
command <- paste("python", "thesaurusPy.py", uniprot, sortie, organisme, sep = " ")
cat("\n CAT 2 :",command)
system(command)
# file.remove(path.copy)
cat("OK\n>the ID correspondences file is done.")
cat(paste("\nID correspondences file (output)", sortie, sep = " : "))
cat(paste("\n\n"))
setwd(mainpath)
visible(mainpanel) <<- T
}
thesaurus_window <- function(f_pos, mainpanel, mainpath) {
uniprot <- c()
return.parameter <- c()
panel_para <- gwindow("Construct an ID correspondences file", parent = f_pos, visible = T)
pp <- gvbox(container = panel_para)
pp$set_borderwidth(10L)
flyt <- gformlayout(container = pp, expand = TRUE)
# Selection of parametres (organism and type of Uniprot file (all or proteome))
gcombobox(c('Caenorhabditis elegans', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae','Arabidopsis thaliana', 'Other'), label = "Organism", selected = 7, container = flyt)
gradio(c("all", "proteome"), selected = 1, horizontal = TRUE, label = "Organism sequences in uniprot file", container = flyt)
# Select the Uniprot file
chdb <- ggroup(container = pp, horizontale = T)
addSpring(chdb)
bouton1 <- gbutton("Uniprot file", container = chdb, handler = function(...) {
uniprot <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
if (is.null(uniprot) == T) {
gmessage('Selected file is null', icon = 'error')
}
if (is.null(uniprot) == F) {
bouton1$set_value(paste(length(uniprot), 'uniprot file selected'))
#cat(paste('\n>File selected : ', uniprot, sep = ''))
}
})
ppb <- ggroup(container = pp)
addSpring(ppb)
gbutton("Construct file", handler = function(h,...) {
return.parameter <<- svalue(flyt)
visible(panel_para) <- F
# Memorization of the selected parameters (organism and type of Uniprot file)
organism <- as.character(return.parameter[1])
sequence <- as.character(return.parameter[2])
# Execution of thesaurusPy.py script when all the parameters are provided
if (is.null(uniprot) == F) {
mainpath <- 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)
fllg <- gformlayout(container = lg)
organismName <- gedit(initial.msg = 'Organism Name', label = "NAME", container = fllg)
visible(panelorganism) <- T
bpc <- ggroup(container = pc); addSpring(bpc)
# 1 : Other organism
bouton1 <- gbutton("OK", handler = function(h,...) {
# Group the different modifications to do
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])
# thesaurus_othero(organism, uniprot, sequence, mainpath)
construct_id(organism, uniprot, sequence, mainpath)
dispose(bpc)
}, container = bpc)
}
else {
construct_id(organism, uniprot, sequence, mainpath)
}
dispose(panel_para)
dispose(ppb)
}
# Test the presence of all elements necessary to execute thesaurusPy.py
else if (is.null(uniprot) == T) {
gmessage('File selected is null', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
else {
gmessage('Error : Unable to construct the ID correspondences file ', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
}, container=ppb)
# Return
gbutton("Return", handler = function(h,...) {
dispose(panel_para)
visible(mainpanel) <<- T
}, container = ppb)
#visible(panel_para) <- T
}
# thesaurus_othero <- function(organism, uniprot, sequence, mainpath) {
#
# cat(paste("\n\nOrganism", organism, sep = " : "))
# cat(paste("\nUniprot file", uniprot, sep = " : "))
#
# cat("\n\n>THESAURUS CONSTRUCTION ... ")
#
# # Creation du dossier correspondant a l'organisme
# organism <- gsub(" ", "-", organism)
# organisme <- gsub("-", "+", organism)
# organisme <- tolower(organisme)
#
# organism.path <- paste(mainpath, organism, sep = '/')
# dir.create(organism.path, showWarnings = FALSE)
#
# sequences <- paste(sequence, "sequences", sep = '-')
# nomsortie <- paste("Thesaurus", "_", organism, "_", sequences, ".txt", sep = '')
# sortie <- paste(organism.path, nomsortie, sep = '/')
#
# setwd(organism.path)
#
# # Construction du thesaurus
# path <- paste(system.file(package = "appinetwork"), "python/thesaurusPy.py", sep = "/")
# file.copy(path, mainpath)
# path.copy <- paste(mainpath, "thesaurusPy.py", sep = "/")
#
# setwd(mainpath)
# setwd("inst")
# command <- paste("python", "thesaurusPy.py", uniprot, sortie, organisme, sep = " ")
# system(command)
# setwd(mainpath)
#
# file.remove(path.copy)
#
# cat("OK\n>Thesaurus construction is done.")
# cat(paste("\nThesaurus file (output)", sortie, sep = " : "))
# cat(paste("\n\n"))
#
# setwd(mainpath)
#
# visible(mainpanel) <- T
#
# }
construct_id = function(organism, uniprot, sequence, mainpath) {
cat(paste("\n\nOrganism", organism, sep = " : "))
cat(paste("\nUniprot file", uniprot, sep = " : "))
cat("\n\n>BUILDING OF THE ID CORRESPONDENCES FILE ... ")
# Create a directory having the name of the organism
organism <- gsub(" ", "-", organism)
organisme <- gsub("-", "+", organism)
organisme <- tolower(organisme)
organism.path <- paste(mainpath, organism, sep = '/')
dir.create(organism.path, showWarnings = FALSE)
sequences <- paste(sequence, "sequences", sep = '-')
nomsortie <- paste("Thesaurus", "_", organism, "_", sequences, ".txt", sep = '')
sortie <- paste(organism.path, nomsortie, sep = '/')
setwd(organism.path)
# execute thesaurusPy.py (python script) to create the ID correspondences file
path <- paste(system.file(package = "appinetwork"), "thesaurusPy.py", sep = "/")
file.copy(path, mainpath)
path.copy <- paste(mainpath, "thesaurusPy.py", sep = "/")
setwd(mainpath)
cat("\n CAT 1 :",mainpath)
command <- paste("python", "thesaurusPy.py", paste0("\"", uniprot, "\""), paste0("\"",sortie, "\""), organisme, sep = " ")
cat("\n CAT 2 :",command)
system(command)
# file.remove(path.copy)
cat("OK\n>the ID correspondences file is done.")
cat(paste("\nID correspondences file (output)", sortie, sep = " : "))
cat(paste("\n\n"))
setwd(mainpath)
visible(mainpanel) <<- T
}
thesaurus_window <- function(f_pos, mainpanel, mainpath) {
uniprot <- c()
return.parameter <- c()
panel_para <- gwindow("Construct an ID correspondences file", parent = f_pos, visible = T)
pp <- gvbox(container = panel_para)
pp$set_borderwidth(10L)
flyt <- gformlayout(container = pp, expand = TRUE)
# Selection of parametres (organism and type of Uniprot file (all or proteome))
gcombobox(c('Caenorhabditis elegans', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae','Arabidopsis thaliana', 'Other'), label = "Organism", selected = 7, container = flyt)
gradio(c("all", "proteome"), selected = 1, horizontal = TRUE, label = "Organism sequences in uniprot file", container = flyt)
# Select the Uniprot file
chdb <- ggroup(container = pp, horizontale = T)
addSpring(chdb)
bouton1 <- gbutton("Uniprot file", container = chdb, handler = function(...) {
uniprot <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
if (is.null(uniprot) == T) {
gmessage('Selected file is null', icon = 'error')
}
if (is.null(uniprot) == F) {
bouton1$set_value(paste(length(uniprot), 'uniprot file selected'))
#cat(paste('\n>File selected : ', uniprot, sep = ''))
}
})
ppb <- ggroup(container = pp)
addSpring(ppb)
gbutton("Construct file", handler = function(h,...) {
return.parameter <<- svalue(flyt)
visible(panel_para) <- F
# Memorization of the selected parameters (organism and type of Uniprot file)
organism <- as.character(return.parameter[1])
sequence <- as.character(return.parameter[2])
# Execution of thesaurusPy.py script when all the parameters are provided
if (is.null(uniprot) == F) {
mainpath <- 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)
fllg <- gformlayout(container = lg)
organismName <- gedit(initial.msg = 'Organism Name', label = "NAME", container = fllg)
visible(panelorganism) <- T
bpc <- ggroup(container = pc); addSpring(bpc)
# 1 : Other organism
bouton1 <- gbutton("OK", handler = function(h,...) {
# Group the different modifications to do
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])
# thesaurus_othero(organism, uniprot, sequence, mainpath)
construct_id(organism, uniprot, sequence, mainpath)
dispose(bpc)
}, container = bpc)
}
else {
construct_id(organism, uniprot, sequence, mainpath)
}
dispose(panel_para)
dispose(ppb)
}
# Test the presence of all elements necessary to execute thesaurusPy.py
else if (is.null(uniprot) == T) {
gmessage('File selected is null', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
else {
gmessage('Error : Unable to construct the ID correspondences file ', icon = 'error')
dispose(ppb)
visible(panel_para) <- F
visible(mainpanel) <<- T
}
}, container=ppb)
# Return
gbutton("Return", handler = function(h,...) {
dispose(panel_para)
visible(mainpanel) <<- T
}, container = ppb)
#visible(panel_para) <- T
}
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