R/biogrid_window_opt.R

In melinagallopin/appinetwork: construction and Analysis of Protein-Protein Interactions (PPI) networks for complexes and biological processes

# rechercheDansThesaurus<-function(i,thesaurus_j,biogridA,biogridB,putative){
#   
#   uniprotthesaurus <- unlist(strsplit(thesaurus_j[2], ";"))
#   
#   
#   for (u in 1:length(uniprotthesaurus)) {
#   if(length(grep(biogridA,uniprotthesaurus[u]))>0 & length(grep(biogridB,uniprotthesaurus[u]))>0){
#         
#     # Recherche pour la proteine A
#     if (biogridA == irefindex2[i,1] && biogridA == uniprotthesaurus[u]) {
#       print("change A")
#       irefindex2[i,1] <- thesaurus_j[1]
#       # Insertion des noms de proteine et de gene
#       irefindex2[i,3] <- thesaurus_j[3]
#       irefindex2[i,14] <- thesaurus_j[4]
#       # Recherche des transposons
#       if (thesaurus_j[6] == "TRUE") {
#         identifiant <- paste("Transposon", irefindex2[i,1], sep = ":")
#         irefindex2[i,1] <- gsub(irefindex2[i,1], identifiant, irefindex2[i,1])
#         nomprot <- paste("Transposon", irefindex2[i,3], sep = ":")
#         irefindex2[i,3] <- gsub(irefindex2[i,3], nomprot, irefindex2[i,3])
#       }
#     # Recherche des proteines putative
#       if (putative == "FALSE") {
#         if (thesaurus_j[5] == "TRUE") {
#           identifiant <- paste("Putative", irefindex2[i,1], sep = ":")
#           irefindex2[i,1] <- gsub(irefindex2[i,1], identifiant, irefindex2[i,1])
#           nomprot <- paste("Putative", irefindex2[i,3], sep = ":")
#           irefindex2[i,3] <- gsub(irefindex2[i,3], nomprot, irefindex2[i,3])
#         }
#       }
#     }
#     # Recherche pour la proteine B
#     if (biogridB == irefindex2[i,2] && biogridB == uniprotthesaurus[u]) {
#       print("change B")
#       irefindex2[i,2] <- thesaurus_j[1]
#       # Insertion des noms de proteine et de gene
#       irefindex2[i,4] <- thesaurus_j[3]
#       irefindex2[i,15] <- thesaurus_j[4]
#       # Recherche des transposons
#       if (thesaurus_j[6] == "TRUE") {
#         identifiant <- paste("Transposon", irefindex2[i,2], sep = ":")
#         irefindex2[i,2] <- gsub(irefindex2[i,2], identifiant, irefindex2[i,2])
#         nomprot <- paste("Transposon", irefindex2[i,4], sep = ":")
#         irefindex2[i,4] <- gsub(irefindex2[i,4], nomprot, irefindex2[i,4])
#       }
#       # Recherche des proteines putative
#       if (putative == "FALSE") {
#         if (thesaurus_j[5] == "TRUE") {
#           identifiant <- paste("Putative", irefindex2[i,2], sep = ":")
#           irefindex2[i,2] <- gsub(irefindex2[i,2], identifiant, irefindex2[i,2])
#           nomprot <- paste("Putative", irefindex2[i,4], sep = ":")
#           irefindex2[i,4] <- gsub(irefindex2[i,4], nomprot, irefindex2[i,4])
#         }
#       }
#     }
#   } 
#   }  
# }
# 
# 
# biogrid_othero <- function(organism, organismID, putative, file, uniprot, pathracine) {
#   
#   cat("\n\n>FORMATING BIOGRID DATABASE")
#   
#   # Creation du dossier correspondant a l'organisme
#   organism <- gsub(" ", "-", organism)
#   organisme <- gsub("-", "+", organism)
#   organisme <- tolower(organisme)
#   
#   organism.path <- paste(pathracine, organism, sep = '/')
#   dir.create(organism.path, showWarnings = FALSE)
#   
#   uniprotfile <- uniprot
#   nomsortie <- paste("ThesaurusBiogrid", "_", organism, ".txt", sep = '')
#   sortie <- paste(organism.path, nomsortie, sep = '/')
#   
#   # Construction du thesaurus
#   cat("\n\n>Thesaurus construction ... ")
#   path <- paste(system.file(package = "appinetwork"), "biogridPy.py", sep = "/")
#   file.copy(path, pathracine)
#   path.copy <- paste(pathracine, "biogridPy.py", sep = "/")
#   
#   command <- paste("python", "biogridPy.py", uniprotfile, sortie, putative, sep = " ")
#   system(command)
#   
#   file.remove(path.copy)
#   
#   # Lecture du thesaurus
#   thesaurus <- read.delim(file = sortie, header = T, sep = "\t")
#   thesaurus <- as.matrix(thesaurus)
#   file.remove(sortie)
#   
#   cat("OK\n>Loading database ... ")
#   
#   # Lecture de la base
#   biogridfile <- file
#   Biogrid <- read.delim(file = biogridfile, header = T, sep = "\t")
#   
#   if (dim(Biogrid)[2] != 24) {
#     cat(paste("\nIncorrect data dimension, read userguide for more informations"))
#     stop()
#   }
#   
#   numParticipants <- rep(2, dim(Biogrid)[1])
#   
#   irefIndex <- cbind(Biogrid[,2], Biogrid[,3], Biogrid[,8], Biogrid[,9], Biogrid[,12], Biogrid[,14], Biogrid[,15], Biogrid[,16], Biogrid[,17], Biogrid[,13], Biogrid[,24], Biogrid[,19], numParticipants, Biogrid[,8], Biogrid[,9])
#   colnames(irefIndex) <- c("uidA", "uidB", "aliasA", "aliasB", "method", "author", "pmids", "taxa", "taxb", "interactionType", "sourceDB", "confidence", "numParticipants", "GeneNameA", "GeneNameB")
#   irefindex <- as.matrix(irefIndex)
#   
#   cat("OK")
#   cat("\n>Formatting database : ")
#   cat(paste(dim(Biogrid)[1]))
#   cat(" lines in database\n")
#   
#   # Remplacement des Id biogrid par les uniprot et suppression des interactions non souhaitees
#   prsbar <- txtProgressBar(min = 1, max = dim(Biogrid)[1], style = 3)
#   N <- dim(irefindex)[1]
#   
#   for (i in 1:N) {
#     
#     # Verification de l'organisme
#     organism <- gsub("-", " ", organism)
#     if (organismID == irefindex[i,8] && organismID == irefindex[i,9]) {
#       irefindex[i,8] <- paste("taxid:", organismID, "(", organism, ")", sep = '')
#       irefindex[i,9] <- paste("taxid:", organismID, "(", organism, ")", sep = '')
#       irefindex[i,7] <- paste("pubmed:", irefindex[i,7], sep = '')
#     }
#     
#     irefindex[i,5] <- paste("", as.character(Biogrid[i,12]), sep = '')
#     irefindex[i,6] <- paste("", as.character(Biogrid[i,14]), sep = '')
#     irefindex[i,10] <- paste("", as.character(Biogrid[i,13]), sep = '')
#     irefindex[i,11] <- paste("", as.character(Biogrid[i,24]), sep = '')
#     irefindex[i,12] <- paste("", as.character(Biogrid[i,19]), sep = '')
#     
#     # Remplacement de l'identifiant
#     biogridA <- irefindex[i,1]
#     biogridB <- irefindex[i,2]
#     irefindex2<<-irefindex
#     apply(thesaurus,1,rechercheDansThesaurus,i=i,biogridA=biogridA,biogridB=biogridB,putative=putative)
#     irefindex<-irefindex2
#     rm(irefindex2)
#     if (irefindex[i,1] == biogridA) {
#       irefindex[i,1] <- paste("Protein", biogridA, sep = ":")
#       irefindex[i,3] <- paste("Protein", irefindex[i,3], sep = ":")
#     }
#     if (irefindex[i,2] == biogridB) {
#       irefindex[i,2] <- paste("Protein", biogridB, sep = ":")
#       irefindex[i,4] <- paste("Protein", irefindex[i,4], sep = ":")
#     }
#     setTxtProgressBar(prsbar, i)
#   }
#   
#   cat("\n>Saving database ... ")
#   
#   setwd(organism.path)
#   database.path <- paste(organism.path, "Databases", sep = '/')
#   dir.create(database.path, showWarnings = FALSE)
#   setwd(database.path)
#   
#   organism <- gsub(" ", "-", organism)
#   outfilename <- paste(organism, "_biogrid.txt", sep = "")
#   write.table(irefindex, file = outfilename, row.names = F, col.names = T, quote = F, sep = "\t")
#   
#   cat(paste("OK\n\n>Formating biogrid database is done.\n\nDatabase file is saved in", database.path, sep = " : "))
#   cat(paste("\n\n"))
#   setwd(pathracine)
#   
#   visible(mainpanel) <- T
#   
# }

construct_id2 = function(organism, uniprot, sequence, mainpath) {
  
  #Construit le "Vrai" fichier thesaurus, celui qui sera enregistré
  
  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)
  
  thesaurus_data = read.delim(file = sortie, header = T, sep = "\t")
  
  file.remove(sortie)
  
  return(thesaurus_data)
}

format_database = function(organism,organismID, putative, file, uniprot, pathracine, other, true_thesaurus) {
  
  # Fonction de formatage de la base de données
  # file: chemin vers fichier Biogrid
  # uniprot: chemin vers fichier uniprot
  # other: stocke le fait que l'organisme en input est où n'est pas dans les choix prédéfinis
  
  cat("\n\n>FORMATING BIOGRID DATABASE ")
  
  mainpath <- getwd()
  
  
  
  if (identical(true_thesaurus, character(0)) == T){
    # si le "Vrai" thesaurus n'est pas fourni :
  
    thesaurus_data = construct_id2(organism, uniprot, sequence = "proteome", mainpath)
    
  }
  if (identical(true_thesaurus, character(0)) == F) {
    # si le "Vrai" thesaurus est fourni :
    thesaurus_data = read.delim(file = true_thesaurus, header = T, sep = "\t")
  }
  
  
  # Creation du dossier correspondant a l'organisme
  organism <- gsub(" ", "-", organism)
  organisme <- gsub("-", "+", organism)
  organisme <- tolower(organisme)
  
  organism.path <- paste(pathracine, organism, sep = '/')
  dir.create(organism.path, showWarnings = FALSE)
  
  uniprotfile <- uniprot
  nomsortie <- paste("ThesaurusBiogrid", "_", organism, ".txt", sep = '')
  sortie <- paste(organism.path, nomsortie, sep = '/')
  
  # Construction du thesaurus
  cat("\n\n>Thesaurus construction ... ")
  
  
  
  path <- paste(system.file(package = "appinetwork"), "biogridPy.py", sep = "/")
  file.copy(path, pathracine)
  path.copy <- paste(pathracine, "biogridPy.py", sep = "/")
  command <- paste("python", "biogridPy.py", uniprotfile, sortie, putative, sep = " ")
  system(command)
  
  file.remove(path.copy)
  
  # Lecture du thesaurus
  thesaurus <- read.delim(file = sortie, header = T, sep = "\t")
  thesaurus <- as.matrix(thesaurus)
  file.remove(sortie)
  
  cat("OK\n>Loading database ... ")
  
  # Lecture de la base
  biogridfile <- file
  Biogrid <- read.delim(file = biogridfile, header = T, sep = "\t")
  
  
  if (dim(Biogrid)[2] != 24) {
    cat(paste("\nIncorrect data dimension, read userguide for more informations"))
    stop()
  }
  
  Biogrid<-as.matrix(Biogrid)
  numParticipants <- rep(2, dim(Biogrid)[1])
  irefIndex <- cbind(Biogrid[,2], Biogrid[,3], Biogrid[,8], Biogrid[,9], Biogrid[,12], Biogrid[,14], Biogrid[,15], Biogrid[,16], Biogrid[,17], Biogrid[,13], Biogrid[,24], Biogrid[,19], numParticipants, Biogrid[,8], Biogrid[,9])
  colnames(irefIndex) <- c("uidA", "uidB", "aliasA", "aliasB", "method", "author", "pmids", "taxa", "taxb", "interactionType", "sourceDB", "confidence", "numParticipants", "GeneNameA", "GeneNameB")
  irefindex <- as.matrix(irefIndex)
  irefindex[,1:15]=trimws(irefindex[,1:15],which = "both")
  
  
  
  
  organism <- gsub("-", " ", organism)
  
  
  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]
  }
  
  cat("\n>Formatting database : ")
  cat(paste(dim(Biogrid)[1]))
  cat(" lines in database\n")
  
  prsbar <- txtProgressBar(min = 1, max = dim(Biogrid)[1], style = 3)
  
  
  
  irefindex[,5] <- paste("", as.character(Biogrid[,12]), sep = '')
  irefindex[,6] <- paste("", as.character(Biogrid[,14]), sep = '')
  irefindex[,10] <- paste("", as.character(Biogrid[,13]), sep = '')
  irefindex[,11] <- paste("", as.character(Biogrid[,24]), sep = '')
  irefindex[,12] <- paste("", as.character(Biogrid[,19]), sep = '')
  

  
  irefindex<-irefindex[organismID == irefindex[,8] & organismID == irefindex[,9],]
      
  
  irefindex[,8] <- paste("taxid:", organismID, "(", organism, ")", sep = '')
  irefindex[,9] <- paste("taxid:", organismID, "(", organism, ")", sep = '')
  irefindex[,7] <- paste("pubmed:", irefindex[,7], sep = '')
  

  
  # eliminate transposons
  thesaurusNotranNoPut<-thesaurus[thesaurus[,6]=="FALSE",]
  
  if(length(thesaurus[thesaurus[,6]==" TRUE",6])>0){
    Tab.transposons<-thesaurus[thesaurus[,6]==" TRUE",]
    Tab.transposons[,2]<-unlist(apply(Tab.transposons,c(1,2), strsplit,split=";")[,2]) 
    for (i in 1:dim(Tab.transposons)[1]){
      if(length(grep(Tab.transposons[i,2],irefindex[,1]))>0)
        irefindex<-irefindex[-grep(Tab.transposons[i,2],irefindex[,1]),]
      if(length(grep(Tab.transposons[i,2],irefindex[,2]))>0)
        irefindex<-irefindex[-grep(Tab.transposons[i,2],irefindex[,2]),]
    }
  }
  
  
  
  # eliminate putative proteins
  if (putative == " TRUE") {
    thesaurusNotranNoPut<-thesaurusNotranNoPut[thesaurusNotranNoPut[,5]=="FALSE",]
    Tab.putatives<-thesaurus[thesaurus[,5]==" TRUE",]
    Tab.putatives[,2]<-unlist(apply(Tab.putatives,c(1,2), strsplit,split=";")[,2]) 
    for (i in 1:dim(Tab.putatives)[1]) {
      if(length(grep(Tab.putatives[i,2],irefindex[,1]))>0)
        irefindex<-irefindex[-grep(Tab.putatives[i,2],irefindex[,1]),]
      if(length(grep(Tab.putatives[i,2],irefindex[,2]))>0)
        irefindex<-irefindex[-grep(Tab.putatives[i,2],irefindex[,2]),]
    }
  }
  
  uniprotthesaurusNotranNoPut<-unlist(apply(thesaurusNotranNoPut,c(1,2), strsplit,split=";")[,2]) # new
  biogridA<-irefindex[,1]
  biogridB<-irefindex[,2]
  
  prsbar <- txtProgressBar(min = 1, max = dim(thesaurusNotranNoPut)[1], style = 3)
  
  
  if (length(thesaurus_data[1,]) != 6) {
    putative_col = rep(NA, length(thesaurus_data[,1]))
    thesaurus_data = cbind(thesaurus_data, putative_col)
    colnames(thesaurus_data)[9] = "Putative"
    
    thesaurus_data = cbind(thesaurus_data, putative_col)
    colnames(thesaurus_data)[10] = "Transposon"
  }
  
  # print(thesaurus_data[1:10,])
  # print(thesaurusNotranNoPut[thesaurusNotranNoPut[,5]==" TRUE",])
  # print(thesaurusNotranNoPut)
  # str(thesaurusNotranNoPut)
  # stop()

  #########################################
  
  # for(i in 1:dim(thesaurusNotranNoPut)[1]){
  #   thesaurus_data[!is.na(thesaurus_data[,1]) & thesaurus_data[,1]==thesaurusNotranNoPut[i,1],9:10] = thesaurusNotranNoPut[i,5:6]
  #   # thesaurus_data[!is.na(thesaurus_data[,1]) & thesaurus_data[,1]==thesaurusNotranNoPut[i,1],] = thesaurusNotranNoPut[i,6]
  #   setTxtProgressBar(prsbar, i)
  # }
  # 
  # write.table(thesaurus_data, file = sortie, row.names = F, col.names = T, quote = F, sep = "\t")
  
  #########################################
  


  for(i in 1:dim(thesaurusNotranNoPut)[1]){
    for (u in 1:length(uniprotthesaurusNotranNoPut[i])){
      irefindex[irefindex[,1]==uniprotthesaurusNotranNoPut[i][u],3]<-thesaurusNotranNoPut[i,3]
      irefindex[irefindex[,1]==uniprotthesaurusNotranNoPut[i][u],14]<-thesaurusNotranNoPut[i,4]
      irefindex[irefindex[,1]==uniprotthesaurusNotranNoPut[i][u],1]<-thesaurusNotranNoPut[i,1]

      irefindex[irefindex[,2]==uniprotthesaurusNotranNoPut[i][u],4]<-thesaurusNotranNoPut[i,3]
      irefindex[irefindex[,2]==uniprotthesaurusNotranNoPut[i][u],15]<-thesaurusNotranNoPut[i,4]
      irefindex[irefindex[,2]==uniprotthesaurusNotranNoPut[i][u],2]<-thesaurusNotranNoPut[i,1]
      thesaurus_data[!is.na(thesaurus_data[,1]) & thesaurus_data[,1]==thesaurusNotranNoPut[i,1],9:10] = thesaurusNotranNoPut[i,5:6]
    }
    setTxtProgressBar(prsbar, i)
  }

  # print(thesaurus_data)
  
  
  #irefindex<-irefindex[(irefindex[,1] != biogridA) &(irefindex[,2] != biogridB),]
  cat("\n>Saving database ... ")
  
  setwd(organism.path)
  database.path <- paste(organism.path, "Databases", sep = '/')
  dir.create(database.path, showWarnings = FALSE)
  setwd(database.path)
  print(database.path)
  organism <- gsub(" ", "-", organism)
  outfilename <- paste(organism, "_biogrid.txt",sep="")
  write.table(irefindex, file = outfilename, row.names = F, col.names = T, quote = F, sep = "\t")
  

  
  
  
  write.table(thesaurus_data, file = sortie, row.names = F, col.names = T, quote = F, sep = "\t")
  
  
  
  
  
  cat(paste("OK\n\n>Formating biogrid database is done.\n\nDatabase file is saved in", database.path, sep = " : "))
  cat(paste("\n\n"))
  
  setwd(pathracine)

  
  
}

biogrid_window2 <- function(f_pos, mainpanel, pana, mainpath) {
    file <- c()
    uniprot <- c()
    return.parameter <- c()

    panel_para <- gwindow("Biogrid database file formatting :", parent = f_pos, visible = T)
    pp <- gvbox(container = panel_para)

    flyt <- gformlayout(container = pp, expand = TRUE)

    # Selection des parametres
    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("Yes", "No"), selected = 1, horizontal = TRUE, label = "Conserve interactions with putative proteins", container = flyt)

    # Selection du fichier
    chdb <- ggroup(container = pp, horizontale = T)
    addSpring(chdb)
    bouton1 <- gbutton("Biogrid file", container = chdb, handler = function(...) {
        file <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
        if (is.null(file) == T) {
            gmessage('Selected Biogrid file is null', icon = 'error')
        }
        if (is.null(file) == F) {
            bouton1$set_value(paste(length(file), 'biogrid file selected'))
            cat(paste('\n>Biogrid file selected : ', file, sep = ''))
        }
    })
    bouton2 <- gbutton("Uniprot file", container = chdb, handler = function(...) {
        uniprot <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
        if (is.null(uniprot) == T) {
            gmessage('Selected Uniprot file is null', icon = 'error')
        }
        if (is.null(uniprot) == F) {
            bouton2$set_value(paste(length(uniprot), 'uniprot file selected'))
            cat(paste('\n>Uniprot file selected : ', uniprot, sep = ''))
        }
    })
      
    true_thesaurus = character(0)
    bouton3 <- gbutton("Thesaurus file*", container = chdb, handler = function(...) {
      true_thesaurus <<- gfile(text = "Select a file", type = "open", multi = F, container = chdb)
      if (is.null(true_thesaurus) == T) {
        gmessage('Selected thesaurus file is null', icon = 'error')
      }
      if (is.null(true_thesaurus) == F) {
        bouton3$set_value(paste(length(true_thesaurus), 'thesaurus file selected'))
        cat(paste('\n>thesaurus file selected : ', true_thesaurus, sep = ''))
      }
    })
    

    ppb <- ggroup(container = pp)
    addSpring(ppb)
    gbutton("Format file", handler = function(h,...) {

        return.parameter <<- svalue(flyt)
        visible(panel_para) <- F
        # Memorisation des parametres de recherche selectionnes
        organism <- as.character(return.parameter[1])
        other = organism
        putative <- as.character(return.parameter[2])
  

        # Execution de la fonction lorsque tous les parametres sont fournis
        if (is.null(file) == F) {
  
            ######################################################################################
            ########################### Execution de la fonction #################################

            pathracine <- getwd()

            if (other == "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 : Autre 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])

                    # biogrid_othero(organism, organismID, putative, file, uniprot, pathracine)
                    
                    format_database(organism,organismID, putative, file, uniprot, pathracine,other, true_thesaurus)

                    dispose(bpc)
                }, container = bpc)

            }
            else {
              
                format_database(organism,organismID, putative, file, uniprot, pathracine,other, true_thesaurus)
              
              
              
                dispose(panel_para)
                dispose(ppb)
              
            }
            visible(mainpanel) <<- T
        }

        # Tests de la presence de tous les elements necessaires a l'execution de la fonction
        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)

	# Retour
	gbutton("Return", handler = function(h,...) {
		dispose(panel_para)
		visible(pana) <<- T
	}, container = ppb)
	
	label_group <- ggroup(container = pp)
	addSpring(label_group)
	label_thesaurus = glabel("*this file is not necessary", container = label_group)
	
	visible(panel_para) <- T

}