correction pb transposon

R/biogrid_window_opt.R

@@ -168,8 +168,8 @@ format_database = function(organism,organismID, putative, file, uniprot, pathrac
   # eliminate transposons
   thesaurusNotranNoPut<-thesaurus[thesaurus[,6]=="FALSE",]
   
-  if(length(thesaurus[thesaurus[,6]==" TRUE",6])>0){
-    Tab.transposons<-thesaurus[thesaurus[,6]==" TRUE",]
+  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)
@@ -182,9 +182,9 @@ format_database = function(organism,organismID, putative, file, uniprot, pathrac
   
   
   # eliminate putative proteins
-  if (putative == " TRUE") {
+  if (putative == "TRUE") {
     thesaurusNotranNoPut <- thesaurusNotranNoPut[thesaurusNotranNoPut[,5] == "FALSE",]
-    Tab.putatives<-thesaurus[thesaurus[,5]==" TRUE",]
+    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)
@@ -296,6 +296,7 @@ biogrid_window2 <- function(f_pos, mainpanel, pana, mainpath) {
     # 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) {

R/intact_window.R

@@ -21,7 +21,7 @@ recup_species = function(intact_tab, taxon) {
   
 }
 
-format_intact = function(organism, organismID, file, pathracine, other) {
+format_intact = function(organism, organismID, file, pathracine, other, thesaurus_file) {
   
   
   cat("\n\n>FORMATING INTACT DATABASE")
@@ -32,6 +32,10 @@ format_intact = function(organism, organismID, file, pathracine, other) {
   
   intact <- read.delim(file = intactFileName, header = T, sep = "\t")
   
+  thesaurus = read.delim(file = thesaurus_file, header = T, sep = "\t", stringsAsFactors = F)
+  
+  
+  
   intact <- intact[,-c(3,4,14)]
   intact <- intact[grep("uniprotkb:", intact[,1]),]
   intact <- intact[grep("uniprotkb:", intact[,2]),]
@@ -161,6 +165,49 @@ format_intact = function(organism, organismID, file, pathracine, other) {
   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 = "")
+  
+  
+  if(length(thesaurus[thesaurus[,10]=="TRUE",]) > 0){
+    
+    Tab.transposons <- thesaurus[thesaurus[,10]=="TRUE",]
+    
+    for (i in 1:dim(Tab.transposons)[1]) {
+      
+      Tab.transposons[i,1]
+      
+      if(length(grep(pattern = Tab.transposons[i,1],irefindex[,1])) > 0) {
+        
+        irefindex <- irefindex[-grep(pattern = Tab.transposons[i,1], irefindex[,1]),] 
+      }
+      if(length(grep(Tab.transposons[i,1],irefindex[,2])) > 0) {
+        irefindex <- irefindex[-grep(pattern = Tab.transposons[i,1], irefindex[,2]),] 
+      }
+      old_uniprot = Tab.transposons[i,7]
+
+      if(length(old_uniprot) > 0) {
+        
+        
+        old_uniprot = unlist(strsplit(Tab.transposons[i,7], split = ";"))
+        
+        for (j in old_uniprot) {
+          
+          
+
+          if(length(grep(pattern = paste0("^",j,"$"),irefindex[,1])) > 0) {
+
+            irefindex <- irefindex[-grep(pattern = paste0("^",j,"$"), irefindex[,1]),]
+          }
+          if(length(grep(pattern = paste0("^",j,"$"), irefindex[,2])) > 0) {
+            irefindex <- irefindex[-grep(pattern = paste0("^",j,"$"), irefindex[,2]),]
+          }
+
+        }
+      }
+      old_uniprot = NULL
+    }
+
+  }
+  
   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 = " : "))
@@ -187,6 +234,7 @@ intact_window <- function(f_pos, mainpanel, pana, mainpath) {
 	# 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) {
@@ -197,6 +245,18 @@ intact_window <- function(f_pos, mainpanel, pana, mainpath) {
 			cat(paste('\n>File selected : ', file, 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)
@@ -249,7 +309,7 @@ intact_window <- function(f_pos, mainpanel, pana, mainpath) {
 
 					# intact_othero(organism, organismID, file, pathracine)
 					
-					format_intact(organism, organismID, file, pathracine, other)
+					format_intact(organism, organismID, file, pathracine, other, true_thesaurus)
 
 					dispose(bpc)		
 				}, container = bpc)
@@ -258,7 +318,7 @@ intact_window <- function(f_pos, mainpanel, pana, mainpath) {
 
 			else {
 			  
-			  format_intact(organism, organismID, file, pathracine, other)
+			  format_intact(organism, organismID, file, pathracine, other, true_thesaurus)
 			  
 			}
 

R/test.R

 rm(list = ls())
+setwd("/home/IPS2/sgosset1/Documents/appinetwork/appinetwork/R")
 library(appinetwork)
 
 

R/thesaurusPy.py

-#!/usr/bin/python
-
-import sys
-import re
-
-try:
-	uniprot = sys.argv[sys.argv.index("thesaurusPy.py")+1]
-except:    
-	print ("ERROR: please, enter uniprot file")
-	sys.exit()
-
-try:
-	thesaurus = sys.argv[sys.argv.index("thesaurusPy.py")+2]
-except:    
-	sys.exit()
-
-try:
-	organism = sys.argv[sys.argv.index("thesaurusPy.py")+3]
-except:    
-	sys.exit()
-
-
-### Recuperation des donnees
-
-fichier = open(uniprot,'r')
-
-donnees = []
-test = 0
-ligne = 'NA'
-liste = []
-ID = 'NA'
-Biogrid = 'NA'
-BIOGRID = []
-NameProt = 'NA'
-Name = 'NA'
-Ref = 'NA'
-Syn = 'NA'
-ORF = 'NA'
-Iso = 'NA'
-ISO = 'NA'
-NIso = 'NA'
-
-for i in fichier :
-
-	i = i.strip("\n")
-
-	# Recuperation du nom principal de la proteine (29, 30-37)
-	if i[0:2] == "ID" :
-		
-		review_state = i[29:39]
-
-		NameProt = re.search(r"(ID)(\s)*(?P<id>\w+)(_)", i)
-		if NameProt is not None:
-			NameProt = NameProt.group('id')
-			NameProt = str(NameProt)
-		else :
-			NameProt = 'NA'
-
-	if review_state == "Unreviewed" :
-		continue
-
-	# Recuperation de l'identifiant uniprot de la proteine et de ses anciens ID
-	if i[0:2] == "AC" :
-		if ID == "NA" :
-			ID = re.search(r"(AC)(\s)*(?P<ac>\w+)(;)", i)
-			if ID is not None:
-				ID = ID.group('ac')
-				ID = str(ID)
-				line = str(i)
-				line = line.strip("AC   ")
-				liste = line.split()
-				if len(liste) > 1 :
-					Iso = ''
-					for j in range(1, len(liste)) :
-						Iso = Iso + liste[j]
-			else :
-				ID = 'NA'
-		else :
-			line = str(i)
-			line = line.strip("AC   ")
-			liste = line.split()
-			if len(liste) > 0 :
-				for j in range(0, len(liste)) :
-					Iso = Iso + liste[j]
-
-
-
-	# Recuperation de la reference du locus (NP)
-	elif i[0:12] == "DR   RefSeq;" :
-		if Ref == "NA" :
-			Ref = re.search(r"(DR   RefSeq; NP_)(?P<rsq>\d+)(.)", i)
-			if Ref is not None:
-				Ref = Ref.group('rsq')
-				Ref = "NP_" + str(Ref)
-			else :
-				Ref = re.search(r"(DR   RefSeq; NP_)(?P<rsq>\d+)(;)", i)
-				if Ref is not None:
-					Ref = Ref.group('rsq')
-					Ref = "NP_" + str(Ref)
-				else :
-					Ref = re.search(r"(DR   RefSeq; XP_)(?P<rsq>\d+)(.)", i)
-					if Ref is not None:
-						Ref = Ref.group('rsq')
-						Ref = "XP_" + str(Ref)
-					else :
-						Ref = re.search(r"(DR   RefSeq; XP_)(?P<rsq>\d+)(;)", i)
-						if Ref is not None:
-							Ref = Ref.group('rsq')
-							Ref = "XP_" + str(Ref)
-						else :
-							Ref = 'NA'
-
-	# Recuperation de l'identifiant biogrid
-	elif i[0:13].upper() == "DR   BIOGRID;" :
-		Biogrid = re.search(r"(DR   BioGrid;)(\s)*(?P<bg>\w+)(;)", i, flags=re.IGNORECASE)
-		if Biogrid is not None:
-			Biogrid = Biogrid.group('bg')
-			Biogrid = str(Biogrid)
-			BIOGRID.append(Biogrid)
-		else :
-			Biogrid = 'NA'
-
-	# Recuperation du nombre d'isoformes
-	elif i[0:2] == "CC" :
-		if NIso == 'NA' :
-			NIso = re.search(r"(Named isoforms=)(?P<is>\d+)(;)", i)
-			if NIso is not None :
-				NIso = NIso.group('is')
-				NIso = str(NIso)
-			else :
-				NIso = 'NA'
-
-	# Recuperation de l'identifiant du gene : Hsapiens, Celegans, Dmelanogaster, Mmusculus, Rnorvegicus, Athaliana
-	#elif i[0:13] == "DR   UniGene;" :
-	#	if organism == "homo+sapiens" :
-	#		if ORF == 'NA' :
-	#			ORF = re.search(r"(DR   UniGene;)(\s)*(Hs.)(?P<ug>\w+)(;)", i)
-	#			if ORF is not None:
-	#				ORF = ORF.group('ug')
-	#				ORF = 'Hs.' + str(ORF)
-	#			else :
-	#				ORF = 'NA'	
-	#	if organism == "caenorhabditis+elegans" :
-	#		if ORF == 'NA' :
-	#			ORF = re.search(r"(DR   UniGene;)(\s)*(Cel.)(?P<ug>\w+)(;)", i)
-	#			if ORF is not None:
-	#				ORF = ORF.group('ug')
-	#				ORF = 'Cel.' + str(ORF)
-	#			else :
-	#				ORF = 'NA'
-	#	if organism == "drosophila+melanogaster" :
-	#		if ORF == 'NA' :
-	#			ORF = re.search(r"(DR   UniGene;)(\s)*(Dm.)(?P<ug>\w+)(;)", i)
-	#			if ORF is not None:
-	#				ORF = ORF.group('ug')
-	#				ORF = 'Dm.' + str(ORF)
-	#			else :
-	#				ORF = 'NA'	
-	#	if organism == "mus+musculus" :
-	#		if ORF == 'NA' :
-	#			ORF = re.search(r"(DR   UniGene;)(\s)*(Mm.)(?P<ug>\w+)(;)", i)
-	#			if ORF is not None:
-	#				ORF = ORF.group('ug')
-	#				ORF = 'Mm.' + str(ORF)
-	#			else :
-	#				ORF = 'NA'
-	#	if organism == "rattus+norvegicus" :
-	#		if ORF == 'NA' :
-	#			ORF = re.search(r"(DR   UniGene;)(\s)*(Rn.)(?P<ug>\w+)(;)", i)
-	#			if ORF is not None:
-	#				ORF = ORF.group('ug')
-	#				ORF = 'Rn.' + str(ORF)
-	#			else :
-	#				ORF = 'NA'	
-	#	if organism == "arabidopsis+thaliana" :
-	#		if ORF == 'NA' :
-	#			ORF = re.search(r"(DR   UniGene;)(\s)*(At.)(?P<ug>\w+)(;)", i)
-	#			if ORF is not None:
-	#				ORF = ORF.group('ug')
-	#				ORF = 'At.' + str(ORF)
-	#			else :
-	#				ORF = 'NA'		
-
-	# Recuperation de l'identifiant du gene : Hsapiens, Celegans, Dmelanogaster, Mmusculus, Rnorvegicus, Athaliana + Ecoli, Scerevisiae
-	elif i[0:10] == "DR   KEGG;" :
-		if organism == "homo+sapiens" :
-			if ORF == 'NA' :
-				ORF = re.search(r"(hsa:)(?P<ug>\S+)(;)", i)
-				if ORF is not None:
-					ORF = ORF.group('ug')
-					ORF = 'hsa:' + str(ORF)
-				else :
-					ORF = 'NA'
-		if organism == "caenorhabditis+elegans" :
-			if ORF == 'NA' :
-				ORF = re.search(r"(cel:)(?P<ug>\S+)(;)", i)
-				if ORF is not None:
-					ORF = ORF.group('ug')
-					ORF = 'cel:' + str(ORF)
-				else :
-					ORF = 'NA'
-		if organism == "drosophila+melanogaster" :
-			if ORF == 'NA' :
-				ORF = re.search(r"(dme:)(?P<ug>\S+)(;)", i)
-				if ORF is not None:
-					ORF = ORF.group('ug')
-					ORF = 'dme:' + str(ORF)
-				else :
-					ORF = 'NA'
-		if organism == "mus+musculus" :
-			if ORF == 'NA' :
-				ORF = re.search(r"(mmu:)(?P<ug>\S+)(;)", i)
-				if ORF is not None:
-					ORF = ORF.group('ug')
-					ORF = 'mmu:' + str(ORF)
-				else :
-					ORF = 'NA'
-		if organism == "rattus+norvegicus" :
-			if ORF == 'NA' :
-				ORF = re.search(r"(rno:)(?P<ug>\S+)(;)", i)
-				if ORF is not None:
-					ORF = ORF.group('ug')
-					ORF = 'rno:' + str(ORF)
-				else :
-					ORF = 'NA'
-		#if organism == "escherichia+coli" :
-		#	if ORF == 'NA' :
-		#		ORF = re.search(r"(eco:)(?P<ug>\S+)(;)", i)
-		#		if ORF is not None:
-		#			ORF = ORF.group('ug')
-		#			ORF = 'eco:' + str(ORF)
-		#		else :
-		#			ORF = 'NA'
-		#if organism == "saccharomyces+cerevisiae" :
-		#	if ORF == 'NA' :
-		#		ORF = re.search(r"(sce:)(?P<ug>\S+)(;)", i)
-		#		if ORF is not None:
-		#			ORF = ORF.group('ug')
-		#			ORF = 'sce:' + str(ORF)
-		#		else :
-		#			ORF = 'NA'	
-
-	# Recuperationdu nom du gene, des synonymes et de l'identifiant du gene
-	if i[0:2] == "GN" :
-
-		# Recuperation des synonymes
-		if test == 1 :
-			ligneSyn = i.split(";")
-			n = len(i)
-			listeLigne = ligneSyn[0].strip("GN   ")
-			laLigne = listeLigne.replace(" ", "")
-			listeSyn = laLigne.split(",")
-			Supprimer = []
-			for k in range(0, len(listeSyn)) : # enlever {...}
-				sup = re.search(r"({)(?P<supp>\S+)(})", listeSyn[k])
-				if sup is not None :
-					sup = sup.group('supp')
-					sup = "{" + str(sup) + "}"
-					listeSyn[k] = listeSyn[k].replace(sup, "")
-				sup = re.search(r"({)(?P<supp>\S+)$", listeSyn[k])
-				if sup is not None :
-					sup = sup.group('supp')
-					sup = "{" + str(sup)
-					listeSyn[k] = listeSyn[k].replace(sup, "")
-				sup = re.search(r"^(?P<supp>\S+)(})", listeSyn[k])
-				if sup is not None :
-					Supprimer.append(k)
-			for s in Supprimer :
-				del listeSyn[s]
-			m = len(listeSyn)
-			if i[n-1] == ";" and m > 0 : # tester si c'est la derniere ligne
-				test = 0
-				listeSyn[m - 1] = listeSyn[m - 1].replace(";", "")
-			elif m == 0 :
-				test = 0
-				listeSyn = []
-			else :
-				del listeSyn[m - 1]
-			if len(listeSyn) > 0 :
-				ajout = ";".join(listeSyn)
-				Syn = Syn + ajout + ";"
-		SYN = re.search(r"(Synonyms=)", i)
-		if SYN is not None :
-			listeLigne = i.split(";")
-			if len(listeLigne) == 2 : # la ligne ne contient que les synonymes, et la liste est complete sur une seule ligne
-				listeLigne[0] = listeLigne[0].strip("GN   Synonyms=")
-				laLigne = listeLigne[0].replace(" ", "")
-				listeSyn = laLigne.split(",")
-				Syn = ''
-				Supprimer = []
-				for k in range(0, len(listeSyn)) : # enlever {...}
-					sup = re.search(r"({)(?P<supp>\S+)(})", listeSyn[k])
-					if sup is not None :
-						sup = sup.group('supp')
-						sup = "{" + str(sup) + "}"
-						listeSyn[k] = listeSyn[k].replace(sup, "")
-					sup = re.search(r"({)(?P<supp>\S+)$", listeSyn[k])
-					if sup is not None :
-						sup = sup.group('supp')
-						sup = "{" + str(sup)
-						listeSyn[k] = listeSyn[k].replace(sup, "")
-					sup = re.search(r"^(?P<supp>\S+)(})", listeSyn[k])
-					if sup is not None :
-						Supprimer.append(k)
-				for s in Supprimer :
-					del listeSyn[s]
-				Syn = ";".join(listeSyn)
-				Syn = Syn + ";"
-			elif len(listeLigne) == 1 : # la ligne ne contient que les synonymes, et la liste ne se termine pas a la premiere ligne, elle est donc sur au moins deux lignes
-				test = 1
-				listeLigne[0] = listeLigne[0].strip("GN   Synonyms=")
-				laLigne = listeLigne[0].replace(" ", "")
-				listeSyn = laLigne.split(",")
-				Syn = ''
-				Supprimer = []
-				for k in range(0, len(listeSyn)) : # enlever {...}
-					sup = re.search(r"({)(?P<supp>\S+)(})", listeSyn[k])
-					if sup is not None :
-						sup = sup.group('supp')
-						sup = "{" + str(sup) + "}"
-						listeSyn[k] = listeSyn[k].replace(sup, "")
-					sup = re.search(r"({)(?P<supp>\S+)$", listeSyn[k])
-					if sup is not None :
-						sup = sup.group('supp')
-						sup = "{" + str(sup)
-						listeSyn[k] = listeSyn[k].replace(sup, "")
-					sup = re.search(r"^(?P<supp>\S+)(})", listeSyn[k])
-					if sup is not None :
-						Supprimer.append(k)
-				for s in Supprimer :
-					del listeSyn[s]
-				del listeSyn[-1]
-				Syn = ";".join(listeSyn)
-				Syn = Syn + ";"
-			else : # la ligne contient diverses informations en plus des synonymes, il faut donc retrouver le fragment concernant les synonymes
-				for j in range(0, len(listeLigne)) :
-					SYN = re.search(r"(Synonyms=)", listeLigne[j])
-					if SYN is not None :
-						if listeLigne[-1] == "" : # la liste se termine sur cette ligne
-							if j == 0 :
-								listeLigne[j] = listeLigne[j].strip("GN   Synonyms=")
-							else :
-								listeLigne[j] = listeLigne[j].strip(" Synonyms=")
-							laLigne = listeLigne[j].replace(" ", "")
-							listeSyn = laLigne.split(",")
-							Syn = ''
-							Supprimer = []
-							for k in range(0, len(listeSyn)) : # enlever {...}
-								sup = re.search(r"({)(?P<supp>\S+)(})", listeSyn[k])
-								if sup is not None :
-									sup = sup.group('supp')
-									sup = "{" + str(sup) + "}"
-									listeSyn[k] = listeSyn[k].replace(sup, "")
-								sup = re.search(r"({)(?P<supp>\S+)$", listeSyn[k])
-								if sup is not None :
-									sup = sup.group('supp')
-									sup = "{" + str(sup)
-									listeSyn[k] = listeSyn[k].replace(sup, "")
-								sup = re.search(r"^(?P<supp>\S+)(})", listeSyn[k])
-								if sup is not None :
-									Supprimer.append(k)
-							for s in Supprimer :
-								del listeSyn[s]
-							Syn = ";".join(listeSyn)
-							Syn = Syn + ";"
-						else : # la liste est sur plusieurs lignes
-							test = 1
-							listeLigne[j] = listeLigne[j].strip(" Synonyms=")
-							laLigne = listeLigne[j].replace(" ", "")
-							listeSyn = laLigne.split(",")
-							Syn = ''
-							Supprimer = []
-							for k in range(0, len(listeSyn)) : # enlever {...}
-								sup = re.search(r"({)(?P<supp>\S+)(})", listeSyn[k])
-								if sup is not None :
-									sup = sup.group('supp')
-									sup = "{" + str(sup) + "}"
-									listeSyn[k] = listeSyn[k].replace(sup, "")
-								sup = re.search(r"({)(?P<supp>\S+)$", listeSyn[k])
-								if sup is not None :
-									sup = sup.group('supp')
-									sup = "{" + str(sup)
-									listeSyn[k] = listeSyn[k].replace(sup, "")
-								sup = re.search(r"^(?P<supp>\S+)(})", listeSyn[k])
-								if sup is not None :
-									Supprimer.append(k)
-							for s in Supprimer :
-								del listeSyn[s]
-							del listeSyn[-1]
-							Syn = ";".join(listeSyn)
-							Syn = Syn + ";"
-					else:
-						SYN = 'NA'
-		else :
-			SYN = 'NA'
-
-		# Recuperation de l'identifiant du gene : Scerevisiae + Ecoli
-		if organism == "saccharomyces+cerevisiae" or organism == "escherichia+coli" :
-			if ORF == "NA" :
-				ligneORF = i.split(";")
-				for k in ligneORF :
-					k = k.replace(" ","")
-					orfs = re.search(r"(.)*(OrderedLocusNames=)(?P<orf>\S+)$", k)
-					if orfs is not None:
-						ORF = orfs.group('orf')
-						ORF = str(ORF)
-						sup = re.search(r"({)(?P<SUP>\S+)(})", ORF)
-						if sup is not None :
-							sup = sup.group('SUP')
-							sup = '{' + sup + '}'
-							ORF = ORF.replace(sup, "")
-					else :
-						orfs = 'NA'
-		if organism == "arabidopsis+thaliana" :
-			if ORF == "NA" :
-				ligneORF = i.split(";")
-				for k in ligneORF :
-					k = k.replace(" ","")
-					k = k.split("{")[0]
-					orfs = re.search(r"(.)*(OrderedLocusNames=)(?P<orf>\S+)$", k)
-					if orfs is not None:
-						ORF = orfs.group('orf')
-						ORF = str(ORF)
-						ORF = ORF.upper()
-						sup = re.search(r"({)(?P<SUP>\S+)(})", ORF)
-						if sup is not None :
-							sup = sup.group('SUP')
-							sup = '{' + sup + '}'
-							ORF = ORF.replace(sup, "")
-					else :
-						orfs = 'NA'
-		# Recuperation du nom du gene
-		if Name == "NA" :
-			ligneName = i.split(";")
-			for k in ligneName :
-				k = k.replace(" ", "")
-				NAME = re.search(r"(Name=)(?P<id>\S+)$", k)
-				if NAME is not None:
-					Name = NAME.group('id')
-					Name = str(Name)
-					sup = re.search(r"({)(?P<SUP>\S+)$", Name)
-					if sup is not None :
-						sup = sup.group('SUP')
-						sup = '{' + sup
-						Name = Name.replace(sup, "")
-				else :
-					NAME = 'NA'
-
-	# A la fin de chaque bloc (chaque proteine) les donnees sont rassemblees sur une meme ligne
-	elif i[0:2] == "//" :
-		if Name == 'NA' :