# modifie mainarams pour adapter au numero de section , nsection et paths
dictToReplace = {
"**POP**":
str(pop),
"**nIndiv**":
str(nbIndivParam),
"**nLoci**":
str(nbMarkerParam),
"**FILEIN**":
str(inputFile),
"**FILEOUT**":
outputFile + "_K" + str(pop) + "_run" + str(rep) + ".txt"
}
mainparamsr = replace_all(dictToReplace, mainparams)
#mainparamsr = mainparams.replace("**POP**",str(pop)).replace("**FILEIN**",str(inputFile)).replace("**FILEOUT**",outputFile+"_K"+str(pop)+"_run"+str(rep)+".txt") # modifie mainparams pour adapter au K
mainparamsOut.write(mainparamsr) # Ecrit le mainparams
mainparamsOut.close()
extraparamsOut.close()
# écriture des scripts pour lancer les annalyses
shOut = open(outputSHDir + "/" + str(count) + "_structure.sh", "w")
shOut.write("module load bioinfo/structure/2.3.4\n")
shOut.write("cd " + workingDir + "/repetition_" + str(rep) +
"/population_" + str(pop) + "/\n")
randomInt = random.randint(1, 60)
shOut.write("sleep %s\n" % randomInt)
shOut.write("structure")
shOut.close()
count += 1
# Récupère le fichier de conf passer en argument
workingObjDir = args.dirPath
replaceParam = args.replaceParam
print("Workink Directory: %s" % workingObjDir.pathDirectory)
dicoReplace = {}
for value in replaceParam.split(","):
old, new = value.split(":")
dicoReplace[old] = new
for fileIn in sorted(workingObjDir.listFiles, key=sort_human):
basename = fileIn.split("/")[-1].split(".")[0]
extention = "." + ".".join(fileIn.split("/")[-1].split(".")[1:])
newName = replace_all(dicoReplace, basename)
if not args.debug:
print("basename", basename)
print("extention", extention)
print("rename file:", basename + extention, "\tto\t",
newName + extention, "\n\n")
if args.debug:
os.rename(fileIn,
workingObjDir.pathDirectory + newName + extention)
print("\nStop time: ", strftime("%d-%m-%Y_%H:%M:%S", localtime()))
print("#################################################################")
print("# End of execution #")
print("#################################################################")
print("############ loop " + str(count) + " ############")
if args.debug: print(">>> FILEIN: " + fileName)
if args.debug:
print(">>> BASENAMEOUT: " + outputResDir + "/" + basenameFile)
dictToReplace.update({
"FILEIN":
str(fileName),
"BASENAMEOUT":
str(outputResDir + "/" + basenameFile),
})
with open(outputSHDir + str(count) + "_script.sh",
"w") as shScriptOut: # not change value here
shtxtReplace = replace_all(dictToReplace, shtxt)
shScriptOut.write(shtxtReplace)
if args.debug: print(">>> base Script with modifications: \n")
if args.debug: print(shtxtReplace)
count += 1
# Not change anythings for headerSGE
headerSGE = """
#!/bin/bash
#$ -N SEB_buildJobArray
#$ -cwd
#$ -V
#$ -e """ + outputTrashDir + """
#$ -o """ + outputTrashDir + """