## Test si min < Max
#if nbRepiParam >= nbRepmParam:
#print("ERROR: nbRepiParam > nbRepmParam")
#exit()
## Test si min < Max
#if nbpopiParam >= nbpopmParam:
#print("ERROR: nbpopiParam > nbpopmParam")
#exit()
# Test si les sous répertoires existent déjà
exist = 0
for rep in range(nbRepiParam,
nbRepmParam + 1): # boucle sur le nombre de répétition
if os.path.exists(workingDir + "/repetition_" + str(rep)):
printCol.yellow("Warning , folder " + workingDir + "/repetition_" +
str(rep) + " already exist !!!!")
exist = 1
if exist == 1:
printCol.yellow("Do you want to remove all analysis? (y/n)\n(" +
outputSHDir + " and /trash will be remove if yes)")
inp = None
while inp == None or inp not in ["y", "n", "yes", "no"]:
inp = input()
if inp in ["y", "yes"]:
os.popen('rm -r ' + workingDir + "/repetition_" + str(rep))
exist = 0
if os.path.exists(outputSHDir):
os.popen('rm -r ' + outputSHDir)
if os.path.exists(outputTrashDir):
os.popen('rm -r ' + outputTrashDir)
elif inp in ["n", "no"]:
str(rep) + "/population_" + str(pop) + "/" +
filename)
os.rename(
workingObjDir.pathDirectory + "/repetition_" +
str(rep) + "/population_" + str(pop) + "/" + filename +
'tmp', workingObjDir.pathDirectory + "/repetition_" +
str(rep) + "/population_" + str(pop) + "/" + filename)
print("Number of file reorder: %s\n" % count)
# Si tous va bien les fichiers sont Ok
# zip du répertoire
nameZip = str(workingObjDir.pathDirectory).split("/")[-2]
zipFile = workingObjDir.pathDirectory + nameZip + ".zip"
if os.path.exists(zipFile):
printCol.yellow(
"\nWARNNING struc2runClumpak : path '%s' already contain file %s\nIt will be remove and rebuild\n"
% (workingObjDir.pathDirectory, zipFile))
os.remove(zipFile)
cmd = "cd " + workingObjDir.pathDirectory + ";zip -r " + zipFile + " repetition_*"
print(
"Zip directory repetition into %s with file name: %s.zip with command:\n\t%s\n"
% (workingObjDir.pathDirectory, zipFile, cmd))
stream = check_output(cmd, shell=True).decode("utf-8")
## build label files
print("Build label files into %s" % workingObjDir.pathDirectory)
labelFile, labelAtopFile, orderlist = buildLabelFile(
labelFileParam, workingObjDir.pathDirectory)
# copy labelAtop into CLUMPAK/distruct
cmd = "cp " + labelAtopFile + " " + clumpakObjDir.pathDirectory + "/distruct/labelsAtop"
print(" - Intput Info:")
print("\t - Working in directory: %s" % pathFileOut.pathDirectory)
print("\t - Fasta were in directory: %s" % pathFastaFile.pathDirectory)
print("\t - Number of threads: %s" % nbThreads)
print("\t - Number of nbBootstrap: %s" % nbBootstrap)
print("\t - Other options are: %s" % raxmlOptionValue)
print(" - Output Info:")
print("\t - Output with result raxml were in directory: %s" % outputraxmlResDir)
print("\t - Output sh were in directory: %s" % outputSHDir)
print("\t - Output trash were in directory: %s\n\n" % outputTrashDir)
# build directory out
if os.path.exists(outputraxmlResDir):
printCol.yellow(" Warning , folder %s already exist !!!!" % outputraxmlResDir )
exist=1
if exist == 1:
printCol.yellow(" Do you want to remove all analysis? (y/n)\n ("+outputSHDir+" and "+outputTrashDir+" will be remove if yes)")
inp = None
while inp == None and inp != "y" and inp != "n" and inp != "yes" and inp != "no":
inp = input()
if inp == "y":
#os.popen('rm -rf '+outputraxmlResDir+" && mkdir "+outputraxmlResDir)
#os.popen('rm -rf '+outputSHDir+" && mkdir "+outputSHDir)
#os.popen('rm -rf '+outputTrashDir+" && mkdir "+outputTrashDir)
shutil.rmtree(outputraxmlResDir)
shutil.rmtree(outputSHDir)
shutil.rmtree(outputTrashDir)
if not os.path.exists(outputraxmlResDir):
print("\t - Suffix is: %s" % args.suffixParam)
print("\t - Ref strain is : %s" % ref)
print("\t - Working directory is: %s" % workingDir)
print("\t - Corresonding CDS ref/strain directory is: %s\n\n" %
correspondingCDSDir)
# liste de toute les souches de proteineOrtho
listSouches = []
# dico de proteine orthologue
dico_ortho = {}
exist = 0
# creer le répertoire contenant les correspondance entre ref et souches
if os.path.exists(correspondingCDSDir):
printCol.yellow(" Warning , folder " + correspondingCDSDir +
" already exist !!!!")
exist = 1
else:
os.makedirs(correspondingCDSDir)
if exist == 1:
printCol.yellow(" Do you want to remove all analysis? (y/n)\n")
inp = None
while inp == None and inp != "y" and inp != "n" and inp != "yes" and inp != "no":
inp = input()
if inp == "y":
os.popen('rm -r ' + correspondingCDSDir + '; mkdir ' +
correspondingCDSDir)
exist = 0
elif inp == "n":
printCol.red(">>>Program exit\n")