" 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")
exit()
# ouverture du fichier de résultat protine ortho pour construire liste de seq ortho
with open(args.proteineOrthoFile, "r") as proteineOrthoFile:
for line in proteineOrthoFile:
if "#" not in line:
tabline = line.split("\t")
souche_contig1 = tabline[0] # nom de la souche et contig
souche_contig2 = tabline[1]
namesouche1 = tabline[0].split("_")[0] # nom de la souche seul
namesouche2 = tabline[1].split("_")[0]
if args.debug == "True":
print(souche_contig1, namesouche1, souche_contig2,
namesouche2) # DEBUG
tabNbPop = []
tabNbRep = [
repo.split("/")[-1].split("_")[-1] for repo in workingObjDir.listDir
if "repetition" in repo
]
for repo in workingObjDir.listDir:
if "repetition" in repo:
workingObjDirPop = directory(repo)
tabNbPop = [
repo.split("/")[-1].split("_")[-1]
for repo in workingObjDirPop.listDir
]
break
if tabNbPop == []:
printCol.red(
"ERROR struc2runClumpak : path '%s' not contain folder 'repetition_*' with population sub-directory. Make sure take results product by script 'make_structure_dir.py' "
% workingObjDir.pathDirectory)
exit()
tabNbRepSort = sorted(tabNbRep, key=int)
tabNbPopSort = sorted(tabNbPop, key=int)
nbRep, nbPop = len(tabNbRep), len(tabNbPop)
print("There are %i repetition of %i population" % (nbRep, nbPop))
# build label files
print("Build label files into %s" % workingObjDir.pathDirectory)
labelFile, labelAtopFile, orderlist = buildLabelFile(
labelFileParam, workingObjDir.pathDirectory)
print("Number of indiv in orderList: %s\n" % len(orderlist))
print("Reorder files tab\n")
##################################################
#Import MODULES_SEB
import sys, os
current_dir = os.path.dirname(os.path.abspath(__file__))+"/"
sys.path.insert(1,current_dir+'../modules/')
from MODULES_SEB import dict2txt, loadInList, dictDict2txt, printCol, relativeToAbsolutePath, existant_file, directory
## Python modules
import argparse
from time import localtime, strftime
import gzip
try:
import egglib3 as egglib
except Exception as e:
printCol.red(str(e))
printCol.red("Must run :\nmodule load compiler/gcc/4.9.3")
exit()
##################################################
## Variables Globales
version="0.1"
VERSION_DATE='28/02/2017'
##################################################
## Main code
##################################################
if __name__ == "__main__":