" 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__":