Commit 6fb74df4 by Paul Igor Costea

Bug fixes

parent a0a9c160
......@@ -43,7 +43,7 @@ def get_arguments():
# OPTIONAL arguments:
parser.add_argument('-b', metavar='FLOAT', type=float, default=40.0)
parser.add_argument('-b', metavar='FLOAT', type=float, default=40.0,
help="Coverage breadth: minimal horizontal genome coverage percentage per sample per species")
parser.add_argument('-d', metavar='FLOAT', type=float, default=5.0,
help="Coverage depth: minimal average vertical genome coverage per sample per species")
......@@ -85,8 +85,8 @@ def debugging(taxids_of_interest, header_cov):
def file_check():
''' Check if required files exist (True / False)'''
args.projdir = args.projdir.rstrip('/')
args.coverage_file = args.projdir+'/'+args.projdir+'.all_cov.tab'
args.percentage_file = args.projdir+'/'+args.projdir+'.all_perc.tab'
args.coverage_file = args.projdir+'/'+args.projdir.split('/')[-1]+'.all_cov.tab'
args.percentage_file = args.projdir+'/'+args.projdir.spit('/')[-1]+'.all_perc.tab'
args.all_samples = args.projdir+'/'+'all_samples'
print("Checking for necessary input files...")
......
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