From 6fb74df427bbce5c1d7dd2e50c7483e0963067c2 Mon Sep 17 00:00:00 2001
From: Paul Igor Costea <paul.igor.costea@embl.de>
Date: Fri, 12 May 2017 16:07:32 +0200
Subject: [PATCH] Bug fixes
---
metaSNV_post.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/metaSNV_post.py b/metaSNV_post.py
index 656e34d..08ec306 100755
--- a/metaSNV_post.py
+++ b/metaSNV_post.py
@@ -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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