diff --git a/metaSNV.py b/metaSNV.py index 91b31d92f08f8e14000d65e636189bb07e8084ca..214d338137fbae32c10493d935a3f74ed20eae50 100755 --- a/metaSNV.py +++ b/metaSNV.py @@ -91,12 +91,11 @@ def get_header(args): f.close() args.ctg_len = args.project_dir + '/bed_header' - def compute_summary(args): '''This information is required by metaSNV_post.py''' project_name = path.basename(args.project_dir) - + cov_dir = path.join(args.project_dir, 'cov') cov_files = glob(cov_dir + '/*.cov') # project_name = path.basename(args.project_dir) @@ -122,7 +121,6 @@ def compute_summary(args): args.project_dir] subprocess.call(cmd) - def split_opt(args): if args.n_splits > 100: @@ -135,15 +133,14 @@ def split_opt(args): for f in older_files: os.unlink(f) - project_name = path.basename(args.project_dir) - + project_name = path.basename(args.project_dir) print("\nCalculating best database split:") # usage createOptimumSplit.sh <all_cov.tab> <all_perc.tab> <geneDefinitions> <INT_NrSplits> <.outfile> cmd = ['python', '{}/src/createOptimumSplit.py'.format(basedir), - "{}/{}.all_cov.tab".format(args.project_dir, project_name), - "{}/{}.all_perc.tab".format(args.project_dir, project_name), + "{}/{}.all_cov.tab".format(args.project_dir, args.project_dir), + "{}/{}.all_perc.tab".format(args.project_dir, args.project_dir), args.ctg_len, str(args.n_splits), path.join(args.project_dir, "bestsplits", "best_split")]