Mercurial > repos > mheinzl > variant_analyzer2
changeset 14:bcdb63df70ce draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Mon, 22 Feb 2021 14:26:13 +0000 |
| parents | 02bf6425fc25 |
| children | 6f4c61123a36 |
| files | read2mut.py |
| diffstat | 1 files changed, 4 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/read2mut.py Mon Feb 22 14:18:57 2021 +0000 +++ b/read2mut.py Mon Feb 22 14:26:13 2021 +0000 @@ -63,6 +63,8 @@ help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.') parser.add_argument('--chimera_correction', action="store_true", help='Count chimeric variants and correct the variant frequencies') + parser.add_argument('--delim_csv', type=str, default=",", + help='Deliminator in csv summary file. Default comma.') return parser @@ -89,6 +91,7 @@ phred_score = args.phred trim = args.trim chimera_correction = args.chimera_correction + delim_csv = args.delim_csv if os.path.isfile(file1) is False: sys.exit("Error: Could not find '{}'".format(file1)) @@ -235,7 +238,7 @@ pure_tags_dict_short = pure_tags_dict csv_data = open(outputFile_csv, "w") - csv_writer = csv.writer(csv_data) + csv_writer = csv.writer(csv_data, delimiter=delim_csv) # output summary with threshold workbook = xlsxwriter.Workbook(outfile)