Mercurial > repos > mheinzl > variant_analyzer2
diff read2mut.py @ 17:f06067bedfc5 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 14:40:07 +0000 |
| parents | 30aec05d04d3 |
| children | d910b6dfd826 |
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--- a/read2mut.py Mon Feb 22 14:33:12 2021 +0000 +++ b/read2mut.py Mon Feb 22 14:40:07 2021 +0000 @@ -63,10 +63,6 @@ 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='Delimiter in csv summary file. Default comma.') - - return parser @@ -238,7 +234,7 @@ pure_tags_dict_short = pure_tags_dict csv_data = open(outputFile_csv, "w") - csv_writer = csv.writer(csv_data, delimiter=delim_csv) + csv_writer = csv.writer(csv_data, delimiter=",") # output summary with threshold workbook = xlsxwriter.Workbook(outfile)