Mercurial > repos > mheinzl > variant_analyzer2
diff read2mut.py @ 26:5cb0bdd578cf 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 16:48:12 +0000 |
| parents | 6ee7044d93b0 |
| children | 5992e30ae50e |
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--- a/read2mut.py Mon Feb 22 16:38:33 2021 +0000 +++ b/read2mut.py Mon Feb 22 16:48:12 2021 +0000 @@ -237,8 +237,8 @@ else: pure_tags_dict_short = pure_tags_dict - csv_data = open(outputFile_csv, "w") - csv_writer = csv.writer(csv_data, delimiter=",") + #csv_data = open(outputFile_csv, "w") + #csv_writer = csv.writer(csv_data, delimiter=",") # output summary with threshold workbook = xlsxwriter.Workbook(outfile) @@ -268,7 +268,7 @@ 'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba', 'in phase', 'chimeric tag') ws1.write_row(0, 0, header_line) - csv_writer.writerow(header_line) + #csv_writer.writerow(header_line) counter_tier11 = 0 counter_tier12 = 0 counter_tier21 = 0 @@ -733,10 +733,10 @@ read_pos3 = read_len_median3 = None line = (var_id, tier, key2[:-5], 'ab1.ba2', read_pos1, read_pos4, read_len_median1, read_len_median4, dcs_median) + details1 + (sscs_mut_ab, sscs_mut_ba, sscs_ref_ab, sscs_ref_ba, add_mut14, chimera) ws1.write_row(row, 0, line) - csv_writer.writerow(line) + #csv_writer.writerow(line) line = ("", "", key2[:-5], 'ab2.ba1', read_pos2, read_pos3, read_len_median2, read_len_median3, dcs_median) + details2 + (sscs_mut_ab, sscs_mut_ba, sscs_ref_ab, sscs_ref_ba, add_mut23, chimera) ws1.write_row(row + 1, 0, line) - csv_writer.writerow(line) + #csv_writer.writerow(line) ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), {'type': 'formula', @@ -767,8 +767,8 @@ else: chimeric_dcs_high_tiers += high_tiers chimera_dict[key1] = (chimeric_dcs, chimeric_dcs_high_tiers) - csv_writer.close() - + #csv_data.close() + # sheet 2 if chimera_correction: header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'chimeras in AC alt (all tiers)', 'chimera-corrected cvrg', 'chimera-corrected AF (all tiers)', 'cvrg (tiers 1.1-2.4)', 'AC alt (tiers 1.1-2.4)', 'AF (tiers 1.1-2.4)', 'chimeras in AC alt (tiers 1.1-2.4)', 'chimera-corrected cvrg (tiers 1.1-2.4)', 'chimera-corrected AF (tiers 1.1-2.4)', 'AC alt (orginal DCS)', 'AF (original DCS)',