Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 29:b14b69697cf6 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Wed, 24 Feb 2021 10:21:07 +0000 |
| parents | afda74e874ac |
| children | e7da54e10e2d |
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| 28:afda74e874ac | 29:b14b69697cf6 |
|---|---|
| 235 if len(value) < thresh: | 235 if len(value) < thresh: |
| 236 pure_tags_dict_short[key] = value | 236 pure_tags_dict_short[key] = value |
| 237 else: | 237 else: |
| 238 pure_tags_dict_short = pure_tags_dict | 238 pure_tags_dict_short = pure_tags_dict |
| 239 | 239 |
| 240 #csv_data = open(outputFile_csv, "w") | 240 csv_data = open(outputFile_csv, "wb") |
| 241 #csv_writer = csv.writer(csv_data, delimiter=",") | 241 csv_writer = csv.writer(csv_data, delimiter=",") |
| 242 | 242 |
| 243 # output summary with threshold | 243 # output summary with threshold |
| 244 workbook = xlsxwriter.Workbook(outfile) | 244 workbook = xlsxwriter.Workbook(outfile) |
| 245 workbook2 = xlsxwriter.Workbook(outfile2, {'in_memory': True}) | 245 workbook2 = xlsxwriter.Workbook(outfile2) |
| 246 workbook3 = xlsxwriter.Workbook(outfile3, {'in_memory': True}) | 246 workbook3 = xlsxwriter.Workbook(outfile3) |
| 247 ws1 = workbook.add_worksheet("Results") | 247 ws1 = workbook.add_worksheet("Results") |
| 248 ws2 = workbook2.add_worksheet("Allele frequencies") | 248 ws2 = workbook2.add_worksheet("Allele frequencies") |
| 249 ws3 = workbook3.add_worksheet("Tiers") | 249 ws3 = workbook3.add_worksheet("Tiers") |
| 250 | 250 |
| 251 format1 = workbook.add_format({'bg_color': '#BCF5A9'}) # green | 251 format1 = workbook.add_format({'bg_color': '#BCF5A9'}) # green |
| 266 'rel. ref.ab', 'rel. ref.ba', 'rel. alt.ab', 'rel. alt.ba', | 266 'rel. ref.ab', 'rel. ref.ba', 'rel. alt.ab', 'rel. alt.ba', |
| 267 'na.ab', 'na.ba', 'lowq.ab', 'lowq.ba', 'trim.ab', 'trim.ba', | 267 'na.ab', 'na.ba', 'lowq.ab', 'lowq.ba', 'trim.ab', 'trim.ba', |
| 268 'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba', | 268 'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba', |
| 269 'in phase', 'chimeric tag') | 269 'in phase', 'chimeric tag') |
| 270 ws1.write_row(0, 0, header_line) | 270 ws1.write_row(0, 0, header_line) |
| 271 #csv_writer.writerow(header_line) | 271 csv_writer.writerow(header_line) |
| 272 counter_tier11 = 0 | 272 counter_tier11 = 0 |
| 273 counter_tier12 = 0 | 273 counter_tier12 = 0 |
| 274 counter_tier21 = 0 | 274 counter_tier21 = 0 |
| 275 counter_tier22 = 0 | 275 counter_tier22 = 0 |
| 276 counter_tier23 = 0 | 276 counter_tier23 = 0 |
| 731 read_pos2 = read_len_median2 = None | 731 read_pos2 = read_len_median2 = None |
| 732 if (read_pos3 == -1): | 732 if (read_pos3 == -1): |
| 733 read_pos3 = read_len_median3 = None | 733 read_pos3 = read_len_median3 = None |
| 734 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) | 734 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) |
| 735 ws1.write_row(row, 0, line) | 735 ws1.write_row(row, 0, line) |
| 736 #csv_writer.writerow(line) | 736 csv_writer.writerow(line) |
| 737 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) | 737 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) |
| 738 ws1.write_row(row + 1, 0, line) | 738 ws1.write_row(row + 1, 0, line) |
| 739 #csv_writer.writerow(line) | 739 csv_writer.writerow(line) |
| 740 | 740 |
| 741 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), | 741 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), |
| 742 {'type': 'formula', | 742 {'type': 'formula', |
| 743 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row + 1, row + 1), | 743 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row + 1, row + 1), |
| 744 'format': format1, | 744 'format': format1, |
| 972 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2)}) | 972 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2)}) |
| 973 row += 3 | 973 row += 3 |
| 974 workbook.close() | 974 workbook.close() |
| 975 workbook2.close() | 975 workbook2.close() |
| 976 workbook3.close() | 976 workbook3.close() |
| 977 csv_data.close() | |
| 977 | 978 |
| 978 | 979 |
| 979 | 980 |
| 980 if __name__ == '__main__': | 981 if __name__ == '__main__': |
| 981 sys.exit(read2mut(sys.argv)) | 982 sys.exit(read2mut(sys.argv)) |