Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 76:56f271641828 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Fri, 26 Mar 2021 07:49:15 +0000 |
parents | 6ccff403db8a |
children | 1797e461d674 |
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75:6ccff403db8a | 76:56f271641828 |
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254 if len(value) < thresh: | 254 if len(value) < thresh: |
255 pure_tags_dict_short[key] = value | 255 pure_tags_dict_short[key] = value |
256 else: | 256 else: |
257 pure_tags_dict_short = pure_tags_dict | 257 pure_tags_dict_short = pure_tags_dict |
258 | 258 |
259 csv_data = open(outputFile_csv, "wb") | 259 csv_data = open(outputFile_csv, "w") |
260 csv_writer = csv.writer(csv_data, delimiter=",") | 260 csv_writer = csv.writer(csv_data, delimiter=",") |
261 | 261 |
262 # output summary with threshold | 262 # output summary with threshold |
263 workbook = xlsxwriter.Workbook(outfile) | 263 workbook = xlsxwriter.Workbook(outfile) |
264 workbook2 = xlsxwriter.Workbook(outfile2) | 264 workbook2 = xlsxwriter.Workbook(outfile2) |
549 ref_positions4 = real_start_end[key1][key2[:-5] + '.ba.2'] | 549 ref_positions4 = real_start_end[key1][key2[:-5] + '.ba.2'] |
550 | 550 |
551 used_keys.append(key2[:-5]) | 551 used_keys.append(key2[:-5]) |
552 counts_mut += 1 | 552 counts_mut += 1 |
553 if (alt1f + alt2f + alt3f + alt4f) > 0.5: | 553 if (alt1f + alt2f + alt3f + alt4f) > 0.5: |
554 total1new_trim, total2new_trim, total3new_trim, total4new_trim = total1new, total2new, total3new, total4new | 554 total1new_trim, total2new_trim, total3new_trim, total4new_trim = total1new, total2new, total3new, total4new |
555 if total1new == 0: | 555 if total1new == 0: |
556 ref1f = alt1f = None | 556 ref1f = alt1f = None |
557 alt1ff = -1 | 557 alt1ff = -1 |
558 alt1ff_trim = -1 | 558 alt1ff_trim = -1 |
559 else: | 559 else: |