Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 76:56f271641828 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Fri, 26 Mar 2021 07:49:15 +0000
parents 6ccff403db8a
children 1797e461d674
comparison
equal deleted inserted replaced
75:6ccff403db8a 76:56f271641828
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: