Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 26:5cb0bdd578cf 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 Mon, 22 Feb 2021 16:48:12 +0000
parents 6ee7044d93b0
children 5992e30ae50e
comparison
equal deleted inserted replaced
25:6ee7044d93b0 26:5cb0bdd578cf
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, "w")
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) 245 workbook2 = xlsxwriter.Workbook(outfile2)
246 workbook3 = xlsxwriter.Workbook(outfile3) 246 workbook3 = xlsxwriter.Workbook(outfile3)
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,
765 if high_tiers == len(tiers): 765 if high_tiers == len(tiers):
766 chimeric_dcs_high_tiers += high_tiers - 1 766 chimeric_dcs_high_tiers += high_tiers - 1
767 else: 767 else:
768 chimeric_dcs_high_tiers += high_tiers 768 chimeric_dcs_high_tiers += high_tiers
769 chimera_dict[key1] = (chimeric_dcs, chimeric_dcs_high_tiers) 769 chimera_dict[key1] = (chimeric_dcs, chimeric_dcs_high_tiers)
770 csv_writer.close() 770 #csv_data.close()
771 771
772 # sheet 2 772 # sheet 2
773 if chimera_correction: 773 if chimera_correction:
774 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)', 774 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)',
775 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', 775 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4',
776 'tier 3.1', 'tier 3.2', 'tier 4.1', 'tier 4.2', 'tier 5', 'tier 6', 'AF 1.1-1.2', 'AF 1.1-2.1', 'AF 1.1-2.2', 776 'tier 3.1', 'tier 3.2', 'tier 4.1', 'tier 4.2', 'tier 5', 'tier 6', 'AF 1.1-1.2', 'AF 1.1-2.1', 'AF 1.1-2.2',