Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 24:cf6f0fb05bad 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 16:31:04 +0000
parents 25625221b88f
children 6ee7044d93b0
comparison
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23:25625221b88f 24:cf6f0fb05bad
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)
770 770 csv_data.close()
771
771 # sheet 2 772 # sheet 2
772 if chimera_correction: 773 if chimera_correction:
773 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)',
774 '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',
775 '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',
971 '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)})
972 row += 3 973 row += 3
973 workbook.close() 974 workbook.close()
974 workbook2.close() 975 workbook2.close()
975 workbook3.close() 976 workbook3.close()
976 csv_data.close() 977
977 978
978 979
979 if __name__ == '__main__': 980 if __name__ == '__main__':
980 sys.exit(read2mut(sys.argv)) 981 sys.exit(read2mut(sys.argv))