Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 58:04741369fc07 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, 12 Mar 2021 14:34:21 +0000
parents 706bf8b59eae
children 0b3df6ea1434
comparison
equal deleted inserted replaced
57:706bf8b59eae 58:04741369fc07
1107 ws1.write_row(row_number, 0, line1) 1107 ws1.write_row(row_number, 0, line1)
1108 csv_writer.writerow(line1) 1108 csv_writer.writerow(line1)
1109 ws1.write_row(row_number + 1, 0, line2) 1109 ws1.write_row(row_number + 1, 0, line2)
1110 csv_writer.writerow(line2) 1110 csv_writer.writerow(line2)
1111 1111
1112 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), 1112 ws1.conditional_format('L{}:M{}'.format(row_number + 1, row_number + 2),
1113 {'type': 'formula', 1113 {'type': 'formula',
1114 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row + 1, row + 1), 1114 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row_number + 1, row_number + 1),
1115 'format': format1, 1115 'format': format1,
1116 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) 1116 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row_number + 1, row_number + 2, row_number + 1, row_number + 2, row_number + 1, row_number + 2)})
1117 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), 1117 ws1.conditional_format('L{}:M{}'.format(row_number + 1, row_number + 2),
1118 {'type': 'formula', 1118 {'type': 'formula',
1119 'criteria': '=OR($B${}="2.1", $B${}="2.2", $B${}="2.3", $B${}="2.4", $B${}="2.5")'.format(row + 1, row + 1, row + 1, row + 1, row + 1), 1119 'criteria': '=OR($B${}="2.1", $B${}="2.2", $B${}="2.3", $B${}="2.4", $B${}="2.5")'.format(row_number + 1, row_number + 1, row_number + 1, row_number + 1, row_number + 1),
1120 'format': format3, 1120 'format': format3,
1121 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) 1121 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row_number + 1, row_number + 2, row_number + 1, row_number + 2, row_number + 1, row_number + 2)})
1122 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), 1122 ws1.conditional_format('L{}:M{}'.format(row_number + 1, row_number + 2),
1123 {'type': 'formula', 1123 {'type': 'formula',
1124 'criteria': '=$B${}>="3"'.format(row + 1), 1124 'criteria': '=$B${}>="3"'.format(row_number + 1),
1125 'format': format2, 1125 'format': format2,
1126 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) 1126 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row_number + 1, row_number + 2, row_number + 1, row_number + 2, row_number + 1, row_number + 2)})
1127 1127
1128 # sheet 2 1128 # sheet 2
1129 if chimera_correction: 1129 if chimera_correction:
1130 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 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'chimeras in AC alt (tiers 1.1-2.5)', 'chimera-corrected cvrg (tiers 1.1-2.5)', 'chimera-corrected AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)', 1130 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 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'chimeras in AC alt (tiers 1.1-2.5)', 'chimera-corrected cvrg (tiers 1.1-2.5)', 'chimera-corrected AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)',
1131 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', 'tier 2.5', 1131 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', 'tier 2.5',