Mercurial > repos > mheinzl > variant_analyzer2
changeset 50:b32c973fe8ab draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Thu, 11 Mar 2021 11:04:05 +0000 |
| parents | aa45100f5b14 |
| children | 26e53b5b8bcb |
| files | read2mut.py |
| diffstat | 1 files changed, 30 insertions(+), 28 deletions(-) [+] |
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--- a/read2mut.py Wed Mar 10 17:46:01 2021 +0000 +++ b/read2mut.py Thu Mar 11 11:04:05 2021 +0000 @@ -1076,34 +1076,36 @@ tier_dict[key1]["tier 2.5"] = tier_dict[key1]["tier 4"] tier_dict[key1]["tier 4"] = 0 lines = change_tier_after_print[key1] - l_i = 0 - for li in lines: - row = li[0] - new_line = li[1] - if l_i == 0: - new_line[1] == "2.5" - ws1.write_row(row, 0, new_line) - else: - ws1.write_row(row + 1, 0, new_line) - - ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), - {'type': 'formula', - 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row + 1, row + 1), - 'format': format1, - 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) - ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), - {'type': 'formula', - '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), - 'format': format3, - 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) - ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), - {'type': 'formula', - 'criteria': '=$B${}>="3"'.format(row + 1), - 'format': format2, - 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) - - l_i += 1 - + + for sample in lines: + l_i = 0 + for li in sample: + row = li[0] + new_line = li[1] + if l_i == 0: + new_line[1] == "2.5" + ws1.write_row(row, 0, new_line) + else: + ws1.write_row(row + 1, 0, new_line) + + ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), + {'type': 'formula', + 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row + 1, row + 1), + 'format': format1, + 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) + ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), + {'type': 'formula', + '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), + 'format': format3, + 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) + ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), + {'type': 'formula', + 'criteria': '=$B${}>="3"'.format(row + 1), + 'format': format2, + 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) + + l_i += 1 + # sheet 2 if chimera_correction: 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)',