Mercurial > repos > mheinzl > variant_analyzer2
changeset 48:e2a655533077 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Wed, 10 Mar 2021 14:37:20 +0000 |
| parents | edf8596463a8 |
| children | aa45100f5b14 |
| files | read2mut.py |
| diffstat | 1 files changed, 48 insertions(+), 7 deletions(-) [+] |
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--- a/read2mut.py Tue Mar 09 12:48:29 2021 +0000 +++ b/read2mut.py Wed Mar 10 14:37:20 2021 +0000 @@ -310,6 +310,7 @@ row = 1 tier_dict = {} chimera_dict = {} + change_tier_after_print = {} for key1, value1 in sorted(mut_dict.items()): counts_mut = 0 chimeric_tag_list = [] @@ -828,7 +829,7 @@ details2 = (total2, total3, total2new, total3new, ref2, ref3, alt2, alt3, ref2f, ref3f, alt2f, alt3f, na2, na3, lowq2, lowq3, beg2, beg3) - sum_highTiers = sum([tier_dict[key1][ij] for ij in tier_dict[key1].keys()[:6]]) + #sum_highTiers = sum([tier_dict[key1][ij] for ij in tier_dict[key1].keys()[:6]]) # assign tiers if ((all(int(ij) >= 3 for ij in [total1new, total4new]) & @@ -898,10 +899,10 @@ counter_tier32 += 1 tier_dict[key1]["tier 3.2"] += 1 - elif (trimmed) and (sum_highTiers > 1): - tier = "2.5" - counter_tier25 += 1 - tier_dict[key1]["tier 2.5"] += 1 + #elif (trimmed) and (sum_highTiers > 1): + # tier = "2.5" + # counter_tier25 += 1 + # tier_dict[key1]["tier 2.5"] += 1 elif (trimmed): tier = "4" @@ -1031,8 +1032,8 @@ read_pos3 = read_len_median3 = None 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) ws1.write_row(row, 0, line) - 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) - ws1.write_row(row + 1, 0, line) + line2 = ("", "", 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) + ws1.write_row(row + 1, 0, line2) ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), {'type': 'formula', @@ -1049,6 +1050,11 @@ '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)}) + if trimmed: + if key1 not in list(mut_read_pos_dict.keys()): + change_tier_after_print[key1] = [((row, line), (row, line2))] + else: + change_tier_after_print[key1].append(((row, line), (row, line2))) row += 3 if chimera_correction: @@ -1063,6 +1069,41 @@ else: chimeric_dcs_high_tiers += high_tiers chimera_dict[key1] = (chimeric_dcs, chimeric_dcs_high_tiers) + + # move tier 4 counts to tier 2.5 if there other mutations with tier <= 2.4 + sum_highTiers = sum([tier_dict[key1][ij] for ij in tier_dict[key1].keys()[:6]]) + if tier_dict[key1]["tier 4"] > 0 and sum_highTiers > 0: + 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 + # 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)',