Mercurial > repos > mheinzl > variant_analyzer2
diff read2mut.py @ 80:8336a4f2b647 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
| author | mheinzl |
|---|---|
| date | Tue, 26 Jul 2022 10:19:28 +0000 |
| parents | d7aea14291e8 |
| children | 612c110305db |
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--- a/read2mut.py Mon Jul 25 13:24:04 2022 +0000 +++ b/read2mut.py Tue Jul 26 10:19:28 2022 +0000 @@ -1367,13 +1367,12 @@ correct_tier = False correct_tier_ref = False 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 + # tier_dict[key1]["tier 2.5"] = tier_dict[key1]["tier 4"] + # tier_dict[key1]["tier 4"] = 0 correct_tier = True - - if tier_dict_ref[key1]["tier 4"] > 0 and sum_highTiers_ref > 0: - tier_dict_ref[key1]["tier 2.5"] = tier_dict_ref[key1]["tier 4"] - tier_dict_ref[key1]["tier 4"] = 0 + elif tier_dict_ref[key1]["tier 4"] > 0 and sum_highTiers_ref > 0: + # tier_dict_ref[key1]["tier 2.5"] = tier_dict_ref[key1]["tier 4"] + # tier_dict_ref[key1]["tier 4"] = 0 correct_tier_ref = True # print(key1, "change tiers from tier 4 to tier 2.5 for {} DCS ...".format(len(change_tier_after_print))) if len(change_tier_after_print) > 0: @@ -1389,12 +1388,16 @@ line1 = tuple(line1) counter_tier25 += 1 counter_tier4 -= 1 - if line1[2] == "ref" and correct_tier_ref and (current_tier == "4") and actual_high_tier: + tier_dict[key1]["tier 2.5"] += 1 + tier_dict[key1]["tier 4"] -= 1 + elif line1[2] == "ref" and correct_tier_ref and (current_tier == "4") and actual_high_tier: line1 = list(line1) line1[1] = "2.5" line1 = tuple(line1) counter_tier25 += 1 counter_tier4 -= 1 + tier_dict_ref[key1]["tier 2.5"] += 1 + tier_dict_ref[key1]["tier 4"] -= 1 ws1.write_row(row, 0, line1) csv_writer.writerow(line1) ws1.write_row(row + 1, 0, line2)