Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 85:d1cd4cd9f18d draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
| author | mheinzl |
|---|---|
| date | Wed, 24 Aug 2022 09:47:08 +0000 |
| parents | e46d5e377760 |
| children | 97bd9c7a1b44 |
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| 84:e46d5e377760 | 85:d1cd4cd9f18d |
|---|---|
| 475 add_mut23 = "" | 475 add_mut23 = "" |
| 476 if key2[:-5] not in tag_dict.keys() and key2[:-5] not in tag_dict_ref.keys(): # skip reads that have not alt or ref | 476 if key2[:-5] not in tag_dict.keys() and key2[:-5] not in tag_dict_ref.keys(): # skip reads that have not alt or ref |
| 477 continue | 477 continue |
| 478 | 478 |
| 479 if (((key2[:-5] in tag_dict.keys()) and (key2[:-5] in pure_tags_dict_short[key1].keys()) and (key1 in tag_dict[key2[:-5]].keys()) and (key2[:-5] not in used_keys)) or ((key2[:-5] in tag_dict_ref.keys()) and (key2[:-5] in pure_tags_dict_ref[key1].keys()) and (key1 in tag_dict_ref[key2[:-5]].keys()) and (key2[:-5] not in used_keys))): | 479 if (((key2[:-5] in tag_dict.keys()) and (key2[:-5] in pure_tags_dict_short[key1].keys()) and (key1 in tag_dict[key2[:-5]].keys()) and (key2[:-5] not in used_keys)) or ((key2[:-5] in tag_dict_ref.keys()) and (key2[:-5] in pure_tags_dict_ref[key1].keys()) and (key1 in tag_dict_ref[key2[:-5]].keys()) and (key2[:-5] not in used_keys))): |
| 480 if key2[:-5] in tag_dict.keys(): | 480 if key2[:-5] in tag_dict.keys() and key1 in tag_dict[key2[:-5]].keys(): |
| 481 variant_type = "alt" | 481 variant_type = "alt" |
| 482 elif key2[:-5] in tag_dict_ref.keys(): | 482 elif key2[:-5] in tag_dict_ref.keys() and key1 in tag_dict_ref[key2[:-5]].keys(): |
| 483 variant_type = "ref" | 483 variant_type = "ref" |
| 484 | 484 |
| 485 if refalttiers is False and variant_type == "ref": # if we only want information about alt tiers, skip all refs | 485 if refalttiers is False and variant_type == "ref": # if we only want information about alt tiers, skip all refs |
| 486 continue | 486 continue |
| 487 | 487 |