comparison read2mut.py @ 85:d1cd4cd9f18d draft default tip

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
comparison
equal deleted inserted replaced
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