From cdcf302ffa8f2a10db71afc289e3e968bfebd0f0 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 11 Dec 2024 18:33:43 +0000 Subject: [PATCH] remove duplicated thing --- tbp_parser/Variant.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/tbp_parser/Variant.py b/tbp_parser/Variant.py index b568704..b362daf 100644 --- a/tbp_parser/Variant.py +++ b/tbp_parser/Variant.py @@ -112,13 +112,6 @@ def extract_annotations(self): self.logger.debug("VAR:The drug ({}) was not found in the annotation dictionary; adding it with a WHO confidence of 'No WHO annotation'".format(drug)) self.annotation_dictionary[drug] = Row(self.logger, self, "No WHO annotation", drug) - if self.gene_name in globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME.keys(): - for antimicrobial in globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME[self.gene_name]: - if antimicrobial not in self.annotation_dictionary.keys(): - self.logger.debug("VAR: The drug ({}) was not found in the gene associated drug list; adding it with a WHO confidence of 'No WHO annotation'".format(antimicrobial)) - self.annotation_dictionary[antimicrobial] = Row(self.logger, self, "No WHO annotation", antimicrobial, source="Mutation effect for given drug is not in TBDB") - - if self.gene_name in globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME.keys(): for antimicrobial in globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME[self.gene_name]: if antimicrobial not in self.annotation_dictionary.keys():