Merge branch 'main' into dev

Dockerfile

@@ -42,7 +42,7 @@ ARG TBP_PARSER_VER
 LABEL base.image="ubuntu:jammy"
 LABEL dockerfile.version="1"
 LABEL software="tbp-parser"
-LABEL software.version="2.2.1"
+LABEL software.version="2.1.1"
 LABEL description="tbp-parser and samtools"
 LABEL website="https://github.com/theiagen/tbp-parser"
 LABEL license="https://github.com/theiagen/tbp-parser/blob/main/LICENSE"

docs/usage.md

@@ -17,11 +17,11 @@ docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.1 #(1)!
 The entrypoint for this Docker image is the `tbp-parser` help message. To run this container *interactively*, you can use the following command:
 
 ``` bash
-docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.1
+docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.1.1
 
 # Once inside the container interactively, you can run the tbp-parser tool
 python3 /tbp-parser/tbp_parser/tbp_parser.py -v
-# v2.2.0
+# v2.2.1
 ```
 
 ### Locally with Python

docs/versioning/exhaustive.md

@@ -66,8 +66,7 @@ The following is a list of every version of `tbp-parser` and a short summary of
     - Earlier versions are now deprecated and will no longer be supported.
 - v2.1.1 - adds the source and comment fields from TBDB to the Laboratorian report; fixes a bug where mmpR5 was not being completly renamed to Rv0678; fixes a bug where mutations that didn't share the same position were being compared
 - v2.2.0 - removes ciprofloxacin, fluoroquinolones, and ofloxacin from gyrA and gyrB and aminoglycosides from rrs in the `globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME` dictionary; if a drug is missing in the TBProfiler JSON's gene_associated_drug field that is present in that global dictionary, it will be added for the mutation.
-- v2.2.1 - fixes a bug where rifampicin was not being renamed to rifampin and resulted in duplicate rows in the laboratorian report 
-- 
+
 ---
 
 The following diagram shows how each version is related to the others without technical details:

tbp_parser/Row.py

@@ -327,6 +327,7 @@ def describe_rationale(self):
     if any(rule in self.mdl_interpretation for rule in globals.RULE_TO_RATIONALE.keys()):
       interpretation = self.mdl_interpretation[0]
       rule = self.mdl_interpretation[1:]
+      self.logger.debug("rule={}".format(rule))
       self.mdl_interpretation = interpretation
       self.logger.debug(globals.RULE_TO_RATIONALE[rule])
       globals.RULE_TO_RATIONALE[rule]

tbp_parser/Variant.py

@@ -112,6 +112,13 @@ 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():
@@ -120,6 +127,7 @@ def extract_annotations(self):
 
       self.logger.debug("VAR:The annotation dictionary has all gene associated drugs included; it now has a length of {}".format(len(self.annotation_dictionary)))
 
+
     else:
       # possibilities 1b and 2: the annotation field has no content or the field does not exist
       self.logger.debug("VAR:The annotation field has no content or does not exist. Now iterating through gene associated drugs and gene-drug combination dictionary.")
@@ -134,7 +142,9 @@ def extract_annotations(self):
             if antimicrobial not in self.annotation_dictionary.keys():
               self.annotation_dictionary[antimicrobial] = Row(self.logger, self, "No WHO annotation", antimicrobial)
 
-    self.logger.debug("VAR:{} annotation(s) extracted, now exiting function".format(len(self.annotation_dictionary)))
+      self.logger.debug("VAR:After iterating through gene_associated_drugs, the annotation dictionary has a length of {}".format(len(self.annotation_dictionary)))
+
+    self.logger.debug("VAR:Annotations extracted, now exiting function")
 
   def apply_expert_rules(self, interpretation_destination):
     """