correct lims report bug

Dockerfile

@@ -3,7 +3,7 @@
 # Shelby Bennett, Erin Young, Curtis Kapsak, & Kutluhan Incekara
 
 ARG SAMTOOLS_VER="1.18"
-ARG TBP_PARSER_VER="1.4.4.9"
+ARG TBP_PARSER_VER="1.4.4.10"
 
 FROM ubuntu:jammy as builder
 
@@ -42,7 +42,7 @@ ARG TBP_PARSER_VER
 LABEL base.image="ubuntu:jammy"
 LABEL dockerfile.version="1"
 LABEL software="tbp-parser"
-LABEL software.version="1.4.4.9"
+LABEL software.version="1.4.4.10"
 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"

README.md

@@ -36,16 +36,16 @@ Again, please use tbp-parser at your own risk and be sure to perform extensive v
 We highly recommend using the following Docker image to run tbp-parser:
 
 ```markdown
-docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.4.4.9
+docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.4.4.10
 ```
 
 The entrypoint for this Docker image is the tbp-parser help message. To run this container interactively, use the following command:
 
 ```markdown
-docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.4.4.9
+docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.4.4.10
 # Once inside the container interactively, you can run the tbp-parser tool
 python3 /tbp-parser/tbp_parser/tbp_parser.py -v
-# v1.4.4.9
+# v1.4.4.10
 ```
 
 ### Locally with Python

tbp_parser/LIMS.py

@@ -347,8 +347,12 @@ def create_lims_report(self):
       drug_name = globals.ANTIMICROBIAL_CODE_TO_DRUG_NAME[antimicrobial_code]
 
       # get the MDL interpretations for all genes **FOR THE LIMS REPORT** associated with this drug             
-      potential_mdl_resistances = globals.DF_LABORATORIAN[globals.DF_LABORATORIAN["antimicrobial"] == drug_name].loc[globals.DF_LABORATORIAN["tbprofiler_gene_name"].isin(gene_dictionary.keys())]["mdl_interpretation"]
+      potential_mdl_resistances = globals.DF_LABORATORIAN[globals.DF_LABORATORIAN["antimicrobial"] == drug_name].loc[globals.DF_LABORATORIAN["tbprofiler_gene_name"].isin(gene_dictionary.keys())]
 
+      # remove any interpretations with failed quality warnings
+      potential_mdl_resistances = potential_mdl_resistances.loc[~potential_mdl_resistances["warning"].str.contains("Failed quality in the mutation position")]
+      potential_mdl_resistances = potential_mdl_resistances["mdl_interpretation"].tolist()
+
       # initalize list of genes responsible for the max resistance
       responsible_gene = set()
 

tbp_parser/__init__.py

@@ -1 +1 @@
-__VERSION__ = "v1.4.4.9"
+__VERSION__ = "v1.4.4.10"