diff --git a/Dockerfile b/Dockerfile index b3adea3..cc8e78c 100644 --- a/Dockerfile +++ b/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" diff --git a/README.md b/README.md index e04fff8..ef0ede5 100644 --- a/README.md +++ b/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 diff --git a/tbp_parser/LIMS.py b/tbp_parser/LIMS.py index c2b6906..e369714 100644 --- a/tbp_parser/LIMS.py +++ b/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() diff --git a/tbp_parser/__init__.py b/tbp_parser/__init__.py index 5b48972..92465a2 100644 --- a/tbp_parser/__init__.py +++ b/tbp_parser/__init__.py @@ -1 +1 @@ -__VERSION__ = "v1.4.4.9" \ No newline at end of file +__VERSION__ = "v1.4.4.10" \ No newline at end of file