Metadata-Version: 2.1
Name: abritamr
Version: 1.0.7
Summary: Running AMRFinderPlus for MDU
Home-page: https://github.com/MDU-PHL/abritamr
Author: Kristy Horan
Author-email: kristyhoran15@gmail.com
Maintainer: Kristy Horan
Maintainer-email: kristyhoran15@gmail.com
License: UNKNOWN
Description: # abriTAMR
        
        [![CircleCI](https://circleci.com/gh/MDU-PHL/abritamr.svg?style=svg&circle-token=a54d59b013a30a507621695e738f0a72e47d6969)](https://circleci.com/gh/MDU-PHL/abritamr)
        
        **_Taming the AMR beast_**
        
        abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or  list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.
        
        _abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia._
        
        ## New look in v 1.0.0
        
        * Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
        * Streamlined output.
        * Presence of virulence factors
        
        ## Install
        
        
        abriTAMR requires [AMRFinder Plus](https://github.com/ncbi/amr), this can be installed with `conda` alone or as part of the abriTAMR `conda` installation (see below).
        
        ```
        conda create -n abritamr -c bioconda ncbi-amrfinder
        conda activate abritamr
        amrfinder -U (to download and install recent DB)
        pip3 install abritamr
        ```
        
        
        ## Command-line tool
        
        ```bash
        abritamr run --help
        
        optional arguments:
          -h, --help            show this help message and exit
          --contigs CONTIGS, -c CONTIGS
                                Tab-delimited file with sample ID as column 1 and path
                                to assemblies as column 2 OR path to a contig file
                                (used if only doing a single sample - should provide
                                value for -pfx). (default: )
          --prefix PREFIX, -px PREFIX
                                If running on a single sample, please provide a prefix
                                for output directory (default: abritamr)
          --species {Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes,Vibrio_cholerae}, -sp {Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes,Vibrio_cholerae}
                                Set if you would like to use point mutations, please
                                provide a valid species. (default: )
          --jobs JOBS, -j JOBS  Number of AMR finder jobs to run in parallel.
                                (default: 16)
        ```
        
        You can also run abriTAMR in `mdu` mode, this will output a spreadsheet which is based on reportable/not-reportable requirements in Victoria. You will need to supply a quality control file (comma separated) (`-q`), with the following columns:
        
        * ISOLATE
        * SPECIES_EXP (the species that was expected)
        * SPECIES_OBS (the species that was observed during the quality control analysis)
        * TEST_QC (PASS or FAIL)
        
        `--sop` refers to the type of collation and reporting pipeline
        * general
          * standard reporting structure for aquired genes, output as reportable and non-reportable
        * salmonella
          * Inferred AST based on validation undertaken at MDU
        
        ```abritamr mdu --help            
          --qc QC, -q QC        Name of checked MDU QC file. (default: )
          --runid RUNID, -r RUNID
                                MDU RunID (default: Run ID)
          --matches MATCHES, -m MATCHES
                                Path to matches, concatentated output of abritamr
                                (default: summary_matches.txt)
          --partials PARTIALS, -p PARTIALS
                                Path to partial matches, concatentated output of
                                abritamr (default: summary_partials.txt)
          --sop {general,salmonella}
                                The MDU pipeline for reporting results. (default:
                                general)
        
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7, <4
Description-Content-Type: text/markdown
