Full Code of pha4ge/hAMRonization for AI

Repository: pha4ge/hAMRonization
Branch: master
Commit: c8184233c52b
Files: 98
Total size: 11.9 MB

Directory structure:
gitextract_2sm_t59v/

├── .dockerignore
├── .github/
│   ├── ISSUE_TEMPLATE/
│   │   └── bug_report.md
│   └── workflows/
│       ├── dockerpublish.yml
│       ├── python_publish.yml
│       └── test_package.yml
├── .gitignore
├── Dockerfile
├── LICENSE.txt
├── README.md
├── docs/
│   ├── hAMRonization_specification_details.csv
│   ├── interactive_report_demo.html
│   └── subgrant/
│       └── PHA4GE_AMR_SubGrant_Orientation.pptx
├── hAMRonization/
│   ├── AbricateIO.py
│   ├── AmrFinderPlusIO.py
│   ├── AmrPlusPlusIO.py
│   ├── AribaIO.py
│   ├── CSStarIO.py
│   ├── DeepArgIO.py
│   ├── FARGeneIO.py
│   ├── GrootIO.py
│   ├── Interfaces.py
│   ├── KmerResistanceIO.py
│   ├── MykrobeIO.py
│   ├── README.md
│   ├── ResFamsIO.py
│   ├── ResFinderIO.py
│   ├── RgiIO.py
│   ├── SraxIO.py
│   ├── Srst2IO.py
│   ├── StarAmrIO.py
│   ├── TBProfilerIO.py
│   ├── __init__.py
│   ├── constants.py
│   ├── hAMRonizedResult.py
│   ├── hamronize.py
│   └── summarize.py
├── schema/
│   ├── PHA4GE AMR Gene & Variant Specification.csv
│   ├── PHA4GE AMR Gene & Variant Specification.json
│   └── csv2json.py
├── setup.cfg
├── setup.py
└── test/
    ├── .gitignore
    ├── README.md
    ├── __init__.py
    ├── data/
    │   ├── dummy/
    │   │   ├── abricate/
    │   │   │   └── report.tsv
    │   │   ├── amrfinderplus/
    │   │   │   └── report.tsv
    │   │   ├── amrplusplus/
    │   │   │   └── gene.tsv
    │   │   ├── ariba/
    │   │   │   ├── report.tsv
    │   │   │   └── report_var.tsv
    │   │   ├── deepARG/
    │   │   │   ├── output.mapping.ARG.
    │   │   │   └── output.mapping.potential.ARG
    │   │   ├── fargene/
    │   │   │   └── retrieved-genes-class_A-hmmsearched.out
    │   │   ├── groot/
    │   │   │   └── groot_report.tsv
    │   │   ├── kmerresistance/
    │   │   │   └── results.res
    │   │   ├── mykrobe/
    │   │   │   ├── empty.json
    │   │   │   └── mykrobe.json
    │   │   ├── pointfinder/
    │   │   │   └── PointFinder_results.txt
    │   │   ├── resfams/
    │   │   │   └── resfams.tblout
    │   │   ├── resfinder/
    │   │   │   └── data_resfinder.json
    │   │   ├── rgi/
    │   │   │   ├── rgi.txt
    │   │   │   ├── rgi_orf.txt
    │   │   │   └── rgi_var.txt
    │   │   ├── srax/
    │   │   │   └── sraX_detected_ARGs.tsv
    │   │   ├── srst2/
    │   │   │   └── report.tsv
    │   │   ├── sstar/
    │   │   │   └── report.tsv
    │   │   ├── staramr/
    │   │   │   ├── pointfinder.tsv
    │   │   │   └── resfinder.tsv
    │   │   └── tbprofiler/
    │   │       └── tbprofiler.json
    │   └── raw_outputs/
    │       ├── abricate/
    │       │   └── report.tsv
    │       ├── amrfinderplus/
    │       │   ├── afp_non_coding.tsv
    │       │   ├── empty_report_with_header.tsv
    │       │   ├── hamronized_non_coding.tsv
    │       │   ├── non_coding_contig.fasta
    │       │   ├── report_nucleotide.tsv
    │       │   └── report_protein.tsv
    │       ├── amrplusplus/
    │       │   └── gene.tsv
    │       ├── ariba/
    │       │   └── report.tsv
    │       ├── deeparg/
    │       │   ├── output.mapping.ARG
    │       │   └── output.mapping.potential.ARG
    │       ├── fargene/
    │       │   └── retrieved-genes-class_A-hmmsearched.out
    │       ├── groot/
    │       │   └── report.tsv
    │       ├── kmerresistance/
    │       │   └── results.res
    │       ├── mykrobe/
    │       │   └── report.json
    │       ├── pointfinder/
    │       │   └── PointFinder_results.txt
    │       ├── resfams/
    │       │   └── resfams.tblout
    │       ├── resfinder/
    │       │   ├── ResFinder_results_tab.txt
    │       │   └── data_resfinder.json
    │       ├── rgi/
    │       │   └── rgi.txt
    │       ├── rgibwt/
    │       │   └── Kp11_bwtoutput.gene_mapping_data.txt
    │       ├── srax/
    │       │   └── sraX_detected_ARGs.tsv
    │       ├── srst2/
    │       │   └── SAMN13064234_srst2_report.tsv
    │       ├── sstar/
    │       │   └── report.tsv
    │       ├── staramr/
    │       │   ├── pointfinder.tsv
    │       │   └── resfinder.tsv
    │       └── tbprofiler/
    │           └── tbprofiler.json
    ├── run_integration_test.sh
    ├── test_interfaces.py
    └── test_parsing_validity.py

================================================
FILE CONTENTS
================================================

================================================
FILE: .dockerignore
================================================
.*
*.egg-info
*.pyc
/docs
/test
/schema
__pycache__


================================================
FILE: .github/ISSUE_TEMPLATE/bug_report.md
================================================
---
name: Bug report
about: Create a report to help us improve
title: "[BUG]"
labels: bug
assignees: ''

---

**Describe the bug**
A clear and concise description of what the bug is.

**Input**
The command-line input you used to run your data.

**Input file**
The file you used as an input to run the data.
Either paste a sample or upload the file.

**Error log**
The error that is thrown when you run the process.

**hAMRonization Version**
The version of hAMRonization you are using. Please ensure it is up to date.

**Expected behavior**
A clear and concise description of what you expected to happen.

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Desktop (please complete the following information):**
 - OS: [e.g. iOS]
 - Browser [e.g. chrome, safari]
 - Version [e.g. 22]

**Additional context**
Add any other context about the problem here.
If applicable, include dependency versions such as pandas version and Python version.


================================================
FILE: .github/workflows/dockerpublish.yml
================================================
name: Publish Docker Image

on:
  release:
    types: [published]

jobs:
  main:
    runs-on: ubuntu-latest
    steps:
      -
        name: Set up QEMU
        uses: docker/setup-qemu-action@v1
      -
        name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v1
      -
        name: Login to DockerHub
        uses: docker/login-action@v1 
        with:
          username: ${{ secrets.DOCKERHUB_USERNAME }}
          password: ${{ secrets.DOCKERHUB_TOKEN }}
      -
        name: Build and push
        id: docker_build
        uses: docker/build-push-action@v2
        with:
          push: true
          tags: finlaymaguire/hamronization:latest
          build-args: |
            SOFTWARE_VERSION=${{ github.event.release.tag_name }}
      -
        name: Image digest
        run: echo ${{ steps.docker_build.outputs.digest }}


================================================
FILE: .github/workflows/python_publish.yml
================================================
# This workflow will upload a Python Package using Twine when a release is created
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

name: python_publish

on:
  release:
    types: [created]

jobs:
  pypi-publish:
    name: Publish release to PyPI
    runs-on: ubuntu-latest
    environment:
      name: pypi
      url: https://pypi.org/p/hAMRonization
    permissions:
      id-token: write
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install setuptools wheel
      - name: Build package
        run: |
          python setup.py sdist bdist_wheel  # Could also be python -m build
      - name: Publish package distributions to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1


================================================
FILE: .github/workflows/test_package.yml
================================================
#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: test_package 

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.10.20, 3.11.15, 3.12.13, 3.13.13, 3.14.4]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest
        pip install .
    - name: Lint hAMRonization library with flake8
      run: |
        pushd hAMRonization
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
        popd
    - name: Run sanity tests
      run: |
          pushd test 
          pytest
          popd
    - name: Run crude test of CLI parser for all tools
      run: |
          pushd test
          bash run_integration_test.sh
          popd
    #- name: Validate all harmonized .json files with SALAD schema
    #  run: |
    #    pip install schema_salad
    #    pushd test/data
    #    for f in *.harmonized.json; do schema-salad-tool ../../schema/antimicrobial_resistance_genomic_analysis_result.schema.yml ${f}; done


================================================
FILE: .gitignore
================================================
.DS_Store
*.egg-info
*.pyc
build
dist


================================================
FILE: Dockerfile
================================================
# base image
FROM docker.io/library/python:3.14.4-alpine3.23

# metadata
LABEL org.opencontainers.image.version=1.2.1
LABEL org.opencontainers.image.base.name="docker.io/library/python:3.14.4-alpine3.23"
LABEL org.opencontainers.image.base.digest="sha256:105efb1f600e4e5d216985f6eeda0ed853ff9b38e65877039781f448ed677a0f"
LABEL org.opencontainers.image.title="hAMRronization"
LABEL org.opencontainers.image.title="Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure"
LABEL org.opencontainers.image.source="https://github.com/pha4ge/hAMRonization"
LABEL org.opencontainers.image.documentation="https://github.com/pha4ge/hAMRonization/blob/master/README.md"
LABEL org.opencontainers.image.licenses="LGPL-3.0-only"
LABEL org.opencontainers.image.authors="Finlay Maguire <finlaymaguire@gmail.com>, Marco van Zwetselaar <io@zwets.it>"
LABEL tags="Genomics"

# add bash so Nextflow can run the container
RUN apk add --no-cache bash && rm -rf /var/cache/apk/*

# set the working directory in the container
WORKDIR /hAMRonization

# copy the sources into the container
COPY . /hAMRonization/src

# install dependencies and clean all up
RUN python -m pip --no-cache-dir install ./src && rm -rf ./src

# command to run on container start without args
CMD ["hamronize", "--help"]


================================================
FILE: LICENSE.txt
================================================
                   GNU LESSER GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.


  This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.

  0. Additional Definitions.

  As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.

  "The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.

  An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
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  A "Combined Work" is a work produced by combining or linking an
Application with the Library.  The particular version of the Library
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  The "Minimal Corresponding Source" for a Combined Work means the
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  The "Corresponding Application Code" for a Combined Work means the
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  1. Exception to Section 3 of the GNU GPL.

  You may convey a covered work under sections 3 and 4 of this License
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  2. Conveying Modified Versions.

  If you modify a copy of the Library, and, in your modifications, a
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   ensure that, in the event an Application does not supply the
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   whatever part of its purpose remains meaningful, or

   b) under the GNU GPL, with none of the additional permissions of
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  3. Object Code Incorporating Material from Library Header Files.

  The object code form of an Application may incorporate material from
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================================================
FILE: README.md
================================================
![Python package](https://github.com/pha4ge/hAMRonization/workflows/test_package/badge.svg)
[![Preprint](https://img.shields.io/badge/Preprint-10.1101/2024.03.07.583950-blue)](https://doi.org/10.1101/2024.03.07.583950)
[![DOI](https://zenodo.org/badge/248040662.svg)](https://zenodo.org/badge/latestdoi/248040662)
[![Docs English](https://img.shields.io/badge/Documentation-English-blue)](https://github.com/pha4ge/hAMRonization/blob/master/docs/subgrant/PHA4GE_AMR_SubGrant_Documentation.pdf)
[![Docs English](https://img.shields.io/badge/Documentation-Español-blue)](https://github.com/pha4ge/hAMRonization/blob/master/docs/subgrant/PHA4GE_hAMRonization_espan%CC%83ol.pdf)


# hAMRonization 

This repo contains the hAMRonization module and CLI parser tools combine the outputs of 
17 disparate antimicrobial resistance gene detection tools into a single unified format.

This is an implementation of the [hAMRonization AMR detection specification scheme](docs/hAMRonization_specification_details.csv) which supports gene presence/absence resistance and mutational resistance (if supported by the underlying tool).

This supports a variety of summary options including an [interactive summary](https://finlaymagui.re/assets/interactive_report_demo.html).

![hAMRonization overview](https://github.com/pha4ge/hAMRonization/blob/master/docs/overview_figure.png?raw=true)


## Installation

This tool requires python>=3.9 and [pandas](https://pandas.pydata.org/)
and the latest release can be installed directly from pip, conda, docker, this repository, or from the galaxy toolshed:
```
pip install hAMRonization
```
[![PyPI version](https://badge.fury.io/py/hamronization.svg)](https://badge.fury.io/py/hamronization)
[![PyPI downloads](https://img.shields.io/pypi/dm/hAMRonization.svg)](https://img.shields.io/pypi/dm/hAMRonization)

Or

```
conda create --name hamronization --channel conda-forge --channel bioconda hamronization
```
![version-on-conda](https://anaconda.org/bioconda/hamronization/badges/version.svg)
![conda-download](https://anaconda.org/bioconda/hamronization/badges/downloads.svg)
![last-update-on-conda](https://anaconda.org/bioconda/hamronization/badges/latest_release_date.svg)


Or to install and run using docker, podman, singularity:
```
docker pull docker.io/finlaymaguire/hamronization:latest
docker run --rm docker.io/finlaymaguire/hamronization:latest hamronize --help
```

Or to install the latest development version:
```
git clone https://github.com/pha4ge/hAMRonization
pip install hAMRonization
```

Alternatively, hAMRonization can also be installed and used in [galaxy](https://galaxyproject.org/) via the [galaxy toolshed](https://toolshed.g2.bx.psu.edu/view/iuc/suite_hamronization/904ab154f8f4).

## Usage

**NOTE**: Only the output format used in the "last updated" version of the AMR prediction tool has been tested for accuracy. Older tool versions or updates which lead to a change in output format may not work. 
In theory, this should only be a problem with major version changes but not all tools follow semantic versioning.
If you encounter any issues with newer tool versions then please create an issue in this repository.

```
usage: hamronize <tool> <options>

Convert AMR gene detection tool output(s) to hAMRonization specification format

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

Tools with hAMRonizable reports:
  {abricate,amrfinderplus,amrplusplus,ariba,csstar,deeparg,fargene,groot,kmerresistance,resfams,resfinder,mykrobe,rgi,srax,srst2,staramr,tbprofiler,summarize}
    abricate            hAMRonize abricate's output report i.e., OUTPUT.tsv
    amrfinderplus       hAMRonize amrfinderplus's output report i.e., OUTPUT.tsv
    amrplusplus         hAMRonize amrplusplus's output report i.e., gene.tsv
    ariba               hAMRonize ariba's output report i.e., OUTDIR/OUTPUT.tsv
    csstar              hAMRonize csstar's output report i.e., OUTPUT.tsv
    deeparg             hAMRonize deeparg's output report i.e.,
                        OUTDIR/OUTPUT.mapping.ARG
    fargene             hAMRonize fargene's output report i.e., retrieved-
                        genes-*-hmmsearched.out
    groot               hAMRonize groot's output report i.e., OUTPUT.tsv (from `groot
                        report`)
    kmerresistance      hAMRonize kmerresistance's output report i.e., OUTPUT.res
    resfams             hAMRonize resfams's output report i.e., resfams.tblout
    resfinder           hAMRonize resfinder's JSON output report (use -j to produce)
    mykrobe             hAMRonize mykrobe's output report i.e., OUTPUT.json
    rgi                 hAMRonize rgi's output report i.e., OUTPUT.txt or
                        OUTPUT_bwtoutput.gene_mapping_data.txt
    srax                hAMRonize srax's output report i.e., sraX_detected_ARGs.tsv
    srst2               hAMRonize srst2's output report i.e., OUTPUT_srst2_report.tsv
    staramr             hAMRonize staramr's output report i.e., resfinder.tsv
    tbprofiler          hAMRonize tbprofiler's output report i.e., OUTPUT.results.json
    summarize           Provide a list of paths to the reports you wish to summarize
```

To look at a specific tool e.g. `abricate`:
```
>hamronize abricate -h 
usage: hamronize abricate <options>

Applies hAMRonization specification to output from abricate (OUTPUT.tsv)

positional arguments:
  report                Path to tool report

optional arguments:
  -h, --help            show this help message and exit
  --format FORMAT       Output format (tsv or json)
  --output OUTPUT       Output location
  --analysis_software_version ANALYSIS_SOFTWARE_VERSION
                        Input string containing the analysis_software_version for abricate
  --reference_database_version REFERENCE_DATABASE_VERSION
                        Input string containing the reference_database_version for abricate

```

Therefore, hAMRonizing abricates output:
```
hamronize abricate ../test/data/raw_outputs/abricate/report.tsv --reference_database_version 3.2.5 --analysis_software_version 1.0.0 --format json
```

To parse multiple reports from the same tool at once just give a list of reports as the argument,
and they will be concatenated appropriately (i.e. only one header for tsv)

```
hamronize rgi --input_file_name rgi_report --analysis_software_version 6.0.0 --reference_database_version 3.2.5 test/data/raw_outputs/rgi/rgi.txt test/data/raw_outputs/rgibwt/Kp11_bwtoutput.gene_mapping_data.txt
```

You can summarize hAMRonized reports regardless of format using the 'summarize'
function:

```
> hamronize summarize -h
usage: hamronize summarize <options> <list of reports>

Concatenate and summarize AMR detection reports

positional arguments:
  hamronized_reports    list of hAMRonized reports

optional arguments:
  -h, --help            show this help message and exit
  -t {tsv,json,interactive}, --summary_type {tsv,json,interactive}
                        Which summary report format to generate
  -o OUTPUT, --output OUTPUT
                        Output file path for summary
```

This will take a list of report and create single sorted report in the 
specified format just containing the unique entries across input reports.
This can handle mixed json and tsv hamronized report formats.

```
hamronize summarize -o combined_report.tsv -t tsv abricate.json ariba.tsv
```

The [interactive summary](https://finlaymagui.re/assets/interactive_report_demo.html) option will produce an html file that can be opened within the browser for navigable data exploration (feature developed
with @alexmanuele).

### Using within scripts

Alternatively, hAMRonization can be used within scripts (the metadata must contain the mandatory metadata that is not included in that tool's output, this can be checked by looking at the CLI flags in `hamronize <tool> --help`):

```
import hAMRonization
metadata = {"analysis_software_version": "1.0.1", "reference_database_version": "2019-Jul-28"}
parsed_report = hAMRonization.parse("abricate_report.tsv", metadata, "abricate")
```

The `parsed_report` is then a generator that yields hAMRonized result objects from the parsed report:

```
for result in parsed_report:
      print(result)
```

Alternatively, you can use the `.write` attribute to export all results left in the generator to a file (if a filepath isn't provided, this will write to stdout).

```parsed_report.write('hAMRonized_abricate_report.tsv')```

You can also output a `json` formatted hAMRonized report:

`parsed_report.write('all_hAMRonized_abricate_report.json', output_format='json')`

If you want to write multiple reports to one file, this `.write` method can accept `append_mode=True` to append rather than overwrite the output file and not include the header (in tsv format).

`parsed_report.write('all_hAMRonized_abricate_report.tsv', append_mode=True)`


### Implemented Parsers

Currently implemented parsers and the last tool version for which they have been validated:

1. [abricate](hAMRonization/AbricateIO.py): last updated for v1.0.0
2. [amrfinderplus](hAMRonization/AmrFinderPlusIO.py): last updated for v4.0.3
3. [amrplusplus](hAMRonization/AmrPlusPlusIO.py): last updated for c6b097a
4. [ariba](hAMRonization/AribaIO.py): last updated for v2.14.6
5. [csstar](hAMRonization/CSStarIO.py): last updated for v2.1.0
6. [deeparg](hAMRonization/DeepArgIO.py): last updated for v1.0.2
7. [fargene](hAMRonization/FARGeneIO.py): last updated for v0.1
8. [groot](hAMRonization/GrootIO.py): last updated for v1.1.2
9. [kmerresistance](hAMRonization/KmerResistanceIO.py): late updated for v2.2.0
10. [mykrobe](test/data/raw_outputs/mykrobe/report.json): last updated for v0.8.1
11. ~pointfinder~ (removed, PointFinder is now integrated in ResFinder)
12. [resfams](hAMRonization/ResFamsIO.py): last updated for hmmer v3.3.2
13. [resfinder](hAMRonization/ResFinderIO.py): last updated for v4.6.0
14. [rgi](hAMRonization/RgiIO.py) (includes RGI-BWT) last updated for v5.2.0
15. [srax](hAMRonization/SraxIO.py): last updated for v1.5
16. [srst2](hAMRonization/Srst2IO.py): last updated for v0.2.0
17. [staramr](hAMRonization/StarAmrIO.py): last updated for v0.8.0
18. [tbprofilder](test/data/raw_outputs/tbprofiler/tbprofiler.json): last updated for v3.0.8

## Implementation Details

### hAMRonizedResult Data Structure

The hAMRonization specification is implemented in the [hAMRonizedResult dataclass](https://github.com/pha4ge/harmonized-amr-parsers/blob/master/hAMRonization/hAMRonization/hAMRonizedResult.py#L6).

This is a simple datastructure that uses positional and key-word args to distinguish mandatory from optional hAMRonization fields. 
It also uses type-hinting to validate the supplied values are of the correct type


Each parser follows a similar strategy, using a common interface.
This has been designed to match the `biopython` `SeqIO` `parse` function 

    >>> import hAMRonization
    >>> filename = "abricate_report.tsv"
    >>> metadata = {"analysis_software_version": "1.0.1", "reference_database_version": "2019-Jul-28"}
    >>> for result in hAMRonization.parse(filename, metadata, "abricate"):
    ...    print(result)

Where the final argument to the `hAMRonization.parse` command is whichever tool is being parsed.

### hAMRonizedResultIterator

An abstract iterator is then implemented to ingest a given AMR tool's report
(via the appropriate subclassed implementation), hAMRonize results i.e. translate the 
original inputs to the fields in the hAMRonization specification, and yield a stream of 
hAMRonizedResult dataclasses.

This iterator also implements a write function to enable outputting the contents 
to a output stream or filehandle in either tsv or json format.

### Tool-specific Iterators

Each tool has a specific subclass of this abstract hAMRonizedResultIterator e.g. `AbricateIO.AbricateIterator`.

These include an attribute containing the mapping of the tools original output report fields to the hAMRonized specification fields (`self.field_mapping`), as well as handling specifying any additional required metadata.

The `parse` method of these subclasses then implements the tool-specific parsing logic required.
This is typically a simple `csv.DictReader` but can be more complex such as the json parsing of `resfinder` output, 
or the modification of output fields required to better fit some tools into the hAMRonization specification.


## Contributing 

We welcome contributions for users in any form (from github issues flagging problems/requests) to pull requests of bug fixes or adding new parsers.

## Setting up a Development Environment

First fork this repository and set up a development environment (replacing `YOURUSERNAME` with your github username:

```
git clone https://github.com/YOURUSERNAME/hAMRonization
conda create -n hAMRonization python pip pytest flake8
conda activate hAMRonization
cd hAMRonization
pip install -e .
```

## Testing and Linting

On every commit github actions automatically runs tests and linting to check
the code. 
You can manually run these in your development environment as well.

To run a full set of integration tests:

    pushd test
    bash run_integration_test.sh
    popd

To run unit tests that verify parsing validity for each tool
as well as generation of valid summaries you can use pytest:

    pip install pytest
    pushd test
    pytest
    popd

Finally to run linting and check whether your code matches the project
code style:

    pushd hAMRonization
    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    flake8 . --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
    popd

## Adding a new parser

If you wish to add a parser for a new tool here are the main steps required:

1. Add an entry into `_RequiredToolMetadata` and `_FormatToIterator` in `hAMRonziation/__init__.py` which points to the appropriate `ToolNameIO.py` containing the tool's Iterator subclass

2. In `ToolNameIO.py` add a `required_metadata` list containing any mandatory fields not implemented by the tool

3. Then add a class `ToolNameIterator(hAMRonizedResultIterator)` and implement the `__init__` methods with the approriate mapping (`self.field_mapping`), and metadata (`self.metadata`).

4. To this class, add a `parse` method which reads an opened file stream into a dictionary per line/result (matching the keys of `self.field_mapping`) and yields the output of `self.hAMRonize` being applied to that dictionary.

5. To add a CLI parser for the tool, create a python file in the `parsers` directory:

    ```
    from hAMRonization import Interfaces
    if __name__ == '__main__': 
        Interfaces.cli_parser('toolname')
    ```

Alternatively, the `hAMRonized_parser.py` can be used as a common script interface to all implemented parsers. 

6. Finally, following the template in `test/test_parsing_validity.py`, please generate a unit test that ensures the parser is working as you intend it to!

If you have any questions about any of this or need any help, please file an issue.

## FAQ

* What's the difference between an Antimicrobial Resistance 'Result' and 'Report'?
  * For the purposes of this project, a 'Report' is an output file (or collection of files) from an AMR analysis tool.
    A 'Result' is a single entry in a report. For example, a single line in an abricate report file is a single Antimicrobial
    Resistance 'Result'.
    
### Known Issues

Here are some known issues that we would welcome input on trying to solve!

#### Limitations of specification

- mandatory fields: `gene_symbol` and `gene_name` are confusing and not usually both present (only consistently used in AFP). Means tools either need 1:2 mapping i.e. single output field maps to both `gene_symbol` and `gene_name` OR have fragile text splitting of single field that won't be robust to databases changes.  Current solution is 1:2 mapping e.g. staramr

- inconsistent nomenclature of terms being used in specification fields: target, query, subject, reference. Need to stick to one name for sequence with which the database is being searched, and one the hit that results from that search.

- `sequence_identity`: is sequence type specific %id amino acids != %id nucleotide but does this matter?

- `coverage_depth` seems to include both tool fields that are average depth of read and just plain overall read-count, 

- `contig_id` isn't general enough when some tools this ID naturally corresponds to a `read_name` (deepARG), individual ORF (resfams), or protein sequence (AFP with protein input): *change to `query_id_name` or similar?*

## Citation
If you use hAMRonization please cite the following publication:
> I Mendes et al. 2024. "hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling". bioRxiv. https://doi.org/10.1101/2024.03.07.583950


================================================
FILE: docs/hAMRonization_specification_details.csv
================================================
Interface Label,Required/Optional,Definition,Value Type,Example,Guidance,Comments,
Input File Name,Mandatory,Name or other identifier of an entry from a sample database.,String,ERR3581801,Tools can have multiple input files (genomic/amino acid). Multiple input files will be accomodated by their corresponding parser. ,,
Input Sequence ID,Optional,The identifier of a molecular sequence being analyzed.,String,DAAGAT010000041.1,Can be left blank if not provided.,,
Input Protein Start ,Optional,The position of the first amino acid in a protein sequence being analyzed (input protein sequence). Also known as the query protein start site in a BLAST search. ,Int,6,"The value should be biologically relevant, and should not start with 0. This field only applies to tools providing gene sequence outputs. Can be left blank if output not provided/applicable.","can start at 1 or 0, fmin/fmax (start at 0), NCBI starts at 1 but CARD database starts at 0",
Input Protein Stop ,Optional,The position of the last amino acid in a protein sequence being analyzed (input protein sequence). Also known as the query protein stop site in a BLAST search. ,Int,307,This field only applies to tools providing gene sequence outputs. Can be left blank if output not provided/applicable.,,
Input Gene Start ,Optional,The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). Also known as the query gene start site in a BLAST search. ,Int,18,,,
Input Gene Stop,Optional,The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). Also known as the query gene stop site in a BLAST search. ,Int,921,,,
Reference Protein Start ,Optional,The position of the first amino acid in a reference protein sequence (sequence being used for comparison). Also known as the subject protein start site in a BLAST search. ,Int,1,This field only applies to tools providing amino acid sequence outputs. Can be left blank if output not provided/applicable.,,
Reference Protein Stop ,Optional,The position of the last amino acid in a reference protein sequence (sequence being used for comparison). Also known as the subject protein stop site in a BLAST search.,Int,300,This field only applies to tools providing gene sequence outputs. Can be left blank if output not provided/applicable.,,
Reference Gene Start ,Optional,The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). Also known as the subject gene start site in a BLAST search.,Int,1,,,
Reference Gene Stop ,Optional,The position of the last nucelotide in a reference sequence (sequence being used for comparison). Also known as the subject gene stop site in a BLAST search.,Int,900,,,
Strand Orientation,Optional,The orientation of a gene in a double stranded DNA replicon. ,String,"(+), sense","Values should be sense or antisense, or the corresponding short form ""+"" or ""-"". The terms ""positive"" and ""negative"" should be avoided. Can be left blank if not provided.","sense or antisense, or use short hand +/-",
Gene Symbol,Mandatory,The short name of a gene or gene product; a single word that does not contain white space characters. It is typically derived from the gene/gene product name.,String,"catA1, blaOXA-101","Acceptable values may represent gene symbols or gene product symbols. ""Gene symbol"" and ""allele"" (based on amino acid variations) may be used interchangeably due to nuances in resistance gene family nomenclature. Parsers should include values from ""gene symbol"" and ""allele"" fields in this category. Either the ""gene symbol"" or the ""gene name"" must be provided.","every aa diff for beta lactamases is a new allele, not the case for all amr gene families; novel allele, leave it blank","Comment: I don't think if it's a novel allele, this should be blank (hence why it's mandatory); it should instead say 'blaOXA', just without a number afterwards designating a specific allele (or it will alternatively list the allele with closest homology)"
Gene Name,Mandatory,"The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.",String,type A-1 chloramphenicol O-acetyltransferase ,"The long name for the gene/protein. Gene names or gene product names are acceptable.  Either the ""gene symbol"" or the ""gene name"" must be provided.",stress long form (describes protein); gene name or protein name?,
Coverage (depth),Optional,Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.,Float,56,The value is expressed as a fold value e.g. 56x.,,
Coverage (%),Optional,The percentage of the reference sequence covered by the sequence of interest.,Float,90,"The sequences can refer to reads and genome, nucelotides and genes, or amino acids and proteins. This value should be normalized and expressed as percentage. Do not include the ""%"" sign in the value. Either ""% Coverage (breadth)"" of ""Coverage (breadth) is required.","Comment: I think this should be mandatory; if you have a hit for a gene, the first question you have is the % identity and % length. This is necessary context to determine whether it's likely a functional protein.",
Coverage (ratio),Optional,The ratio of the reference sequence covered by the sequence of interest.,,450/500,"The sequences can refer to reads and genome, nucelotides and genes, or amino acids and proteins. This value should not be normalized and expressed as the ratio of actual positions being compared e.g. 450/500. Either ""% Coverage (breadth)"" of ""Coverage (breadth) is required.",,
Sequence Identity,Optional,Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.,Float,1,"The sequences can refer to reads and genome, nucelotides and genes, or amino acids and proteins. The value should be expressed as a percentage. Do not include the ""%"" sign in the value.",,
Reference Database ID,Mandatory,"Database containing references genomes for genome annotation, gene identification, characterization etc.",String,"ncbi, ResFinder",,,
Reference Database Version,Mandatory,Version of a particular database.,String,,,ISSUE: No standards available for database versioning,
Reference Accession,Mandatory,"A persistent, unique identifier of a molecular sequence database entry.",String,NF000491.1 ,,,
Reference Gene Length,Optional,The length (number of positions) of a gene sequence being used as a reference for comparison.,Int,657,,"more specific term under ""Genetic Sequence Length (NCIT:C135487)""",
Reference Protein Length,Optional,The length (number of positions) of a protein sequence being used as a reference for comparison.,Int,219,,,
Input Gene Length,Optional,The length (number of positions) of a gene sequence being analyzed (input gene sequence).,Int,657,,"more specific term under ""Genetic Sequence Length (NCIT:C135487)""",
Input Protein Length,Optional,The length (number of positions) of a protein sequence being analyzed (input protein sequence).,Int,219,,,
Drug Class,Optional,"A set of medications and other compounds that have similar chemical structures, the same mechanism of action (i.e., bind to the same biological target), a related mode of action, and/or are used to treat the same disease.",String,Phenicol,Standardized terms from the ChEBI ontology should be used. Find terms using https://www.ebi.ac.uk/ols/ontologies/chebi. Can be left blank if not provided.,,
Antimicrobial Agent ,Optional,"A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.",String,CHLORAMPHENICOL,This should describe a specific agent. Standardized terms from the ChEBI ontology should be used. Find terms using https://www.ebi.ac.uk/ols/ontologies/chebi. Can be left blank if not provided.,,
Resistance mechanism,Optional,Cellular processes in a pathogen that result in antimicrobial drug resistance.,String,target alteration,Standardized terms from the ChEBI ontology should be used. Find terms using https://www.ebi.ac.uk/ols/ontologies/aro. Can be left blank if not provided. ,,
Analysis Software Name,Mandatory,"The name of a computer package, application, method or function.",String,amrfinder,Not typically included in an AMR prediction output. The user may have to provide the value.,,
Analysis Software Version,Mandatory,"A version number is a unique number or set of numbers assigned to a specific release of a software program, file, firmware, device driver, or even hardware. Typically, as updates and entirely new editions of a program or driver are released, the version number will increase.",String,1.2.5,Not typically included in an AMR prediction output. The user may have to provide the value. Semantic versioning is strongly recommended.,https://semver.org/,"Comment: the version of the gene database is more typical than the software, so this should perhaps not be required"
Genetic Variation Type,Mandatory,"The type of genetic variant (e.g. gene presence, gene absence, protein variant, nucleotide variant).",String,protein_mutation,,,
Variant Frequency,Optional,The frequency of the variant in the data.,Float,0.5,,,
Nucleotide Mutation,Optional,The nucleotide sequence change(s) detected in the sequence being analyzed compared to a reference in HGVS format.,String,c.1349C>T,,,
Nucleotide Mutation Interpretation,Optional,The description of the HGVS encoded nucelotide mutation(s) for clinical interpretation. ,String,This is a subst found in rpoB at position 1349 where the reference has a C and the sample has a T,,,
Protein Mutation,Optional,The protein sequence change(s) detected in the sequence being analyzed compared to a reference in HGVS format.,String,p.Ser450Leu,,,
Protein Mutation Interpretation,Optional,The description of the HGVS encoded protein mutation(s) for clinical interpretation. ,String,This is a amino acid subst found in rpoB at position 450 where the reference has a Serine and the sample has a Leucine,,,


================================================
FILE: docs/interactive_report_demo.html
================================================
<!DOCTYPE html>
<html>
  <head>
    <title>hAMRonized Results</title>
    <link rel='icon' href="https://pha4ge.org/wp-content/uploads/2020/06/logo-clear.png">
    <!-- Required meta tags -->
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
    <!-- Bootstrap CSS -->
    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
    <!-- custom CSS. Must be after botostrap -->
    <!-- pha4ge dark blue: #1c4f77 -->
    <!-- pha4ge light blue: #4879a1 -->
    <style>
      .search_hit{
        background-color: paleturquoise;
      }
      .selected{
        background-color: gold;
      }
      .search_hit.selected{
        background-color: springgreen;
      }
      .amr_hit:hover{
        background-color: lemonchiffon;
      }
      td
        {
          padding:0 15px;
         }
      .phage-blue{
        background-color: #1c4f77;
        color: white;
      }
      .phage-blue-light{
        background-color: #4879a1;
        color: white;
      }
      .sticky{
        position: sticky;
        top: 6rem;
      }
      .selection-bar{
        max-height: 48rem;
      }
      .data-display{
        max-height: 36rem;
      }
      .scroll-x{
        overflow-x: auto;
      }
      .scroll-y{
        overflow-y: auto;
      }
    /* custom table bg-colors
    currently broken. TODO make it work... breaks hover.
    .table-striped>tbody>tr:nth-child(even)>td,
    .table-striped>tbody>tr:nth-child(even)>th {
       background-color: ##99d8c9; // Choose your own color here
     }
   .table-striped>tbody>tr:nth-child(odd)>td,
   .table-striped>tbody>tr:nth-child(odd)>th {
      background-color: #e5f5f9; // Choose your own color here
    } */
    </style>
  </head>
  <body>
    <!-- Navbar -->
    <nav class="navbar sticky-top navbar-light bg-light">
        <a class="navbar-brand" href="#">
          <img src="https://pha4ge.org/wp-content/uploads/2020/04/logob.png" width="320" height="74" alt="">
        </a>
        <div class="form-inline my-2 my-lg-0">
      <input id="gene-search" class="form-control mr-sm-2" onkeyup="geneSearch()" placeholder="Search" aria-label="Search">
      <button id="results-only" class="btn btn-outline-success my-2 my-sm-0" onclick="showOnlyResults()">Show Only Genomes With Hits</button>
      <button id="restore-table" class="btn btn-outline-primary my-2 my-sm-0" onclick="restoreTable()" style="display:none">Restore Results</button>
    </div>

    </nav>
    <div class="container-flex">
      <div class="row">
        <div class="col col-lg-9 col-md-12" id="dynamic-table">
            <!--<input type='button' onclick='CreateTableFromJSON()' value='make table'/>-->
        </div>
        <div class="col">
          <div class="sticky selection-bar scroll-y">
            <div class="row">
              <div class="col">
                <div class="card">
                    <div class="card-header phage-blue-light">
                      Search Results
                    </div>
                    <ul class="list-group list-group-flush">
                      <li class="list-group-item d-flex justify-content-between align-items-center">Total hits:<span class="badge badge-primary badge-pill" id="nhits-badge">0</span></li>
                      <li class="list-group-item d-flex justify-content-between align-items-center">Genomes with hits:<span class="badge badge-primary badge-pill" id="ngenomes-badge">0</span></li>
                      <li class="list-group-item d-flex justify-content-between align-items-center">Tools with hits:<span class="badge badge-primary badge-pill" id="ntools-badge">0</span></li>
                      <li class="list-group-item d-flex justify-content-between align-items-center">
                        <div>
                          <span data-toggle="tooltip" data-placement="bottom" class="badge badge-dark text-light badge-pill" title="Indicates the number of genomes in which at least one tool found a hit matching the search query, but not all tools did.">
                            ?
                          </span>
                          Differential results:
                        </div>
                        <span class="badge badge-primary badge-pill" id="ndiff-badge">0</span>
                      </li>
                    </ul>
                  </div>
                </div>
              </div>

          <div class="row">
            <div class="col">
              <div class="card">
                <div class="card-header phage-blue-light">
                  Selected
                </div>
                <ul id="selected-genes" class="list-group list-group-flush">
                  <!--populated by JS -->
                </ul>
                <div class="row">
                  <div class="col-6">
                    <button type="button" class="btn btn-info btn-block selection-button" onclick="displayAmrData()" disabled>Compare</button>
                  </div>
                  <div class="col-6">
                    <button type="button" class="btn btn-warning btn-block selection-button" onclick="clearSelected()" disabled>Clear</button>
                  </div>
                </div>
              </div>
            </div>
          </div>
        </div>
        </div>
      </div>
   </div>
   <div id="select-container" class="container-flex phage-blue-light">
     <div class="row bg-light">
       <div class="container-fluid"  id="data-display">
       </div>
     </div>
  </div>
 <!-- JavaScript -->
 <!-- jQuery first, then Popper.js, then Bootstrap JS -->
 <script src="https://code.jquery.com/jquery-3.4.1.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"></script>
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 <script type='text/javascript'>
//parse JSON
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