From 402a8441c44386dfb96a91dc21ddf8072ebd4266 Mon Sep 17 00:00:00 2001
From: Luis Pedro Coelho <luis@luispedro.org>
Date: Tue, 19 Dec 2023 13:27:49 +1000
Subject: [PATCH] DOC barebones rtd (by copying README)

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+# argNorm
+
+[![Python package](https://github.com/BigDataBiology/argNorm/actions/workflows/python-package.yml/badge.svg)](https://github.com/BigDataBiology/argNorm/actions/workflows/python-package.yml)
+[![Downloads](https://pepy.tech/badge/argNorm)](https://pepy.tech/project/argNorm)
+![](https://img.shields.io/badge/status-alpha-red?style=flat) 
+
+Antibiotic resistance gene (ARG) normalization by mapping to the [antibiotic resistance ontology (ARO)](https://obofoundry.org/ontology/aro.html) by CARD.
+
+Right now, many tools exist for annotating ARGs in genomes and metagenomes.
+However, each tool will output in its own format.
+The [hAMRonization](https://github.com/pha4ge/hAMRonization) package can normalize file formats, but each tool will use different names/identifiers (_e.g._, `TetA` or `TETA` or `tet(A)` or `tet-A` are all different ways to spell the same gene name).
+For a small number of isolate genomes, a human user can still quickly evaluate the outputs.
+However, for metagenomics, especially for large-scale projects, this becomes infeasible.
+Thus, `argNorm` normalizes the _output vocabulary_ of these tools by mapping all tools to the same ontology (ARO).
+
+This is a beta-quality implementation (subject to changes and some bugs may remain), but you're welcomed to try it and provide feedback.
+
+We welcome your feedback on the [Issues Page](https://github.com/BigDataBiology/argNorm/issues). 
+
+## Supported tools
+
+Note that CARD RGI already uses ARO, thus there is no need to use argNorm.
+
+- [x] [DeepARG](https://bench.cs.vt.edu/deeparg) (v1.0.2)
+- [x] [ARGs-OAP](https://galaxyproject.org/use/args-oap/) (v2.3)
+- [x] [ABRicate](https://github.com/tseemann/abricate) (v1.0.1) with NCBI (v3.6), ResFinder (v4.1.11), MEGARes (v2.0), ARG-ANNOT (v5)
+- [x] [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder/src/master/) (v4.0)
+- [x] [AMRFinderPlus](https://github.com/ncbi/amr) (v3.10.30)
+<!-- Hamronized output
+
+- [x] [deeparg](https://bitbucket.org/gusphdproj/deeparg-largerepo/src/master/database/v2/features.fasta)
+- [x] [sarg](https://smile.hku.hk/SARGs/static/images/Ublastx_stageone2.3.tar.gz)
+- [x] [ncbi](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMRProt)
+- [x] [argannot](https://github.com/tseemann/abricate/tree/master/db/argannot)
+- [x] [megares](https://github.com/tseemann/abricate/tree/master/db/megares)
+- [x] [resfinder](https://bitbucket.org/genomicepidemiology/resfinder_db) -->
+
+<!-- Raw output
+
+- [x] [deeparg](https://bitbucket.org/gusphdproj/deeparg-largerepo/src/master/database/v2/features.fasta)
+- [ ] [sarg](https://smile.hku.hk/SARGs/static/images/Ublastx_stageone2.3.tar.gz)
+- [x] [ncbi](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMRProt)
+- [x] [argannot](https://github.com/tseemann/abricate/tree/master/db/argannot)
+- [x] [megares](https://github.com/tseemann/abricate/tree/master/db/megares)
+- [ ] [resfinder](https://bitbucket.org/genomicepidemiology/resfinder_db) -->
+
+## Installation
+
+```bash
+pip install argnorm
+```
+
+## Basic usage
+
+Use `argnorm -h` to see available options.
+
+```bash
+argnorm [tool] -i [original_annotation.tsv] -o [annotation_result_with_aro.tsv]
+```
+
+## Examples
+
+```bash
+argnorm argsoap --mode reads -i examples/raw/args-oap.sarg.reads.tsv -o tmp
+argnorm argsoap --mode reads -i examples/hamronized/args-oap.sarg.reads.tsv -o tmp --hamronized
+argnorm argsoap --mode orfs -i examples/raw/args-oap.sarg.orfs.tsv -o tmp
+argnorm argsoap --mode orfs -i examples/hamronized/args-oap.sarg.orfs.tsv -o tmp --hamronized
+
+argnorm deeparg -i examples/raw/deeparg.deeparg.orfs.tsv -o tmp
+argnorm deeparg -i examples/hamronized/deeparg.deeparg.orfs.tsv -o tmp --hamronized
+
+argnorm abricate --db ncbi -i examples/raw/abricate.ncbi.tsv -o tmp
+argnorm abricate --db megares -i examples/raw/abricate.megares.tsv -o tmp
+argnorm abricate --db argannot -i examples/raw/abricate.argannot.tsv -o tmp
+
+argnorm abricate --db ncbi -i examples/hamronized/abricate.ncbi.tsv -o tmp --hamronized
+argnorm abricate --db megares -i examples/hamronized/abricate.megares.tsv -o tmp --hamronized
+argnorm abricate --db argannot -i examples/hamronized/abricate.argannot.tsv -o tmp --hamronized
+argnorm abricate --db resfinder -i examples/hamronized/abricate.resfinder.tsv -o tmp --hamronized
+
+argnorm resfinder -i examples/raw/resfinder.resfinder.orfs.tsv -o outputs/raw/resfinder.resfinder.orfs.tsv
+argnorm resfinder -i examples/raw/resfinder.resfinder.reads.tsv -o outputs/raw/resfinder.resfinder.reads.tsv
+
+argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.tsv
+
+```
diff --git a/mkdocs.yml b/mkdocs.yml
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+site_name: "argNorm: Normalize ARG annotations to ARO"
+repo_url: "https://github.com/BigDataBiology/argNorm"
+repo_name: "GitHub"
+
+theme:
+    name: readthedocs
+    highlightjs: true
+    html_show_sourcelink: false
+    prev_next_buttons_location: both
+
+nav:
+        - 'argNorm': index.md
+