Merge branch 'develop' of https://github.com/metagentools/MetaCoAG in…

…to develop

.github/workflows/pypi-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/testing_python_conda.yml

@@ -0,0 +1,45 @@
+name: CI conda
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    strategy:
+      matrix:
+        os: [macos-12, ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+        with:
+          fetch-depth: 0
+
+      # Setup conda env
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: metacoag
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: "Setup graphbin on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      
+      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=graphbin --cov-report=xml --cov-append

README.md

@@ -10,7 +10,7 @@
 [![PyPI version](https://badge.fury.io/py/metacoag.svg)](https://badge.fury.io/py/metacoag)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/metacoag/badges/downloads.svg)](https://anaconda.org/bioconda/metacoag)
 
-[![CI](https://github.com/metagentools/MetaCoAG/actions/workflows/testing.yml/badge.svg)](https://github.com/metagentools/MetaCoAG/actions/workflows/testing.yml)
+[![CI](https://github.com/metagentools/MetaCoAG/actions/workflows/testing_python.yml/badge.svg)](https://github.com/metagentools/MetaCoAG/actions/workflows/testing_python.yml)
 ![GitHub](https://img.shields.io/github/license/Vini2/MetaCoAG)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![CodeQL](https://github.com/metagentools/MetaCoAG/actions/workflows/codeql.yml/badge.svg)](https://github.com/metagentools/MetaCoAG/actions/workflows/codeql.yml)

docs/citation.md

@@ -32,3 +32,4 @@ URL = {https://doi.org/10.1089/cmb.2022.0262},
 eprint = {https://doi.org/10.1089/cmb.2022.0262},
 abstract = { Metagenomics enables the recovery of various genetic materials from different species, thus providing valuable insights into microbial communities. Metagenomic binning group sequences belong to different organisms, which is an important step in the early stages of metagenomic analysis pipelines. The classic pipeline followed in metagenomic binning is to assemble short reads into longer contigs and then bin these resulting contigs into groups representing different taxonomic groups in the metagenomic sample. Most of the currently available binning tools are designed to bin metagenomic contigs, but they do not make use of the assembly graphs that produce such assemblies. In this study, we propose MetaCoAG, a metagenomic binning tool that uses assembly graphs with the composition and coverage information of contigs. MetaCoAG estimates the number of initial bins using single-copy marker genes, assigns contigs into bins iteratively, and adjusts the number of bins dynamically throughout the binning process. We show that MetaCoAG significantly outperforms state-of-the-art binning tools by producing similar or more high-quality bins than the second-best binning tool on both simulated and real datasets. To the best of our knowledge, MetaCoAG is the first stand-alone contig-binning tool that directly makes use of the assembly graph information along with other features of the contigs. }
 }
+```

docs/usage.md

@@ -98,4 +98,14 @@ metacoag --assembler megahit --graph /path/to/graph_file.gfa --contigs /path/to/
 
 ```
 metacoag --assembler flye --graph /path/to/assembly_graph.gfa --contigs /path/to/assembly.fasta --paths /path/to/assembly_info.txt --abundance /path/to/abundance.tsv --output /path/to/output_folder
-```
+```
+
+# Output
+
+The output of MetaCoAG will contain the following main files and folders.
+
+* `contig_to_bin.tsv` containing the comma separated records of `contig id, bin number`
+* `bins` containing the identified bins (FASTA file for each bin)
+* `low_quality_bins` containing the identified low-quality bins, i.e., having a fraction of marker genes lower than `bin_mg_threshold` (FASTA file for each bin)
+* `*.frag.faa`, `*.frag.ffn` and `*.frag.gff` files containing FragGeneScan output
+* `*.hmmout` containing HMMER output