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Merge pull request #18 from moshi4/develop
Bump to v2.0.0
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‎.github/workflows/ci.yml‎

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jobs:
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CI:
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Python ${{ matrix.python-version}}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Poetry
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- name: Install Rye
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
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echo "$HOME/.rye/shims" >> $GITHUB_PATH
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- name: Install Dependencies
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run: poetry install -n
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- name: Setup Python ${{matrix.python-version}} & Dependencies
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run: |
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rye pin ${{ matrix.python-version }}
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rye sync --update-all --all-features
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- name: Run ruff lint check
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run: poetry run ruff check --diff
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run: rye run ruff check --diff
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- name: Run ruff format check
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run: poetry run ruff format --check --diff
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run: rye run ruff format --check --diff
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- name: Run pytest
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run: poetry run pytest
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run: rye run pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src | tee pytest-coverage.txt
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- name: Pytest Coverage Comment
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uses: MishaKav/pytest-coverage-comment@main
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with:
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pytest-coverage-path: pytest-coverage.txt
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junitxml-path: pytest.xml
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if: ${{ matrix.os=='ubuntu-latest' && matrix.python-version=='3.12' }}

‎.github/workflows/publish_to_pypi.yml‎

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on:
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release:
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types: [released]
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workflow_dispatch:
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jobs:
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publish_to_pypi:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install Poetry
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- name: Install Rye
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
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echo "$HOME/.rye/shims" >> $GITHUB_PATH
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- name: Build
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run: poetry build
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run: rye build
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- name: Publish
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run: poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD
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run: rye publish -u $PYPI_USERNAME --token $PYPI_PASSWORD -y

‎.gitignore‎

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output/
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example/
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.vscode/
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notebooks/
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**.fna.gz
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.pot
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# Django stuff:
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*.log
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# *.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.11.6
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hooks:
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- id: ruff
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name: ruff lint check
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types_or: [python, pyi]
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args: [--fix]
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- id: ruff-format
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name: ruff format check
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types_or: [python, pyi]

‎README.md‎

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## Installation
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`Python 3.8 or later` is required for installation.
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`Python 3.9 or later` is required for installation.
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[fastANI](https://github.com/ParBLiSS/FastANI) or [skani](https://github.com/bluenote-1577/skani) is required to calculate ANI.
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**Install bioconda package:**
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1. Calculate ANI between all-vs-all microbial genomes by fastANI (or skani).
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If no similarity detected by fastANI, NA is output. In that case, NA is replaced by 0.0.
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If previous result available at the time of re-run, reuse previous result.
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2. Clustering ANI matrix by scipy's UPGMA method.
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2. Clustering ANI matrix by scipy UPGMA method.
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3. Using clustered matrix, draw ANI clustermap by seaborn.
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## Usage
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### Options
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$ ANIclustermap --help
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usage: ANIclustermap -i [Genome fasta directory] -o [output directory]
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Draw ANI(Average Nucleotide Identity) clustermap
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optional arguments:
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-i I, --indir I Input genome fasta directory (*.fa|*.fna[.gz]|*.fasta)
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-o O, --outdir O Output directory
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-m , --mode ANI calculation mode ('fastani'[default]|'skani')
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-t , --thread_num Thread number parameter (Default: MaxThread - 1)
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--overwrite Overwrite previous ANI calculation result (Default: OFF)
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--fig_width Figure width (Default: 10)
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--fig_height Figure height (Default: 10)
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--dendrogram_ratio Dendrogram ratio to figsize (Default: 0.15)
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--cmap_colors cmap interpolation colors parameter (Default: 'lime,yellow,red')
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--cmap_gamma cmap gamma parameter (Default: 1.0)
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--cmap_ranges Range values (e.g. 80,90,95,100) for discrete cmap (Default: None)
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--cbar_pos Colorbar position (Default: (0.02, 0.8, 0.05, 0.18))
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--annotation Show ANI value annotation (Default: OFF)
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--annotation_fmt Annotation value format (Default: '.3g')
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-v, --version Print version information
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-h, --help Show this help message and exit
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Usage: ANIclustermap [OPTIONS]
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Draw ANI(Average Nucleotide Identity) clustermap
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╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────╮
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│ * --indir -i Input genome fasta directory (*.fa|*.fna[.gz]|*.fasta) [required] │
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│ * --outdir -o Output directory [required] │
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│ --mode ANI calculation tool (fastani|skani) [default: fastani] │
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│ --thread_num -t Thread number parameter [default: MaxThread - 1] │
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│ --overwrite Overwrite previous ANI calculation result │
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│ --fig_width Figure width [default: 10] │
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│ --fig_height Figure height [default: 10] │
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│ --dendrogram_ratio Dendrogram ratio to figsize [default: 0.15] │
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│ --cmap_colors cmap interpolation colors parameter [default: lime,yellow,red] │
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│ --cmap_gamma cmap gamma parameter [default: 1.0] │
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│ --cmap_ranges Range values (e.g. 80,90,95,100) for discrete cmap │
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│ --cbar_pos Colorbar position [default: 0.02, 0.85, 0.04, 0.15] │
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│ --annotation Show ANI value annotation │
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│ --annotation_fmt Annotation value format [default: .3g] │
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│ --quiet No print log on screen │
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│ --version -v Print version information │
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│ --help -h Show this message and exit. │
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╰──────────────────────────────────────────────────────────────────────────────────────────────────────╯
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### Example Command
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7 genomes minimal dataset. Click [here](https://github.com/moshi4/ANIclustermap/wiki/dataset/minimal_dataset.zip) to download dataset (Size=3.6MB).
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7 genomes minimal dataset. Click [here](https://github.com/moshi4/ANIclustermap/raw/main/example/input/minimal_dataset.zip) to download dataset.
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ANIclustermap -i ./minimal_dataset/ -o ./ANIclustermap_result
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## Output Contents
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ANIclustermap outputs 3 types of files.
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ANIclustermap outputs 3 types of result files.
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- **`ANIclustermap.[png|svg]`** ([example1](https://github.com/moshi4/ANIclustermap/blob/main/example/output/05_normal_dataset/ANIclustermap.png), [example2](https://github.com/moshi4/ANIclustermap/blob/main/example/output/06_normal_dataset_annotation/ANIclustermap.png))
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ANI clustermap result figure.
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## Gallery
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Example gallery of 33 genomes normal dataset.
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If you want to try it for yourself, click [here](https://github.com/moshi4/ANIclustermap/wiki/dataset/normal_dataset.zip) to donwload dataset (Size=63.5MB).
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If you want to try it for yourself, click [here](https://github.com/moshi4/ANIclustermap/raw/main/example/input/normal_dataset.zip) to donwload dataset.
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**Normal parameter:**
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result01 \
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--fig_width 15
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![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/01_ANIclustermap.png)
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**Change cmap_gamma parameter:**
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result02 \
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--fig_width 15 --cmap_gamma 0.5
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![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/02_ANIclustermap.png)
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**Change cmap_colors(=white,orange,red) paramter:**
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result03 \
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![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/03_ANIclustermap.png)
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**Change cmap_ranges paramter:**
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result04 \
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> See [this issue](https://github.com/moshi4/ANIclustermap/issues/1) for more details.
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**Add ANI value annotation parameter:**
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
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ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result05 \
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![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/05_ANIclustermap.png)

‎example/example_run.sh‎

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ANIclustermap -i ./input/minimal_dataset -o ${OUTDIR}/01_minimal_dataset \
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--fig_width 8 --fig_height 5
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ANIclustermap -i ./input/minimal_dataset -o ${OUTDIR}/02_minimal_dataset_annotation \
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--fig_width 8 --fig_height 5 --annotation
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--fig_width 8 --fig_height 5 --annotation
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ANIclustermap -i ./input/small_dataset -o ${OUTDIR}/03_small_dataset \
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--fig_width 15
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--fig_width 15
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ANIclustermap -i ./input/small_dataset -o ${OUTDIR}/04_small_dataset_annotation \
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--fig_width 15 --annotation
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--fig_width 15 --annotation
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/05_normal_dataset \
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--fig_width 15
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--fig_width 15
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/06_normal_dataset_annotation \
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--fig_width 20 --annotation
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--fig_width 20 --annotation
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# Normal parameter
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result01 \
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--fig_width 15
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# Change cmap_gamma parameter
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result02 \
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--fig_width 15 --cmap_gamma 0.5
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# Change cmap_colors parameter
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result03 \
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--fig_width 15 --cmap_colors white,orange,red
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# Change cmap_ranges parameter
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result04 \
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--fig_width 15 --cmap_ranges 80,85,90,92.5,95,97.5,100
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# Add ANI value annotation parameter
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ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result05 \
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--fig_width 20 --fig_height 15 --annotation

‎example/input/minimal_dataset.zip‎

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‎example/input/normal_dataset.zip‎

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‎example/input/small_dataset.zip‎

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‎example/output/01_minimal_dataset/ANIclustermap.png‎

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