Merge pull request #9 from maxibor/dev

Version 1.0.0-beta

.github/workflows/publish_pypi.yml

@@ -1,25 +1,25 @@
 name: publish-pypi
 
-on: 
+on:
   release:
     types: [published, edited]
 
 jobs:
-    build-and-publish:
-      name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
-      runs-on: ubuntu-18.04
-      steps:
-        - uses: actions/checkout@v1
-        - name: Setup Python 3.7
-          uses: actions/setup-python@v1
-          with:
-            python-version: 3.7
-        - name: Build sam2lca
-          run: |
-            pip install wheel
-            python setup.py sdist bdist_wheel
-        - name: Publish distribution 📦 to PyPI
-          uses: pypa/gh-action-pypi-publish@master
-          with:
-            password: ${{ secrets.PYPI_TOKEN }}
-
+  build-and-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.9"
+      - name: Build sam2lca
+        run: |
+          pip install wheel
+          python setup.py sdist bdist_wheel
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/sam2lca_ci.yml

@@ -2,17 +2,16 @@ name: sam2lca-CI
 
 on: [push, pull_request]
 
-
 jobs:
   sam2lca_ci:
     name: sam2lca_ci
-    runs-on: 'ubuntu-latest'
+    runs-on: "ubuntu-latest"
     if: "!contains(github.event.head_commit.message, '[skip_ci]')"
     steps:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.7
+          python-version: 3.9
           mamba-version: "*"
           channels: conda-forge,bioconda,defaults
           channel-priority: true
@@ -26,15 +25,6 @@ jobs:
       - name: Test with pytest
         shell: bash -l {0}
         run: |
-          pip install -e .
-          pip install pytest
-          # pytest
-      - name: Check sam2lca help message
-        shell: bash -l {0}
-        run: |
-          sam2lca --help
-      - name: Check sam2lca on test data
-        shell: bash -l {0}
-        run: |
-          sam2lca -m test update-db
-          sam2lca -m test analyze -b -t tests/data/taxonomy/test.tree tests/data/aligned.sorted.bam
+          pip install .
+          pip install pytest pytest-console-scripts
+          pytest -s -vv --script-launch-mode=subprocess

.gitignore

@@ -106,4 +106,7 @@ venv.bak/
 .nextflow
 .vscode/
 mappings
-aligned.sorted.sam2lca.*
+aligned.sorted.sam2lca.*
+sam2lca_test_dbdir
+sam2lca.egg-info
+.DS_Store

CHANGELOG.md

@@ -0,0 +1,40 @@
+# Changelog
+
+All notable changes to [sam2lca](https://github.com/maxibor/sam2lca) will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## 1.0.0beta
+
+### Added
+
+- Added sam2lca tutorial
+- Add Custom acc2tax with json
+- Total number of reads is computed early on to provide progress bar
+- unit and integration testing with PyTest
+- Total Descendant read counts for each taxon
+- GTDB taxonomy and acc2tax added
+- 18s acc2tax added
+- XN and XR flag in bam output for, respectively, Taxon name and rank
+- Add edit distance threshold filtering
+
+### Changed
+
+- Code refactoring for speedup, making use of multithreading on shared dictionaries
+- Improve logging and replace prints statements with logging.info
+- ete3 has been replaced by taxopy
+- Unclassified TAXID is now `12908` by default
+- RocksDB params changed
+- TAXID of LCA is only attributed to alignment segments passing threshold
+- Identity threshold is now a range selection in CLI.
+
+## Dependencies
+
+- ete3 removed
+- ordered-set removed
+- pytest-console-scripts 1.3.1
+- scipy
+- Jinja2 pinned version ot 3.1 (see [RTD issue](https://github.com/readthedocs/readthedocs.org/issues/9038) )
+
+### Removed

README.md

@@ -1,11 +1,18 @@
-![sam2lca-CI](https://github.com/maxibor/sam2lca/workflows/sam2lca-CI/badge.svg) [![Documentation Status](https://readthedocs.org/projects/sam2lca/badge/?version=latest)](https://sam2lca.readthedocs.io/en/latest/?badge=latest)
+![](docs/img/sam2lca_logo_text.png)
+
+<p align="center">
+    <a href="https://github.com/maxibor/sam2lca/actions"><img src="https://github.com/maxibor/sam2lca/workflows/sam2lca-CI/badge.svg"/></a>
+    <a href="https://sam2lca.readthedocs.io"><img src="https://readthedocs.org/projects/sam2lca/badge/?version=latest"/></a>
+    <a href="https://pypi.org/project/sam2lca"><img src="https://img.shields.io/badge/install%20with-pip-blue"/></a>
+</p>
+
 # sam2lca
 
-[Lowest Common Ancestor](https://en.wikipedia.org/wiki/Lowest_common_ancestor) from a SAM/BAM/CRAM sequence alignment file
+[Lowest Common Ancestor](https://en.wikipedia.org/wiki/Lowest_common_ancestor) from a [SAM/BAM/CRAM](<https://en.wikipedia.org/wiki/SAM_(file_format>) sequence alignment file.
 
-## Quick start
+## TLDR
 
-Quick analyis of sequencing reads aligned to a DNA database
+Analysis of sequencing reads aligned to a DNA database with NCBI accession numbers, using the NCBI taxonomy
 
 ```bash
 sam2lca analyze myfile.bam
@@ -16,31 +23,42 @@ See all options
 ```bash
 sam2lca --help
 sam2lca update-db --help
+sam2lca list-db --help
 sam2lca analyze --help
 ```
 
+> For further infos, check out the [sam2lca documentation](https://sam2lca.readthedocs.io) and [tutorial](https://sam2lca.readthedocs.io/en/latest/tutorial.html)
+
 ## Installation
 
-### From source
+### With [Conda](https://docs.conda.io/en/latest/) (recommended)
 
 ```bash
-git clone [email protected]:maxibor/sam2lca.git
-conda env create -f environment.yml
-conda activate sam2lca
-pip install git+ssh://[email protected]/maxibor/sam2lca.git
+conda install -c conda-forge -c bioconda -c maxibor sam2lca
 ```
 
-### From Conda
+### With [pip](https://pypi.org/project/pip/)
 
 ```bash
-conda install -c conda-forge -c bioconda -c maxibor sam2lca
+pip install sam2lca
 ```
-### From Pypi
+
+### For development purposes, from the dev branch
 
 ```bash
-pip install sam2lca
+git clone [email protected]:maxibor/sam2lca.git
+git checkout dev
+conda env create -f environment.yml
+conda activate sam2lca
+pip install -e .
+```
+
+or
+
+```bash
+pip install git+ssh://[email protected]/maxibor/sam2lca.git@dev
 ```
 
 ## Documentation
 
-The documentation of sam2lca, including tutorials, is available here: [sam2lca.readthedocs.io](https://sam2lca.readthedocs.io)
+The documentation of sam2lca, including tutorials, is available here: [sam2lca.readthedocs.io](https://sam2lca.readthedocs.io)

conda/meta.yaml

@@ -21,13 +21,12 @@ requirements:
     - python
     - click >=7.0
     - pip >=20.0.2
-    - conda-forge::ete3 >=3.1.1
+    - bioconda::taxopy=0.9.2
     - bioconda::pysam >=0.15.2
     - conda-forge::rocksdb >=6.10.1
     - conda-forge::python-rocksdb >=0.7.0
     - conda-forge::xopen >=0.9.0
     - tqdm >=4.45.0
-    - ordered-set >=4.0.2
     - pandas >=1.1.4
 
 test:

docs/source/contributing.md

@@ -0,0 +1,45 @@
+# Contributing
+
+We welcome any contributions !
+
+To further develop sam2lca, or add documentation, please read further:
+
+## Clone the sam2lca repository, and checkout the dev branch
+
+```bash
+git clone [email protected]:maxibor/sam2lca.git
+git checkout dev
+```
+
+## Install and activate the development environment
+
+```bash
+conda env create -f environment.yml
+conda activate sam2lca
+```
+
+## Install sam2lca with pip in editable mode
+
+```bash
+pip install -e .
+```
+
+## Run the unit and integration tests
+
+```bash
+pytest -s -vv --script-launch-mode=subprocess
+```
+
+## Build the documentation
+
+```bash
+cd docs
+make html
+```
+
+The docs are built in the `docs/build/html` directory
+
+### Claim your sticker
+
+Thanks for contributing to sam2lca !
+If you want to spread the word about sam2lca, please get in touch with me to claim your sticker (maxime_borry[at]eva.mpg.de) !