align-trim 1.1.0__tar.gz

align_trim-1.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect, please ensure you have checked existing issues before submitting a new issue.
+labels: [bug]
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ align_trim ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file (from stderr with --verbose enabled), the report TSV generated with `--report`, and your primer scheme bedfile are all helpful.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Install method _(eg. pip, conda, source)_
+        * Version of align_trim _(eg. 1.1, 1.5, 1.8.2)_

align_trim-1.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest an idea for the align_trim, please ensure you have checked existing feature requests before submitting a new suggestion to avoid duplicates.
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

align_trim-1.1.0/.github/workflows/pytest.yml

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+name: pytest
+on:
+  push:
+    paths:
+      - "align_trim/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - "uv.lock"
+      - ".github/workflows/pytest.yml"
+
+jobs:
+  ci:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-22.04, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: install project
+        run: uv sync --python ${{ matrix.python-version }} --locked --all-extras --dev
+
+      - name: run tests
+        run: uv run --python  ${{ matrix.python-version }} pytest

align_trim-1.1.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package to PyPI 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:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      url: https://pypi.org/p/align_trim
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

align_trim-1.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.DS_store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

align_trim-1.1.0/.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.1
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [--fix, --show-fixes]
+      # Run the formatter.
+      - id: ruff-format
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.7.11
+    hooks:
+      - id: uv-lock
+      - id: uv-export

align_trim-1.1.0/LICENSE

@@ -0,0 +1,19 @@
+Copyright (c) 2017-2018 Nick Loman & the ZiBRA Project & the ARTIC project
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

align_trim-1.1.0/PKG-INFO

@@ -0,0 +1,133 @@
+Metadata-Version: 2.4
+Name: align_trim
+Version: 1.1.0
+Summary: Soft-clip primer sites for SAM/BAM files generated from amplicon sequencing runs
+Project-URL: Repository, https://github.com/artic-network/align_trim.git
+Project-URL: Issues, https://github.com/artic-network/align_trim/issues
+Author-email: Nick Loman <n.j.loman@bham.ac.uk>, Sam Wilkinson <s.a.j.wilkinson@bham.ac.uk>, Chris Kent <c.g.kent@bham.ac.uk>
+Maintainer-email: Sam Wilkinson <s.a.j.wilkinson@bham.ac.uk>, Chris Kent <c.g.kent@bham.ac.uk>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.9
+Requires-Dist: numpy
+Requires-Dist: primalbedtools>=0.10.1
+Requires-Dist: pysam
+Description-Content-Type: text/markdown
+
+# align_trim
+
+Stand alone version of ARTIC's fieldbioinformatics align_trim.py
+
+## Installation  
+
+From conda
+```bash
+conda install bioconda::align_trim 
+```
+from pypi
+```bash
+pip install align_trim
+```
+from source
+```bash
+git clone https://github.com/artic-network/align_trim.git
+cd align_trim
+uv sync
+uv run align_trim --help
+```
+
+## Command Line Interface
+
+### Basic Usage
+
+```bash
+align_trim [OPTIONS] BEDFILE
+```
+
+The tool reads alignment data from either a SAM/BAM file or stdin and outputs trimmed alignments to stdout in SAM format by default.
+
+### Required Arguments
+
+- `BEDFILE`: BED file containing the amplicon primer scheme in [v3](https://doi.org/10.5281/zenodo.16366659) format. 
+
+### Optional Arguments
+
+#### Input/Output Options
+
+- `--samfile`, `-s` : Sorted SAM/BAM file containing the aligned reads, if this is not provided (or '-') then 'align_trim' will read from stdin.
+- `--output`, `-o` : Output file path. Format determined by extension (.sam/.bam). If not provided or '-', writes SAM to stdout
+
+#### Processing Options
+
+- `--normalise`, `-n` : Normalise to target depth N per amplicon using a greedy per-read algorithm. Each read is kept only if it brings the amplicon depth closer to the target. Use 0 for no normalisation (default: 0)
+- `--min-mapq`, `-m` : Minimum mapping quality to keep an aligned read (default: 20)
+- `--primer-match-threshold`, `-p` : Add this many bases of padding to the 5' end of primer coordinates to allow fuzzy matching for reads with barcodes/adapters (default: 35)
+
+#### Primer and Read Handling
+
+- `--no-trim-primers` : Do not trim primers from reads (by default, primers are trimmed)
+- `--allow-incorrect-pairs` : Allow reads to be assigned to amplicons even if primers are not correctly paired
+- `--require-full-length` : Require all reads to start and stop in primer sites (do not use with rapid barcoding)
+
+#### Output and Reporting
+
+- `--report`, `-r` : Output detailed report TSV to specified filepath
+- `--amp-depth-report`, `-a` : Output mean depth for each amplicon as TSV to specified filepath
+- `--no-read-groups` : Do not divide reads into pool-based read groups in SAM/BAM output
+
+#### General Options
+
+- `--verbose`, `-v` : Enable debug mode with detailed logging to stderr
+- `--version` : Show version information
+- `--help` : Show help message
+
+### Examples
+
+#### Basic trimming with primer removal
+```bash
+align_trim primers.bed --samfile input.bam --output trimmed.bam
+```
+
+#### Normalize coverage and generate reports
+```bash
+align_trim primers.bed --samfile input.bam --normalise 100 \
+  --report alignment_report.tsv --amp-depth-report depth_report.tsv \
+  --output normalized.bam
+```
+
+#### Process from stdin with verbose output
+```bash
+samtools view -h input.bam | align_trim primers.bed --verbose > trimmed.sam 2> verbose.out.txt
+```
+
+#### Strict full-length read filtering
+```bash
+align_trim primers.bed --samfile input.bam --require-full-length \
+  --min-mapq 30 --output filtered.bam
+```
+
+#### Allow mismatched primer pairs with custom threshold
+```bash
+align_trim primers.bed --samfile input.bam --allow-incorrect-pairs \
+  --primer-match-threshold 50 --output relaxed.bam
+```
+
+### Output Formats
+
+The tool supports multiple output formats based on file extension:
+- `.sam` - SAM format (text)
+- `.bam` - BAM format (binary, compressed)
+- No extension or `-` - SAM format to stdout
+
+### Report Files
+
+When using `--report`, a tab-separated file is generated with the following columns:
+- `chrom`: Reference chromosome/contig
+- `QueryName`: Read name
+- `ReferenceStart`/`ReferenceEnd`: Alignment coordinates
+- `PrimerPair`: Primer pair assignment
+- `Primer1`/`Primer2`: Individual primer information
+- `CorrectlyPaired`: Boolean indicating proper primer pairing
+- Additional alignment metrics
+
+The `--amp-depth-report` generates a summary of coverage depth per amplicon.

align_trim-1.1.0/README.md

@@ -0,0 +1,117 @@
+# align_trim
+
+Stand alone version of ARTIC's fieldbioinformatics align_trim.py
+
+## Installation  
+
+From conda
+```bash
+conda install bioconda::align_trim 
+```
+from pypi
+```bash
+pip install align_trim
+```
+from source
+```bash
+git clone https://github.com/artic-network/align_trim.git
+cd align_trim
+uv sync
+uv run align_trim --help
+```
+
+## Command Line Interface
+
+### Basic Usage
+
+```bash
+align_trim [OPTIONS] BEDFILE
+```
+
+The tool reads alignment data from either a SAM/BAM file or stdin and outputs trimmed alignments to stdout in SAM format by default.
+
+### Required Arguments
+
+- `BEDFILE`: BED file containing the amplicon primer scheme in [v3](https://doi.org/10.5281/zenodo.16366659) format. 
+
+### Optional Arguments
+
+#### Input/Output Options
+
+- `--samfile`, `-s` : Sorted SAM/BAM file containing the aligned reads, if this is not provided (or '-') then 'align_trim' will read from stdin.
+- `--output`, `-o` : Output file path. Format determined by extension (.sam/.bam). If not provided or '-', writes SAM to stdout
+
+#### Processing Options
+
+- `--normalise`, `-n` : Normalise to target depth N per amplicon using a greedy per-read algorithm. Each read is kept only if it brings the amplicon depth closer to the target. Use 0 for no normalisation (default: 0)
+- `--min-mapq`, `-m` : Minimum mapping quality to keep an aligned read (default: 20)
+- `--primer-match-threshold`, `-p` : Add this many bases of padding to the 5' end of primer coordinates to allow fuzzy matching for reads with barcodes/adapters (default: 35)
+
+#### Primer and Read Handling
+
+- `--no-trim-primers` : Do not trim primers from reads (by default, primers are trimmed)
+- `--allow-incorrect-pairs` : Allow reads to be assigned to amplicons even if primers are not correctly paired
+- `--require-full-length` : Require all reads to start and stop in primer sites (do not use with rapid barcoding)
+
+#### Output and Reporting
+
+- `--report`, `-r` : Output detailed report TSV to specified filepath
+- `--amp-depth-report`, `-a` : Output mean depth for each amplicon as TSV to specified filepath
+- `--no-read-groups` : Do not divide reads into pool-based read groups in SAM/BAM output
+
+#### General Options
+
+- `--verbose`, `-v` : Enable debug mode with detailed logging to stderr
+- `--version` : Show version information
+- `--help` : Show help message
+
+### Examples
+
+#### Basic trimming with primer removal
+```bash
+align_trim primers.bed --samfile input.bam --output trimmed.bam
+```
+
+#### Normalize coverage and generate reports
+```bash
+align_trim primers.bed --samfile input.bam --normalise 100 \
+  --report alignment_report.tsv --amp-depth-report depth_report.tsv \
+  --output normalized.bam
+```
+
+#### Process from stdin with verbose output
+```bash
+samtools view -h input.bam | align_trim primers.bed --verbose > trimmed.sam 2> verbose.out.txt
+```
+
+#### Strict full-length read filtering
+```bash
+align_trim primers.bed --samfile input.bam --require-full-length \
+  --min-mapq 30 --output filtered.bam
+```
+
+#### Allow mismatched primer pairs with custom threshold
+```bash
+align_trim primers.bed --samfile input.bam --allow-incorrect-pairs \
+  --primer-match-threshold 50 --output relaxed.bam
+```
+
+### Output Formats
+
+The tool supports multiple output formats based on file extension:
+- `.sam` - SAM format (text)
+- `.bam` - BAM format (binary, compressed)
+- No extension or `-` - SAM format to stdout
+
+### Report Files
+
+When using `--report`, a tab-separated file is generated with the following columns:
+- `chrom`: Reference chromosome/contig
+- `QueryName`: Read name
+- `ReferenceStart`/`ReferenceEnd`: Alignment coordinates
+- `PrimerPair`: Primer pair assignment
+- `Primer1`/`Primer2`: Individual primer information
+- `CorrectlyPaired`: Boolean indicating proper primer pairing
+- Additional alignment metrics
+
+The `--amp-depth-report` generates a summary of coverage depth per amplicon.