Initial implementation of bwapy

[nh13]

This PR gets a minimal API for running bwa aln and bwa mem on single-ended (fragment) reads. Paired reads are not supported.

The motivation is to replace the usage of https://github.com/fulcrumgenomics/bwa-aln-interactive in https://github.com/fulcrumgenomics/prymer and elsewhere. We can then use pybwa along with latest supported release of bwa.

Improved documentation (e.g. additional examples, verbose docstrings), as well as test coverage are planned to be added at a later date. I did examine differences in alignments on a few SRA samples (see this gist), with only differences in bwa mem (as described in the docs) found.

Live docs in its current form can be found here: https://pybwa--1.org.readthedocs.build/en/1/. I used sphinx since I couldn't get mkdocs to play nicely with cython code.

Finally, I made a few design decisions I'd like to highlight for posterity. I split out the options for bwa into separate classes, for the use case where we want to align reads, examine alignments, loosen/update options, then re-align, and iterate.

The BwaAlnOptions requires that the options are changed via setting properties rather than directly in the constructor. It wouldn't be hard to add this functionality in a later PR. The same occurs for BwaMemOptions, but there's a required finalize method that needs to be called before it can be used with the aligner, which either the user can call, or the align method will call (with copy=True to copy rather than modifying in-place).

[codecov]

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[msto]

I don’t know if it’s codified, I learned it through experience.

…

On Tue, Dec 17, 2024 at 9:13 PM Tim Fennell ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In pyproject.toml <#1 (comment)>: > +[tool.poetry] +name = "bwapy" +version = "0.0.1-dev" +description = "Python bindings for BWA" +authors = ["Nils Homer"] +license = "MIT" +readme = "README.md" +homepage = "https://github.com/fulcrumgenomics/bwapy" +repository = "https://github.com/fulcrumgenomics/bwapy" +keywords = ["bioinformatics"] +packages = [{ include = "bwapy" }] +classifiers = [ + "Development Status :: 3 - Alpha", + "Environment :: Console", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Software Development :: Documentation", + "Topic :: Software Development :: Libraries :: Python Modules", +] +include = [ + "LICENSE", + { path = "bwapy/**/*.so", format = "wheel" }, + { path = "**/*.so", format = "wheel" }, + { path = "*.so", format = "wheel" }, + #{ path = "*.so", format = "wheel" } +] + +[tool.poetry.build] +generate-setup-file = false +script = "build.py" + +[tool.poetry.dependencies] +python = ">=3.9.0,<4.0" +pysam = ">=0.22.1" +typing_extensions = { version = ">=3.7.4", python = "<3.12" } + +[tool.poetry.group.dev.dependencies] +# dependencies for linting, style checking, and unit testing +mypy = ">=1.7.0" +pytest = ">=7.4.0" +pytest-cov = ">=2.8.1" +ruff = "0.4.8" +setuptools = ">=68.0.0" Is this a policy written down somewhere or an emergent policy? — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAANOFO66NYWKYDWMYHO4TT2GDK4ZAVCNFSM6AAAAABTSJJNSCVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDKMJQGYYTGMJZHA> . You are receiving this because you commented.Message ID: ***@***.***>