puretabix 2.0.0

Pure python implementation Tabix reader.

Pure Tabix

This is a pure-python Tabix index parser. Useful as an alternative to PySAM and PyTabix for rapid read access by position to Tabix indexed block gzipped files such as VCFs and other common bioinfomatics formats.

See https://samtools.github.io/hts-specs/tabix.pdf and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042176 for information about Tabix and the detailed file format specification.

from puretabix import TabixIndexedFile

tabix_indexed_file = TabixIndexedFile(open('somefile.vcf.gz', 'rb'), open('somefile.vcf.gz.tbi', 'rb'))
tabix_indexed_file.fetch("1", 1000, 5000)

development

TL;DR: pip install -e .[dev] && pre-commit install

pip install -e .[dev]  # Install using pip including development extras
pre-commit install  # Enable pre-commit hooks
pre-commit run --all-files  # Run pre-commit hooks without committing
# Note pre-commit is configured to use:
# - seed-isort-config to better categorise third party imports
# - isort to sort imports
# - black to format code
pip-compile  # Freeze dependencies
pytest  # Run tests
coverage run --source=puretabix -m pytest && coverage report -m  # Run tests, print coverage
mypy .  # Type checking
pipdeptree  # Print dependencies
scalene --outfile tests/perf_test.txt --profile-all --cpu-sampling-rate 0.0001 tests/perf_test.py  # performance measurements

Global git ignores per https://help.github.com/en/github/using-git/ignoring-files#configuring-ignored-files-for-all-repositories-on-your-computer

For release to PyPI see https://packaging.python.org/tutorials/packaging-projects/

python3 setup.py sdist && python3 -m twine upload dist/*

acknowledgements

Inspired by @yangmqglobe code in https://github.com/cggh/scikit-allel/pull/297