pybiosyntax

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pybiosyntax provides Python bindings for libbiosyntax, a small C99 reimplementation of BioSyntax's biological text highlighting model.

The C core is vendored under vendor/libbiosyntax. Source installs build the bundled C library. Wheels include the compiled shared library.

python -m pip install .

The bundled C library is installed inside the Python package. No separate libbiosyntax installation is required.

Usage

import biosyntax as bs

line = "chr1\t42\trs1\tA\tT\t99\tPASS\n"
for span in bs.highlight_line("vcf", line):
    print(span, bs.class_name(span.class_id), span.slice(line))

The package also installs a small ANSI-rendering CLI:

biosyntax sample.vcf
python -m biosyntax --format fastq reads.fastq

For source-tree development, reinstall after changes. This rebuilds and installs the bundled C library.

python -m pip install .
python examples/basic.py

To build distribution artifacts, use a PEP 517 frontend such as build:

python -m pip install build
python -m build

License

The Python binding is licensed under the MIT License. The bundled libbiosyntax C library is licensed under the GNU Lesser General Public License version 2.1 or later.

Documentation

The documentation is in docs/ and can be built with MkDocs.

python -m pip install mkdocs
mkdocs serve

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for kojix2 from gravatar.com kojix2

Credits

Author: libbiosyntax contributors

License expression

MIT AND LGPL-2.1-or-later
View SPDX License List

Requires

Python >=3.10

Tags

pybiosyntax biosyntax bioinformatics syntax-highlighting ctypes fasta fastq sam vcf

Classifiers

Report project as malware

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