pybiosyntax 0.1.0

Python bindings for libbiosyntax with a bundled C build

pybiosyntax

pybiosyntax provides Python bindings for libbiosyntax.

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

Documentation

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

python -m pip install mkdocs
mkdocs serve

• Documentation index
  • Installation
  • Usage
  • API reference
  • Command line
  • Development
  • Vendoring