pybiosyntax
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
1 maintainer
Metadata
1 maintainer
Release files for pybiosyntax 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| pybiosyntax-0.1.1.tar.gz | 43.3 kB | With provenance | Details |
Built distributions (wheels)
Total release size: 2.4 MB
Release files / pybiosyntax-0.1.1.tar.gz
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| Size | 43.3 kB |
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