pyblast4-archive 0.1.11

Rudimentary BLAST archive reading in Python

pyblast4_archive

This library provides limited Python bindings to the CBlast4_archive and related objects from the NCBI C++ Toolkit. CBlast4_archive allows the programmer to interpret BLAST output in format 11 "BLAST archive format (ASN.1)," and this Python library aims to make such interpretation possible in Python.

Installation

The latest portable binary wheel for your platform can be installed from PyPI using pip.

python -m pip install pyblast4_archive

Alternatively, you can build the library yourself.

Getting started

The main class of interest in this library is Blast4Archive. To load Blast4Archive objects from a binary ASN.1 BLAST Archive file, use the from_path classmethod.

fomr pyblast4_archive import Blast4Archive

archives = Blast4Archive.from_path("blast_results.asn1", "asn_binary")

or for a text ASN.1 file,

archives = Blast4Archive.from_path("blast_results.asn1", "asn_text")

To decode query IDs from the archives, use decode_query_ids.

from pyblast4_archive import decode_query_ids

decoded_queries = decode_query_ids(archives)

Likewise, to decode subejct IDs, use decode_subject_ids.

from pyblast4_archive import decode_subject_ids

decoded_subjects = decode_subject_ids(archives)

To decode BLAST database OIDs, a SeqDB object is needed. SeqDB objects can be constructed from a path to the BLAST DB and its database type ("nucleotide" or "protein").

from pyblast4_archive import SeqDB

db = SeqDB("/path/to/blast/db", "nucleotide")

Then, to decode database OIDs, use decode_database_oids.

from pyblast4_archive import decode_database_oids

decoded_oids = decode_database_oids(archives, db)

Dependencies

This software depends on the NCBI C++ Toolkit and Boost.Python.

Portable binary wheels

Since this software provides Python bindings for a C++ library, it must be compiled, unlike a pure Python library. Pre-built portable binary wheels for many platforms are avaiable on the Python Package Index (PyPI). The full process for building these wheels is described by the package.yml GitHub Actions workflow file.

Supported platforms

The platforms for which I am currently building portable wheels to upload to PyPI are listed below. For other platforms, it might be necessary to build this library yourself.

Linux, glibc (manylinux)

Architectures

• x86_64
• i686
• aarch64
• s390x
• ppc64le

Python implementations

• CPython 3.11
• CPython 3.12
• CPython 3.13 (+ free threading)
• CPython 3.14 (+ free threading)
• PyPy 3.11

macOS

Architectures

• x86_64
• aarch64

Python implementations

• CPython 3.11
• CPython 3.12
• CPython 3.13 (+ free threading)
• CPython 3.14 (+ free threading)

macOS versions

• macOS 15 (Sequoia)
• macOS 26 (Tahoe)

Dependency licenses

Portable binary wheels operate by bundling the main library with its transitive dependencies. This is accomplished with auditwheel on Linux or delocate on macOS and is abstractly similar to static linking. Source code for these transitive dependencies are not included in the Git repository for this library since those wanting to build this library themselves will most likely prefer to download the transitive dependencies from a package manager or else build them from upstream sources.

The sources for the transitive dependencies are included in the source tarballs accompanying each release of this software on GitHub. (Due to file size limitations, the source tarballs available from PyPI do not currently include these dependencies.) Dependency sources for Linux can be found under the deps/linux directory, and dependency sources for macOS can be found under the deps/macos directory.

Both the binaries and sources of the transitive dependencies are obtained from the package manager of the system used for building. For Linux, the manylinux_2_28 container (based on AlmaLinux 8) was used. The manylinux_2_28 container uses the default AlmaLinux 8 repositories, Extra Packages for Enterprise Linux, and a custom DNF repository hosted at https://www.cs.uky.edu/~acta225/manylinux_packages/almalinux/8 . For macOS, the default Homebrew taps hombrew/core and homebrew/cask were used, as well as a custom actapia/cibuildwheel_packages tap.

For Linux dependencies, the RPM .spec file and any patches associated with the package are included. For macOS dependencies, the Homebrew Formula .rb file is included. In both cases, any patches for the pakcage have been pre-applied.

Full license texts for each dependency may be found with the dependency's source code under deps/. Additionally, the LICENSES.linux and LICENSES.macos files summarize the licenses of the transitive dependencies bundled in the portable wheels.

License

This software is licensed under the GNU General Public License, Version 3, which may be found at LICENSE.