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.
1 maintainer
Metadata
1 maintainer
Release files for pyblast4-archive 0.1.12
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