BinSeqs - Support for binary sequence formats in Bioython

BinSeqs is a Python package intended to enrich the SeqIO framework from Biopython by adding support for some binary sequence formats.

Deprecation Warning

This code has now been merged into Biopython. Starting from Biopython release 1.75, all you need to do to support the formats below is to load the Bio.SeqIO module.

Consequently, this project will no longer be maintained. It will remain available online but will not be updated. All improvements and bug fixes will occur in the Biopython repository.

You can still use this module until Biopython 1.75 is released and available on your system. After that, loading the incenp.bio.seqio module will be a no-op and a DeprecationWarning will be emitted.

Formats supported

• xdna format, used by DNA Strider and Serial Cloner: reading and writing supported
• snapgene format, used by SnapGene: reading support only
• gck format, used by Gene Construction Kit: reading support only

Usage

The BinSeqs parsers and writers are not designed to be used independently and should instead be used through the Biopython's SeqIO module.

Simply import the incenp.bio.seqio module to make the parsers and writers available to Biopython's SeqIO:

from Bio import SeqIO
import incenp.bio.seqio

records = list(SeqIO.parse('snapgene_file.dna', 'snapgene'))
SeqIO.write(records, 'serialcloner_file.xdna', 'xdna')

Copying

BinSeqs is free software and distributed under the terms of a BSD-like license. The full license is included in the LICENSE.txt file of the source distribution.

Homepage

The project is located at https://incenp.org/dvlpt/binseqs.html (homepage) and https://git.incenp.org/damien/binseqs (repository and bug tracker).

Download

Download the latest release tarball:

Or install through PyPI:

pip install incenp.binseqs