Support for binary sequence formats in Biopython
Project description
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 supportedsnapgene
format, used by SnapGene: reading support onlygck
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).
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