Support for binary sequence formats in Biopython
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.
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
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
module will be a no-op and a DeprecationWarning will be emitted.
xdnaformat, used by DNA Strider and Serial Cloner: reading and writing supported
snapgeneformat, used by SnapGene: reading support only
gckformat, used by Gene Construction Kit: reading support only
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')
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.
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