Support for some binary sequence formats for BioPython.
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Damien Goutte-Gattat 4078e160ab Write Features segment to SnapGene file. 2 years ago
incenp Write Features segment to SnapGene file. 2 years ago
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README.md

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.

Formats supported

  • xdna format, used by DNA Strider and Serial Cloner: reading and writing supported
  • snapgene format, used by SnapGene: 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 and contact

The latest source code is available at git://git.incenp.org/binseqs.git and may also be browsed using the Gitweb interface at https://incenp.org/dvlpt/gitweb/?p=binseqs.git;a=summary.

To contact the author, use the following address: Damien Goutte-Gattat dgouttegattat@incenp.org