Support for some binary sequence formats for BioPython.
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Damien Goutte-Gattat f8d6fa804a Prepare first release. 1 month ago
incenp Apply PEP8 and PEP263. 4 months 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

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