Check if Biopython already knows about our formats (which will be the case starting from Biopython 1.75) before loading the parsers. Emit a warning if the parsers are already available in Biopython so that the user will know she no longer needs to load our module.
|2 years ago|
|incenp||2 years ago|
|.gitignore||2 years ago|
|AUTHORS||2 years ago|
|LICENSE.txt||3 years ago|
|MANIFEST.in||2 years ago|
|NEWS||2 years ago|
|README.md||2 years ago|
|setup.py||2 years ago|
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.
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.