[Biopython-dev] [Biopython - Bug #2235] SeqRecord from Bio.SwissProt.SProt lacks annotation information

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Tue Apr 16 13:48:14 UTC 2013

Issue #2235 has been updated by Peter Cock.

Assignee changed from Peter Cock to Biopython Dev Mailing List

Bug #2235: SeqRecord from Bio.SwissProt.SProt lacks annotation information

Author: Peter Cock
Status: In Progress
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: Not Applicable

This also affects Bio.SeqIO as it calls Bio.SwissProt.SProt to parse "swiss" format files into SeqRecord objects:

The _SequenceConsumer called by the SequenceParser (both defined in Bio/SwissProt/SProt.py) records only the bare minimum of sequence, id, name and description.

It should implement methods for more of the consumer events (i.e. Swiss-Prot line types), storing the data in a format as close as possible to the SeqRecord objects produced by Bio.GenBank

I plan to tackle this after the next release of Biopython, together with a more detailed set of tests for Bio.SeqIO that look at the annotation and database cross references of SeqRecord objects.

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