[Biopython-dev] [Bug 2526] New: SeqFeature's .id property is not preserved in BioSQL
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Jun 20 15:01:17 UTC 2008
http://bugzilla.open-bio.org/show_bug.cgi?id=2526
Summary: SeqFeature's .id property is not preserved in BioSQL
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: BioSQL
AssignedTo: biopython-dev at biopython.org
ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
As per the title, a SeqFeature's .id property is not preserved after a
save/retreive in BioSQL.
I found this while working on Bug 2235, where my modified "swiss" parser
creates SeqRecord objects with SeqFeature object which may have their .id set.
Note that in GenBank and EMBL, the SeqFeature objects do not have their id
property set, and so are not affected.
I need to review the BioSQL schema to see if there is a suitable field that
Biopython is ignoring, and if there is, use it. If not, we can probably use a
tagged qualifier - ideally with the same name as the other Bio* projects.
See also test_BioSQL_SeqIO.py revision 1.17 which includes a word arround to
avoid this limitation.
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