[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


           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.

Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list