[Biopython-dev] [Bug 2422] New: BioSQL shouldn't just ignore the taxon_id

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2422

           Summary: BioSQL shouldn't just ignore the taxon_id
           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


In Bug 1921 biopython/BioSQL/Loader.py was changed to ignore the taxon_id, in
order to avoid a foreign key constraint when the taxon id was not already
defined (e.g. from loading an up to date NCBI taxonomy).

We should see how BioPerl and BioJava handle this situation...

One crude option (which would still be an improvement on the current situation)
is to check if the taxon_id is defined, and if it is, then store the record
with this included, and if not, issue a warning and store the sequence but
omitting the taxon id.


-- 
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.