[Biopython-dev] [Bug 2475] BioSQL.Loader should reuse existing taxon entries in lineage

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2475


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #36 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-08 11:56 EST -------
as the main use cases are now covered, I'm marking this bug as fixed.

For SeqRecord objects with no taxonomy information, nothing has changed.

For SeqRecord objects with taxonomy information AND an NCBI taxon ID, we now
record either the full taxonomy via Bio.Entrez if requested, or a stub entry
which can be completed by running load_ncbi_taxonomy.pl later.

For the atypical case of sequences with taxonomy information but NO NCBI taxon
ID, the old behaviour continues - new entries will be created in the taxon
tables for the given lineage, without attempting to match existing entries.  To
do this properly would require some clever heuristics.

If this final situation is a real issue, we can re-visit this.


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