[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





------- Comment #27 from biopython-bugzilla at maubp.freeserve.co.uk  2008-04-10 08:07 EST -------
Regarding inserting the lineage into the taxon/taxon_tables, the tree structure
is stored in two ways.  Firstly, using the taxon.parent field, and secondly
using the left/right fields.

Over on the BioSQL mailing list we've established that updating the left/right
values by recalulating them takes about 10 minutes - doing this from Biopython
when adding a new sequence does not seem ideal.

We could add missing taxonomy nodes to the tables (based on the Bio.Entrez
data), and record the tree structure using the taxon.parent field, but leave
the left/right values as NULL.

This should be enough for Biopython to recover the full linege when retrieving
a sequence - we need to check BioSQL.BioSeq._retrieve_taxon() is happy.

If the user wants the left/right values, they would have to (re)run the BioSQL
load_ncbi_taxonomy.pl script (which is slow).


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