[Gusdev-gusdev] LoadTaxonomy.pm

[<pi...@pc...>]

The LoadTaxonomy plugin was written to load taxonomy information from tables
downloaded from NCBI. It was intended that the plugin update and not replace
rows in the taxonomy tables and that the taxon_ids remain stable. It was
assumed that NCBI didn't replace their tax_ids but in  fact they do although at
a low rate. This results in duplications in the taxon_ids that represent the
same taxonomic group. There is a merged.dmp file included in their tar ball
that contains a list of old to new tax_id mappings and seems to be cumulative.
I have written them to confirm that all replacements are in the file and that
it is cumulative.

I would like to add a subroutine to the LoadTaxon plugin  that would be called
first to replace the deprecated ncbi_tax_ids in sres.taxon with their
replacements
and then continue with the plugin as it is. This would require the addition of
another option for the merged.dmp file. I was not going to make this an
optional task but I will try to build in a time saver for first time use.

Any comments? Please respond quickly as I need to run the plugin ASAP.

                                          -Debbie