[Gusdev-gusdev] Re: Load Taxon and Load NRDB

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

Yes, they both were written to enter new data or update existing data. I 
recently modified LoadTaxon.pm and haven't had a chance to send a final 
e-mail although I did send an e-mail outlining the problem. I'll cc to 
the gusdev-gusdev list.

LoadTaxon was modified to merge taxon_ids using the merged.dmp file that 
is in the tar ball from NCBI. There is a new command line argument. 
--merged that is required.  Unfortunately, the plugin was incompletely 
tested because I had a bug which affected the merged sub but was not 
obvious in tests until after I ran the plugin with commit on and then 
only by querying the db. The bug resulted in duplications but only with 
a very small number of ncbi_tax_id. I  think I fixed the bug and it  
looked OK in tests but anyone running the plugin should be aware.

For updates with LoadNRDB, the three options --maketemp, --plugin, 
--delete should be included on the command line.

                                                                                                                                                     
-Debbie



Ed Robinson wrote:

>Debbie,
>
>How do LoadTaxon and LoadNRDB work for Updates?  Do I just run
>them as if I am doing a new installation and they can tell
>that these are updates?  I think that is what I saw in the
>LoadNRDB pluggin, but I wanted to make sure that this is correct.
>
>thanks for any pointers you can offer.
>
>-Ed
>
>-----------------
>Ed Robinson
>Program Specialist
>Center for Tropical and Emerging Global Diseases
>and Dept. of Genetics
>University of Georgia, Athens, GA 30602
>ero...@ug.../(706) 542.1447
>  
>