[Bioperl-l] load_seqdatabase didn't load the taxon ids

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Dec 14 18:56:46 EST 2005

> Thanks for your help. But I've loaded the taxon tables.
> Only thing I'm doing differently is loading my data from a fasta file
> instead of the genbank, swissprot format. Does that matter anyhow?

A FASTA file usually contains much less non-sequence information than a
Genbank or Swissprot file. The latter usually
have /taxon_id, /organism, /strain fields etc which I assume can be used
to make the correct links in the BioSQL database.

Depending on what is stored in the ">" lines in your FASTA file, you may
need to write a custom SeqProccesor class, as Hilmar Lapp has mentioned
before in his replies to you:

See http://bioperl.org/pipermail/bioperl-l/2005-August/019579.html

Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium

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