[Bioperl-l] Taxon id null with load_seqdatabase.pl
hlapp at gmx.net
Sun Jan 14 12:17:21 EST 2007
George, I presume you are still loading fasta-formatted files? These
do not have a syntax for parsing or figuring out the species, so
bioperl won't have one. If you somehow know the species/taxon, you
can use that same SeqProcessor module you created to also set the
Better yet, also add the NCBI taxon ID, which is the most effective
On Jan 10, 2007, at 9:33 PM, George Heller wrote:
> Hi all.
> I just loaded Arabidopsis data into the bioentry and biosequence
> tables in my Postgres database using load_seqdatabase.pl. I had
> loaded the taxon data prior to this, using the
> load_ncbi_taxonomy.pl. Yet, I see the taxon_id field in the
> bioentry field is blank, after the loading.
> Can anyone tell me why this might be happening? And perhaps what
> needs to be done to correct this?
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: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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