[Bioperl-l] load_seqdatabase didn't load the taxon ids
angshu96 at gmail.com
Wed Dec 14 22:14:14 EST 2005
On 12/14/05, Jason Stajich <jason.stajich at duke.edu> wrote:
> Well let's try to think this through together Angshu - how do you
> think the loading mechanism should be guessing what the species is
> for a FASTA file.... (Hint: it doesn't)
> On Dec 14, 2005, at 5:42 PM, Angshu Kar wrote:
> > Hi Torsten,
> > 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?
> > Thanks,
> > Angshu
> > On 12/14/05, Torsten Seemann
> > <torsten.seemann at infotech.monash.edu.au> wrote:
> >> Angshu,
> >>> After running the load_seqdatabase.pl I see that it hasn't loaded
> >>> the
> >>> bioentry table with the taxon ids from the taxon table!!! Could
> >>> you please
> >>> suggest a remedy to this?
> >> Did you put the taxons in the database first ?
> >>> From bioperl-cvs/biosql-schema/INSTALL :
> >> "With bioperl and bioperl-db installed you are ready to load some
> >> data.
> >> It is advisable to pre-load the NCBI taxonomy database (use
> >> scripts/load_taxonomy.pl in the biosql-schema package, the details
> >> are
> >> in its documentation)."
> >> Use bioperl-cvs/biosql-schema/scripts/load_ncbi_taxonomy.pl :
> >> "Usage: load_ncbi_taxonomy.pl" ... (try --help option)
> >> The BioPerl authors have been very patient answering your
> >> questions so
> >> far, but I think you should read the INSTALL files in biosql-
> >> schema and
> >> bioperl-db first before asking further questions.
> >> --
> >> Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
> >> Victorian Bioinformatics Consortium
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> Jason Stajich
> Duke University
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