[Bioperl-l] Beginner Script Error

Cavin Ward-Caviness cavin.wardcaviness at gmail.com
Mon Sep 14 02:25:51 UTC 2009


I am very new to perl and bioperl and figured I'd start learning by trying
to run a simple script to get BLAST data.  Here is the code I am trying to
run

use Bio::Perl;

$seq = get_sequence('swiss',"ROA1_HUMAN");

# uses the default database - nr in this case
$blast_result = blast_sequence($seq);

write_blast(">roa1.blast",$blast_result);

Instead of creating a file of the blast results I get the following error
message
Bio::SeqIO: swiss cannot be found.
Exception
Msg: Failed to load module Bio::SeqIO:swiss

It seems as though I may simply be missing the proper module.  I am running
bioperl 1.5.9_4 installed using the Perl Package Manager from the
instructions on the bioperl wiki page.  If I am simply missing a module
please let me know which one it is - and any other helpful modules that
someone in the bioinformatics field is likely to use.

Thanks,
Cavin



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