[Bioperl-l] Bio::Perl::get_sequence for Swiss-Prot doesn't work

Amir Karger akarger at CGR.Harvard.edu
Wed Jun 28 15:49:54 EDT 2006


>perl -MBio::Perl -e '$database="swiss", $id="P09651", $format="fasta";'
-e '$sequence = get_sequence($database, $id);'

-------------------- WARNING ---------------------
MSG: acc (P09651) does not exist
---------------------------------------------------
>perl -MBio::Perl -e '$database="swiss", $id="ROA1_HUMAN",
$format="fasta";' -e '$sequence = get_sequence($database, $id);'

-------------------- WARNING ---------------------
MSG: id (ROA1_HUMAN) does not exist
---------------------------------------------------

But of course, it does exist: http://ca.expasy.org/uniprot/ROA1_HUMAN
Same error for a couple other proteins.
Works for a GenBank protein.

perl 5.8.6
Perl.pm,v 1.23.2.1 2005/10/09 15:16:18 jason Exp

This worked a few months ago.
What's going on?

-Amir Karger



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