I want to query uniprot/KB by accesion number to retrieve species names only.I have write this script:
#!/usr/bin/perl
use strict;
use warnings;
use Bio::Seq;
use Bio::DB::SwissProt;
use SWISS::Entry;
print "Please enter the accession number ... ";
$_ = <STDIN>;
my $db_obj = Bio::DB::SwissProt->new;
my $seq_obj = $db_obj->get_Seq_by_acc($_);
if( defined $seq->species ) {
print "Sequence coming from ",$species->binomial," [",$species->common_name,"]\n";
}
exit 0;
but it throws me this error
Name of the protein: Bio::Species=HASH(0x3bb03d8)
Can you help me understand what doesn't work ? Thanks you.
•
written
by
anicet.ebou
This doesn't really answer your question, but you could also have a look at the Swissknife PERL package, http://swissknife.sourceforge.net/docs/
I think the OP is already using it (isn't the module SWISS::Entry part of swissknife ?)
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The script is below.
Where is the error message ?
This doesn't look like an error message but like a variable that wasn't properly dereferenced.