[Bioperl-l] More on ACC NR -> Species name

[Henrik Nilsson]

Thanks everyone for your kind input on the matter!

>You can get the seq from genbank via
>Bio::DB::GenBank, and then ask for the species with
>$seq->species() [this will return a Bio::Species object]

Yes, this would be exactly what I am looking for. My being a bioperl
newcomer, I'm not sure how to implement your elegant solution. The
following code, for example, doesn't really do the trick:

-----------------------
#!/usr/bin/perl -w
use strict;                     
use Bio::Perl;                  
use IO::String;                  
use Bio::Perl qw( get_sequence );
use Bio::DB::GenBank;
use Bio::Species;
use Bio::Root::Root;

my ($seq_object, $seq_id, $seq_as_string, $species);

$seq_object = get_sequence('genbank',"AF429427"); 
$seq_id  = $seq_object->display_id;  
$seq_as_string = $seq_object->seq();  
$species = $seq_object->species();

print "seq_id: $seq_id\n";
print "sequence: $seq_as_string\n";
print "species: $species\n";
exit;
----------------------

although it does output

seq_id: AF429427
sequence: TTGTAGCTGGCCGTAAACT ...
species: Bio::Species=HASH(0x8658bf0)

i.e. it does fetch the sequence and seq_id, but not the species.

What am I doing wrong?

Yours gratefully,

Henrik N