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

[James Wasmuth]

The Bio::Species object you've created (Bio::Species=HASH(0x8658bf0)) 
can be manipulated to give you what you want from it, eg. common name, 
species.

To get species use

$self->species( $species )


Have a look at the documentation for it at 
http://doc.bioperl.org/releases/bioperl-1.2/Bio/Species.html

James



Henrik Nilsson wrote:

>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
>
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>  
>

-- 

Nematode Bioinformatics
Blaxter Nematode Genomics Group
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