[Bioperl-l] extracting 'species' from ncbi records

[Jason Stajich]

$seq->species() returns and object (Bio::Species)

You want
next unless $seq->species->species() =~ /.../;


On Fri, 17 Jan 2003, Charles Hauser wrote:

> All,
>
> I am trying to parse species names from GenBank records.
>
> the following code fails:
>
> my $seqio = Bio::SeqIO->new('-format' => 'GenBank', -fh => \*FH);
> while( my $seq = $seqio->next_seq ) {
> 	next unless $seq->species() =~/reinhardtii/;
> 	foreach my $feat ( $seq->top_SeqFeatures ) {
> 	............
>
>
>
> Do I need to call Bio::Species directly?
>
> 	my $species = Bio::Species->new();
>
> Chuck
>
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu