[Bioperl-l] fetch method of Bio::Index::Fasta

[Simon Chan]

Hi All,

I'm trying to index a bunch of fasta files for easy sequence fetching.
So, I take a look at Bio::Index::Fasta

my $Index = Bio::Index::Fasta->new( -filename => "output", -write_flag => 1);

### Each element of @array contains path to fasta file
$Index->make_index(@array);


foreach my $id (@array) {

        my $line = $Index->fetch($id);  
        print "ID: " . $line->display_id() . " \n";


}



In the docs, it says that the fetch method returns a Seq object.  Thus, I can run
the Seq methods, like display_id(), desc(), etc.  However, running the fetch method
appears to not return anything to me!  Therefore, once I get to the print line, the
program dies because I'm trying to call a method on an undefined variable. That is,
$line is undefined.


Perhaps, there is more documentation to view?  I've taken a look at:
http://doc.bioperl.org/releases/bioperl-1.0/Bio/Index/AbstractSeq.html#POD2

Well, that's about it.  Many thanks for your input, All! ;-)

Simon

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