Monks,

I am currently making use of the Bio::DB::GenBank module from BioPerl to conduct searches for medical terms across a number of databases in turn.

Using the docs as a guide, I have written the following subroutine which should make this possible: 

sub search {
    my ( $db, @keywords ) = @_;
    my ( $gb, $query, $seqio );

    $gb     = new Bio::DB::GenBank;
    $query  = Bio::DB::Query::GenBank->new(
                       -query => join(" ", @keywords),
                       -db    => $db
                       );

    $seqio  = $gb->get_Stream_by_query($query);
    
    print "Search for [", join(" ", @keywords), "] on $db returned ", 
+$query->count, " results.\n";

    while ( my $seq = $seqio->next_seq() ) {
        # do something with the data
    }
}

[download]

I am encountering problems when trying to extract each sequence object from the stream, however, in that calls to $seqio->next_seq() never seem to return an object. I am certain data is being retrieved from the database (the count of records retrieved and obtained from $query is > 0).

Has anyone made use of this module and had a similar problem? If so, can you suggest a way to correct the issue?

Thanks in advance,

-- Foxcub
#include www.liquidfusion.org.uk

In reply to Retrieving Search Results from a Bio::DB::GenBank Query by Tanalis

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