[Bioperl-l] How to retrieve/parse RefSeq contig entries with Bio::DB::Query::GenBank?

[Jason Stajich]

I think we deliberately bail on these - need someone to figure out how 
to parse them correctly.

-jason
On Dec 5, 2004, at 3:14 PM, Rumen Kostadinov wrote:

> Hi,
>
>
> Is there a way to retrieve and parse RefSeq contig entries with bioperl
> using the Bio::DB::Query::GenBank?
>
> e.g.
> NT_079581
>
> I get weird parsing when doing:
>
>    my $query_string = param('query');
>    my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide',
>                                             -query=>$query_string);
>    my $count = $query->count;
>    my @ids   = $query->ids;
>
>    # get a genbank database handle
>    my $gb = new Bio::DB::GenBank;
>
>    my $stream = $gb->get_Stream_by_query($query);
>    while (my $seq = $stream->next_seq) {
>        print "<tr><td>";
>        print '<a href="map.pl?acc='.$seq->accession_number().';">';
>        print $seq->accession_number(), '</a> ';
>        print "<td>", $seq->desc(), br;
>    }
>
> Sincerely,
> Rumen Kostadinov
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/