[Bioperl-l] Re: Bio::DB::GFF trouble + Blast question

[Scott Cain]

Venky,

It is not all that clear to me why in this case you need to, but you
need to specify the class of the object, in this case 'Gene'.

Here is an example script that works for me:

#!/usr/bin/perl
use strict;
use Bio::DB::GFF;
my $db = Bio::DB::GFF->new(-adaptor => 'dbi::mysql',
                           -dsn     => 'fly');
my @genes = $db->get_feature_by_name(-class=>'Gene',-name=>'CG6665');
print $genes[0]->seq,"\n";

Scott

On Thu, 2003-07-03 at 11:58, bioperl-l-request at portal.open-bio.org
wrote:
> Message: 12
> Date: Thu, 03 Jul 2003 01:43:57 -0700
> From: Venky Nandagopal <venky at OCF.Berkeley.EDU>
> Subject: [Bioperl-l] Bio::DB::GFF trouble + Blast question
> To: bioperl-l at portal.open-bio.org
> Message-ID: <oprrp7vjpxqwe008 at mail.ocf.berkeley.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> Hi,
> 
> I have a couple of problems: (1) I use a database created using 
> process_gadfly.pl to access the D.mel genome, via Bio::DB::GFF. I have a 
> utility script that returns the sequence of a gene given the CG number, 
> using 	@genes = get_feature_by_name(CG####); 	print $genes[0]->seq;
> This script seems to work fine for most CG numbers, except for CG6667, 
> which is the ID for the dorsal gene. For some reason, no sequence is 
> returned by the seq() method. The gene object is not undefined though, 
> since $genes[0]->asString returns "gene:gadfly(CG6667)"; similarly the 
> start, end, strand methods work fine. I have tried getting transcripts 
> instead of the gene etc etc, but CG6667 refuses to yield any sequence. Can 
> anyone provide an explanation for this?
> 
> 
> (2) This is not directly connect to Bioperl, but BLAST reports sometimes 
> provide Expect values in the form "Expect(3)=0.0". What does the 3 refer 
> to? Sometimes it says "Expect(7+)=1e-23".
> 
> 
> Thanks
> Venky

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory