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

[Venky Nandagopal]

Scott,

Thanks for the reply. I should have been more careful with my email -- my 
script actually has the following lines

@genes = $db->get_feature_by_name("Gene" => $gene_id);
print $genes[0]->seq;

The script works for every other CG number I've tried --- it only fails for 
CG6667, which makes me think that there must be something wierd going on 
with Bio::DB::GFF, not the script.

Venky



On 03 Jul 2003 13:46:08 -0400, Scott Cain <cain at cshl.org> wrote:

> 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
>



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