[Bioperl-l] Multiple gene segment problem

[Lincoln Stein]

There may be several genes with the same name. Call segment() in a list 
context to get them all.

Lincoln

On Saturday 11 March 2006 01:05, Marco Blanchette wrote:
> Dear all--
>
> One more unusual behavior from the latest GadFly gff3 database loaded into
> mySQL... I had been following Lincoln Stein advice as to how populate a
> Bio::DB::GFF mySQL database with GadFly. Everything seemed to work nicely
> but somehow, while calling for gene segment based on CG ids, I hit a CG
> with more than one assignment as in
>
> #!/usr/bin/perl
>
> use strict;
> use Bio::DB::GFF;
>
> my $agg1 = Bio::DB::GFF::Aggregator->new(    -method => 'pre_mRNA',
>                                             -sub_parts    =>
> ['exon','five_prime_UTR','three_prime_UTR'],
>                                         );
>
> my $dmdb = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',
>                       -dsn =>
> 'dbi:mysql:database=dmel_421;host=riolab.net', -user => 'guest',
>                       -aggregators=> [$agg1],
>                       );
>
> my @hits = ('CG2086', 'CG17894', 'CG32912');
>
> for my $gene (@hits){
>     my $tg = $dmdb->segment(-name => $gene);
>     print "$gene is ", $tg->length,  " nt long\n";
> }
>
> When I tried to get the segment for gene CG32912, I get the following:
>
> ------------- EXCEPTION  -------------
> MSG: multiple segment exception
> STACK Bio::DB::GFF::_multiple_return_args
> /Library/Perl/5.8.6/Bio/DB/GFF.pm:953
> STACK Bio::DB::GFF::segment /Library/Perl/5.8.6/Bio/DB/GFF.pm:938
> STACK toplevel test.pl:19
>
> --------------------------------------
>
> Any clue??? Any fix???
>
> ______________________________
> Marco Blanchette, Ph.D.
>
> mblanche at uclink.berkeley.edu
>
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
>
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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PLEASE CONTACT MY ASSISTANT, 
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