[Bioperl-l] Bio::DB::SeqFeature::Segment problem

[Jason Stajich]

One would have to see some of your GFF to know better.  It sounds like  
you have chr1 defined in multiple places.

Did you use the bp_seqfeature_load script to load the data in one go -  
it should catch it if you have non-unique IDs.

-jason
On Apr 30, 2009, at 9:40 AM, Jon Flowers wrote:

>
> Dear colleagues,
>
> I have set up a mySQL database and loaded a GFF3 and fasta file using
> Bio::DB::SeqFeature::Store::GFF3Loader.  Everything appears to be  
> working
> normally except when I attempt to create a  
> Bio::DB::SeqFeature::Segment
> object.
>
> The following works as expected:
>
> my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
> 				                                 -dsn => 'dbi:mysql:foo',
> 				                                 -user => 'myuser',
> 				                                 -pass => 'mypassword',
> 				                                 -write => '1');
>
> my @features = $db->features(-seq_id=>'chr1',
>                                              -start=>1,
>                                              -end=>10000,
>                                              -types=>['gene']);
>
> However, when I try to create a segment object using either of the two
> following method calls I get an error:
>
> my $segment  = $db->segment('chr1',1=>10000);
>
> my $segment  = $db->segment( -seq_id => 'chr1', -start => '1', -end =>
> '10000');
>
> -------------------------------- EXCEPTION
> ------------------------------------
>
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types  
> or
> -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment
> /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:1178
> STACK toplevel trial.pl:42
> -------------------------------------------------------
>
> Calling in list context (which is not defined in the documentation)  
> produces
> an array of 22 identical scalars = 'chr1:1..10000'.
>
> Any ideas?
>
> Thanks
>
> Jonathan
>
> -- 
> View this message in context: http://www.nabble.com/Bio%3A%3ADB%3A%3ASeqFeature%3A%3ASegment-problem-tp23319982p23319982.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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Jason Stajich
jason at bioperl.org