[Bioperl-l] how to find SeqFeature at specific sequence location

[Chris UI]

One should be able to do this via Bio::DB::SeqFeature::Store.  However, going from a Bio::Seq to that is the tricky part.

chris

Sent from my iPad

On Jul 12, 2011, at 6:12 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> I've done it before by taking a segment of the sequence and looking for features in that.
> 
> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',-dsn=> 'hapmap:gbrowsemysql')or die "Can't open database:",Bio::DB::GFF->error,"\n";
> my $segment = $db->segment(-class=>'Chromosome',-name=> "Chr1", -start=>$start, -end=>$end);
> my @repeats = $segment->features(-types=> ['match:UCSC_REPEATMASK']);
> 
> --Russell
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Adam Witney
>> Sent: Wednesday, 13 July 2011 6:04 a.m.
>> To: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] how to find SeqFeature at specific sequence
>> location
>> 
>> Hi,
>> 
>> Is there an easy way of finding the SeqFeatures at a specific base
>> location on a Bio::Seq? I guess I can do it by calling
>> get_all_SeqFeatures and testing start/stop coordinates, but just
>> wondered if there was a better way.
>> 
>> Thanks
>> 
>> Adam
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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