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

[Smithies, Russell]

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
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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