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

[Adam Witney]

Thanks for your replies guys.

I was trying to do it from the BioSQL schema and Bio::DB::BioDB but after some further investigation it looks like Bio::DB::GFF or Bio::DB::SeqFeature::Store are the only ways to do it

Thanks

adam

On 13 Jul 2011, at 01:06, Chris UI wrote:

> 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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