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

[Adam Witney]

Thanks Roy,

I had given up and switched to Bio::DB::SeqFeature::Store which works fine (as suggested by Chris). But I may go back and give this a try to see how it works.

Thanks again

adam

On 22 Jul 2011, at 12:02, Roy Chaudhuri wrote:

> Hi Adam,
> 
> Sorry for the late reply. You can do this direct from BioSQL using a BioQuery:
> 
> #!/usr/bin/perl
> use warnings FATAL=>qw(all);
> use Modern::Perl;
> use Bio::DB::BioDB;
> use Bio::DB::Query::BioQuery;
> my ($accession, $start, $end)=qw(U00096 1000 1001);
> my $dbadap=Bio::DB::BioDB->new(-database=>'biosql', -dbname=>'mydatabase', -user=>'myuser', -pass=>'mypass', -driver=>'mysql');
> my @where=("entry.accession_number='$accession'",
> "location.start < $end",
> "location.end > $start");
> my $query=Bio::DB::Query::BioQuery->new(-datacollections=>['Bio::SeqFeatureI feat', 'Bio::Annotation::SimpleValue=>Bio::SeqFeatureI term::primary_tag',
> 'Bio::PrimarySeqI=>Bio::SeqFeatureI entry',
> 'Bio::SeqFeatureI=>Bio::LocationI'],
> -where=>\@where
> );
> my $result=$dbadap->get_object_adaptor('Bio::SeqFeatureI')->find_by_query($query);
> while (my $feat=$result->next_object) {
>   say join "\t", $feat->primary_tag, $feat->get_tagset_values(qw(gene locus_tag product)), $feat->location->to_FTstring;
> }
> 
> Cheers,
> Roy.
> 
> On 13/07/2011 23:03, Adam Witney wrote:
>> 
>> 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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