Raw content of Bio::EnsEMBL::ExternalData::SNPSQL::WebAdaptor
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#
# Ensembl module for Bio::EnsEMBL::ExternalData::SNPSQL::WebAdaptor.pm
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::ExternalData::SNPSQL::WebAdaptor - Web accelerated (light objects) for SNPs
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
This object is derived from SNPSQL::DBAdaptor.
Method get_Ensembl_SeqFeatures_clone_web() is there only to speed up
Web work. It loads only minimal set of sequence features into
Variation objects . To get a fullset of Variation attributes method
get_SeqFeature_by_id() is call on select objects, only. Additionally
it needs an attribute determined by the display resolution on how far
apart the features have to be to be drawn.
=head1 AUTHOR - Ewan Birney
This modules is part of the Ensembl project
Email birney@ebi.ac.uk
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::ExternalData::SNPSQL::WebAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor;
use Bio::EnsEMBL::ExternalData::Variation;
use Bio::EnsEMBL::Utils::Eprof qw( eprof_start eprof_end);
@ISA = qw(Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor);
# new is inherieted from SNPSQL::DBAdaptor
=head2 get_Ensembl_SeqFeatures_clone_web
Title : get_Ensembl_SeqFeatures_clone_web
Usage :
Function:
Example :
Returns : a list of lightweight Variation features.
Args : scalar in nucleotides (should default to 50)
array of accession.version numbers
=cut
sub get_Ensembl_SeqFeatures_clone_web {
my ($self,$glob,@acc) = @_;
if (! defined $glob) {
$self->throw("Need to call get_Ensembl_SeqFeatures_clone_web with a globbing parameter and a list of clones");
}
if (scalar(@acc) == 0) {
$self->throw("Calling get_Ensembl_SeqFeatures_clone_web with empty list of clones!\n");
}
#lists of variations to be returned
my @variations;
my %hash;
my $string;
foreach my $a (@acc) {
$a =~ /(\S+)\.(\d+)/;
$string .= "'$1',";
$hash{$1}=$2;
}
$string =~ s/,$//;
my $inlist = "($string)";
# db query to return all variation information in current GoldenPath; confidence attribute is gone!!
# data are preprocessed to contain only relevent information (RefSNP.mapweight is not needed)
# denormalized SubSNP in
my $query = qq{
SELECT start, end, strand,
acc, version, refsnpid,
tcsid, hgbaseid
FROM GPHit
WHERE acc in $inlist
ORDER BY acc,start
};
&eprof_start('snp-sql-query');
my $sth = $self->prepare($query);
my $res = $sth->execute();
&eprof_end('snp-sql-query');
my $snp;
my $cl;
&eprof_start('snp-sql-object');
SNP:
while( (my $arr = $sth->fetchrow_arrayref()) ) {
my ($begin, $end, $strand,
$acc, $ver, $snpuid,
$tscid, $hgbaseid
) = @{$arr};
my $acc_version="$acc.$ver";
if ( defined $snp && $snp->end+$glob >= $begin && $acc_version eq $cl) {
#ignore snp within glob area
next SNP;
}
next SNP if $hash{$acc} != $ver;
#
# prepare the output objects
#
### mega dodginess here: ideally, a Variation should be allowed to
### have several Locations. However, a Variation is-a SeqFeature,
### which can only have one. So instead, we'll return a list of
### Varations, each with a separate single location, but otherwise
### identical. That's clean-room engineering for you :-)
my $key=$snpuid.$acc; # for purpose of filtering duplicates
my %seen; # likewise
if ( ! $seen{$key} ) {
## we're grabbing all the necessary stuff from the db in one
## SQL statement for speed purposes, so we have to do some
## duplicate filtering here.
$seen{$key}++;
#Variation
$snp = new Bio::EnsEMBL::ExternalData::Variation
(-start => $begin,
-end => $end,
-strand => $strand,
-original_strand => $strand,
-score => 1,
-source_tag => 'dbSNP',
);
my $link = new Bio::Annotation::DBLink;
$link->database('dbSNP');
$link->primary_id($snpuid);
$link->optional_id($acc_version);
#add dbXref to Variation
$snp->add_DBLink($link);
if ($hgbaseid) {
my $link2 = new Bio::Annotation::DBLink;
$link2->database('HGBASE');
$link2->primary_id($hgbaseid);
$link2->optional_id($acc_version);
$snp->add_DBLink($link2);
}
if ($tscid) {
my $link3 = new Bio::Annotation::DBLink;
$link3->database('TSC-CSHL');
$link3->primary_id($tscid);
$link3->optional_id($acc_version);
#add dbXref to Variation
$snp->add_DBLink($link3);
}
$cl=$acc_version;
# set for compatibility to Virtual Contigs
$snp->seqname($acc_version);
#add SNP to the list
push(@variations, $snp);
} # if ! $seen{$key}
} # while a row from select statement
&eprof_end('snp-sql-object');
return @variations;
}
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