Raw content of Bio::EnsEMBL::Lite::SNPAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::GeneLiteAdaptor -
MySQL Database queries to retrieve genes quickly from denormalized tables.
=head1 SYNOPSIS
=head1 METHODS
=cut
package Bio::EnsEMBL::Lite::SNPAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::SNP;
use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all_by_Slice
Arg 1 : Bio::EnsEMBL::Slice $slice
The slice we want SNPs on
Function : retrieve all the SNPs on this slice.
uses Lite databases transcript to get info
Returntype: listreference of Bio::EnsEMBL::ExternalData::Variation
Exceptions: none
Caller : Bio::EnsEMBL::Slice
=cut
sub fetch_all_by_Slice {
my ($self, $slice ) = @_;
my @snps;
my $from_strand = $slice->strand();
# warn "LITE snps....";
# wherever this slice is, it needs to be converted to
# a toplevel slices since all snps in the lite database
# are stored on toplevel seqregions
my @projection = @{$slice->project('toplevel')};
my $link_col_idx = 12;
my @link_dbs = ('dbSNP', 'WI', 'HGBASE', 'TSC-CSHL', 'ANO');
my %link_cache = ();
foreach my $segment (@projection) {
my $from_start = $segment->from_start();
my $from_end = $segment->from_end();
my $top_slice = $segment->to_Slice();
my $top_slice_start = $top_slice->start();
my $top_slice_end = $top_slice->end();
my $top_slice_strand = $top_slice->strand();
my $sth = $self->prepare
("SELECT internal_id, chr_start, chr_end, chr_strand, type, " .
" range_type, validated, alleles, snpclass, mapweight, ".
" ambiguity, source, id_refsnp, id_wi, id_hgbase, id_tsc, " .
" id_ano " .
"FROM snp " .
"WHERE chr_name = ? " .
"AND chr_start >= ? " .
"AND chr_start <= ? " .
"AND chr_end >= ?");
$sth->execute($top_slice->seq_region_name(),
$top_slice_start - 500,
$top_slice_end,
$top_slice_start);
while(my $arrayref = $sth->fetchrow_arrayref()) {
my @links = ();
# loop over the last columns of the row to retrieve a single external
# database link for each column
for(my $i = 0; $i < scalar(@link_dbs); $i++) {
my $link_id = $arrayref->[$link_col_idx + $i];
next if(!$link_id);
my $link_db = $link_dbs[$i];
my $link = $link_cache{"$link_db:$link_id"};
if(!$link) {
$link = Bio::EnsEMBL::DBEntry->new_fast
({'dbname' => $link_db,
'primary_id' => $link_id,
'display_name' => $link_id});
$link_cache{"$link_db:$link_id"} = $link;
}
push @links, $link;
}
#create a snp object through a fast (hacky) constructor
my $status = $arrayref->[6];
$status =~ s/-/ /;
if($status && $status ne 'no info') {
$status = "proven $status";
} else {
$status = 'suspected';
}
# coordinates must be adjusted so that they are first
# relative to the start of the top level slice (rather than absolute)
# and then adjusted so they are relative to the start of the
# original requested slice (w/ from_start)
my($start,$end,$strand);
if($top_slice_strand == 1) {
$start = $arrayref->[1] - $top_slice_start + $from_start;
$end = $arrayref->[2] - $top_slice_start + $from_start;
$strand = $arrayref->[3];
} else {
$start = $top_slice_end - $arrayref->[2] + $from_start;
$end = $top_slice_end - $arrayref->[1] + $from_start;
$strand = $arrayref->[3] * -1;
}
push @snps, Bio::EnsEMBL::SNP->new_fast({
'dbID' => $arrayref->[0],
'_gsf_start' => $start,
'_gsf_end' => $end,
'_snp_strand' => $strand,
'_gsf_score' => 1,
'_type' => $arrayref->[4],
'_range_type' => $arrayref->[5],
'_validated' => $arrayref->[6],
'status' => $status,
'alleles' => $arrayref->[7],
'_ambiguity_code' => $arrayref->[10],
'_snpclass' => $arrayref->[8],
'_mapweight' => $arrayref->[9],
'_source' => $arrayref->[11],
'_source_tag' => $arrayref->[11],
'link' => \@links,
'_unique_id' => "$arrayref->[0]:$arrayref->[1]"
});
}
}
return \@snps;
}
sub fetch_all_by_Slice_transcript_ids {
my $self = shift;
my $slice = shift;
my $transcript_ids = shift;
my $DB = shift || 'core';
my $snps = $self->fetch_all_by_Slice( $slice );
my %SNPS = ();
foreach my $transid ( @{$transcript_ids||[]} ) {
# warn "TRANSCRIPT: $transid";
my $sth = $self->prepare(qq(select gs.snp_id, gs.type, gs.aminoacid_start,
gs.aminoacid_offset, gs.wildtype_aminoacid,
gs.aminoacids, s.internal_id, s.chr_start
from gene_snp as gs, snp as s
where gs.transcript_id = ? and gs.db = "$DB" and
gs.snp_id = s.snp_id
));
$sth->execute( $transid );
while(my $a = $sth->fetchrow_arrayref()) {
$SNPS{"$a->[6]:$a->[7]"}{$transid} = [ @$a ];
}
}
foreach my $snp ( @$snps ) {
$snp->{'_transcripts'} = {};
my $snptype = '99:';
if( $SNPS{$snp->{'_unique_id'}} ) {
#warn ">>> $snp->{'_unique_id'}";
foreach my $transid ( keys %{$SNPS{$snp->{'_unique_id'}}} ) {
my $a = $SNPS{$snp->{'_unique_id'}}{$transid};
$snp->{'_transcripts'}{$transid} = $a;
$snptype = $a->[1] if $a->[1] lt $snptype;
}
}
$snp->{'_local_type'} = $snptype;
}
return $snps;
}
sub fetch_attributes_only_lite{
my $self = shift;
my $refsnp_id = shift;
my $source = shift || 'dbSNP';
my $WHERE = $source eq 'dbSNP' ? "id_refsnp = ? and source='dbSNP'" : "id_ano=? and source='non-dbSNP'";
my %SNPS = qw( 12 dbSNP 13 WI 14 HGBASE 15 TSC-CSHL 16 ANO );
my $QUERY = "select internal_id, chr_start, chr_end, chr_strand, type, range_type,
validated, alleles, snpclass, mapweight, ambiguity, source,
id_refsnp, id_wi, id_hgbase, id_tsc, id_ano, chr_name
FROM snp
WHERE $WHERE";
my $sth = $self->prepare( $QUERY );
eval { $sth->execute($refsnp_id);};
return [] if $@;
my @snps = ();
my %link_hash;
my $link;
while(my $arrayref = $sth->fetchrow_arrayref()) {
my @links = ();
foreach( sort keys %SNPS ) {
my $V = $arrayref->[ $_ ];
if( $V && $V ne '' ) {
unless($link = $link_hash{"$SNPS{$_}:$V"}) {
$link_hash{"$SNPS{$_}:$V"} = $link = Bio::EnsEMBL::DBEntry->new_fast( {'_dbname' => $SNPS{$_}, '_primary_id' => $V });
}
push @links, $link;
}
}
#create a snp object through a fast (hacky) constructor
my $STATUS = $arrayref->[6];
$STATUS =~s/-/ /;
$STATUS = ( $STATUS && $STATUS ne 'no info' ) ? "proven $STATUS" : 'suspected';
my $snp = Bio::EnsEMBL::SNP->new_fast(
{ 'dbID' => $arrayref->[0],
'_snp_strand' => $arrayref->[3],
'_gsf_score' => 1,
'_type' => $arrayref->[4],
'_range_type' => $arrayref->[5],
'_validated' => $arrayref->[6],
'status' => $STATUS,
'alleles' => $arrayref->[7],
'_ambiguity_code' => $arrayref->[10],
'_snpclass' => $arrayref->[8],
'_mapweight' => $arrayref->[9],
'_source' => $arrayref->[11],
'_source_tag' => $arrayref->[11],
'link' => \@links });
return $snp;
}
return undef;
}
1;
]]>