Raw content of Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor
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# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor
#
# Copyright (c) 2004 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor
=head1 SYNOPSIS
$vdb = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(...);
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
# tell the variation database where core database information can be
# be found
$vdb->dnadb($db);
$va = $vdb->get_VariationAdaptor();
$vfa = $vdb->get_VariationFeatureAdaptor();
$sa = $db->get_SliceAdaptor();
# Get a VariationFeature by its internal identifier
$vf = $va->fetch_by_dbID(145);
# get all VariationFeatures in a region
$slice = $sa->fetch_by_region('chromosome', 'X', 1e6, 2e6);
foreach $vf (@{$vfa->fetch_all_by_Slice($slice)}) {
print $vf->start(), '-', $vf->end(), ' ', $vf->allele_string(), "\n";
}
# fetch all genome hits for a particular variation
$v = $va->fetch_by_name('rs56');
foreach $vf (@{$vfa->fetch_all_by_Variation($v)}) {
print $vf->seq_region_name(), $vf->seq_region_start(), '-',
$vf->seq_region_end(),"\n";
}
=head1 DESCRIPTION
This adaptor provides database connectivity for VariationFeature objects.
Genomic locations of variations can be obtained from the database using this
adaptor. See the base class BaseFeatureAdaptor for more information.
=head1 AUTHOR - Graham McVicker
=head1 CONTACT
Post questions to the Ensembl development list ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor;
use Bio::EnsEMBL::Variation::VariationFeature;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
our @ISA = ('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor');
=head2 fetch_all_by_Variation
Arg [1] : Bio::EnsEMBL:Variation::Variation $var
Example : my @vfs = @{$vfa->fetch_all_by_Variation($var)};
Description: Retrieves all variation features for a given variation. Most
variations should only hit the genome once and only a return
a single variation feature.
Returntype : reference to list Bio::EnsEMBL::Variation::VariationFeature
Exceptions : throw on bad argument
Caller : general
Status : Stable
=cut
sub fetch_all_by_Variation {
my $self = shift;
my $var = shift;
if(!ref($var) || !$var->isa('Bio::EnsEMBL::Variation::Variation')) {
throw('Bio::EnsEMBL::Variation::Variation arg expected');
}
if(!defined($var->dbID())) {
throw("Variation arg must have defined dbID");
}
return $self->generic_fetch("vf.variation_id = ".$var->dbID());
}
=head2 fetch_all_genotyped_by_Slice
Arg [1] : Bio::EnsEMBL:Variation::Slice $slice
Example : my @vfs = @{$vfa->fetch_all_genotyped_by_Slice($slice)};
Description: Retrieves all variation features that have been gentoyped for a given slice.
Most variations should only hit the genome once and only a return
a single variation feature.
Returntype : reference to list Bio::EnsEMBL::Variation::VariationFeature
Exceptions : throw on bad argument
Caller : general
Status : Stable
=cut
sub fetch_all_genotyped_by_Slice{
my $self = shift;
my $slice = shift;
my $constraint = "vf.flags & 1";
#call the method fetch_all_by_Slice_constraint with the genotyped constraint
return $self->fetch_all_by_Slice_constraint($slice,$constraint);
}
# method used by superclass to construct SQL
sub _tables { return (['variation_feature', 'vf'],
[ 'source', 's']); }
sub _default_where_clause {
my $self = shift;
return 'vf.source_id = s.source_id';
}
sub _columns {
return qw( vf.variation_feature_id vf.seq_region_id vf.seq_region_start
vf.seq_region_end vf.seq_region_strand vf.variation_id
vf.allele_string vf.variation_name vf.map_weight s.name vf.validation_status vf.consequence_type);
}
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
#
# This code is ugly because an attempt has been made to remove as many
# function calls as possible for speed purposes. Thus many caches and
# a fair bit of gymnastics is used.
#
my $sa = $self->db()->dnadb()->get_SliceAdaptor();
my @features;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my ($variation_feature_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $variation_id,
$allele_string, $variation_name, $map_weight, $source_name, $validation_status, $consequence_type );
$sth->bind_columns(\$variation_feature_id, \$seq_region_id,
\$seq_region_start, \$seq_region_end, \$seq_region_strand,
\$variation_id, \$allele_string, \$variation_name,
\$map_weight, \$source_name, \$validation_status, \$consequence_type);
my $asm_cs;
my $cmp_cs;
my $asm_cs_vers;
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
my $dest_slice_start;
my $dest_slice_end;
my $dest_slice_strand;
my $dest_slice_length;
if($dest_slice) {
$dest_slice_start = $dest_slice->start();
$dest_slice_end = $dest_slice->end();
$dest_slice_strand = $dest_slice->strand();
$dest_slice_length = $dest_slice->length();
}
FEATURE: while($sth->fetch()) {
#get the slice object
my $slice = $slice_hash{"ID:".$seq_region_id};
if(!$slice) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
$slice_hash{"ID:".$seq_region_id} = $slice;
$sr_name_hash{$seq_region_id} = $slice->seq_region_name();
$sr_cs_hash{$seq_region_id} = $slice->coord_system();
}
#
# remap the feature coordinates to another coord system
# if a mapper was provided
#
if($mapper) {
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
($sr_name,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($sr_name));
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"} ||=
$sa->fetch_by_region($cmp_cs_name, $sr_name,undef, undef, undef,
$cmp_cs_vers);
} else {
$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
$sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
$asm_cs_vers);
}
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length) {
next FEATURE;
}
}
$slice = $dest_slice;
}
$validation_status = 0 if (!defined $validation_status);
my @states = split(',',$validation_status);
my @types = split(',',$consequence_type); #get the different consequence types
# consequence_type
push @features, $self->_create_feature_fast('Bio::EnsEMBL::Variation::VariationFeature',
#push @features, Bio::EnsEMBL::Variation::VariationFeature->new_fast(
#if use new_fast, then do not need "-" infront of key, i.e 'start' => $seq_region_start,
{'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'slice' => $slice,
'allele_string' => $allele_string,
'variation_name' => $variation_name,
'adaptor' => $self,
'dbID' => $variation_feature_id,
'map_weight' => $map_weight,
'source' => $source_name,
'validation_code' => \@states,
'consequence_type' => \@types || 'INTERGENIC',
'_variation_id' => $variation_id});
}
return \@features;
}
=head2 list_dbIDs
Arg [1] : none
Example : @feature_ids = @{$simple_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all simple features in
the current db
Returntype : list of ints
Exceptions : none
Caller : general
Status : At Risk
=cut
sub list_dbIDs {
my $self = shift;
return $self->_list_dbIDs('variation_feature');
}
=head2 get_all_synonym_sources
Args[1] : Bio::EnsEMBL::Variation::VariationFeature vf
Example : my @sources = @{$vf_adaptor->get_all_synonym_sources($vf)};
Description : returns a list of all the sources for synonyms of this
VariationFeature
ReturnType : reference to list of strings
Exceptions : none
Caller : general
Status : At Risk
: Variation database is under development.
=cut
sub get_all_synonym_sources{
my $self = shift;
my $vf = shift;
my %sources;
my @sources;
if(!ref($vf) || !$vf->isa('Bio::EnsEMBL::Variation::VariationFeature')) {
throw("Bio::EnsEMBL::Variation::VariationFeature argument expected");
}
if (!defined($vf->{'_variation_id'}) && !defined($vf->{'variation'})){
warning("Not possible to get synonym sources for the VariationFeature: you need to attach a Variation first");
return \@sources;
}
#get the variation_id
my $variation_id;
if (defined ($vf->{'_variation_id'})){
$variation_id = $vf->{'_variation_id'};
}
else{
$variation_id = $vf->variation->dbID();
}
#and go to the varyation_synonym table to get the extra sources
my $source_name;
my $sth = $self->prepare(qq{SELECT s.name
FROM variation_synonym vs, source s
WHERE s.source_id = vs.source_id
AND vs.variation_id = ?
});
$sth->bind_param(1,$variation_id,SQL_INTEGER);
$sth->execute();
$sth->bind_columns(\$source_name);
while ($sth->fetch){
$sources{$source_name}++;
}
@sources = keys(%sources);
return \@sources;
}
1;
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