Skip to content
Snippets Groups Projects
Commit bb9171f3 authored by Kieron Taylor's avatar Kieron Taylor :angry:
Browse files

Removing ancient Ensembl::Lite package that is neither used nor functional

parent 400b9e14
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
modules/Bio/EnsEMBL/Lite/DBAdaptor.pm deleted 100755 → 0
+ 0
− 64
View file @ 400b9e14
=head1 LICENSE
Copyright (c) 1999-2011 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
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <dev@ensembl.org>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Lite::DBAdaptor
=head1 SYNOPSIS
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-user => 'anonymous',
-dbname => 'homo_sapiens_lite_20_34c',
-host => 'ensembldb.ensembl.org',
-driver => 'mysql'
);
$snp_adaptor = $db->get_SNPAdaptor();
@snps = @{ $snp_adaptor->fetch_all_by_Slice($slice) }
=head1 DESCRIPTION
This is a database connection to the denormalised lite database. It
allows for the rapid creation of drawable objects that are too slow
to retreive from normalised data sources. Formerly this included many
Ensembl objects such as genes, transcript, exons, etc. but is now
limited to just SNPs.
=head1 METHODS
=cut
package Bio::EnsEMBL::Lite::DBAdaptor;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::EnsEMBL::DBSQL::DBAdaptor);
sub get_available_adaptors{
my %pairs = ("SNP", "Bio::EnsEMBL::Lite::SNPAdaptor");
return (\%pairs);
}
1;
modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm deleted 100644 → 0
+ 0
− 271
View file @ 400b9e14
=head1 LICENSE
Copyright (c) 1999-2011 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
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <dev@ensembl.org>.
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;
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment