From bb9171f3219ebe952e163f3f9f32d48ace040a8b Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Wed, 25 May 2011 14:14:28 +0000
Subject: [PATCH] Removing ancient Ensembl::Lite package that is neither used
nor functional
---
modules/Bio/EnsEMBL/Lite/DBAdaptor.pm | 64 ------
modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm | 271 -------------------------
2 files changed, 335 deletions(-)
delete mode 100755 modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
delete mode 100644 modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
diff --git a/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm b/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
deleted file mode 100755
index 99136a9d2c..0000000000
--- a/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
+++ /dev/null
@@ -1,64 +0,0 @@
-=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;
diff --git a/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm b/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
deleted file mode 100644
index 117e990448..0000000000
--- a/modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
+++ /dev/null
@@ -1,271 +0,0 @@
-=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;
-
--
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