diff --git a/modules/Bio/EnsEMBL/DBSQL/CrossMatchDBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CrossMatchDBAdaptor.pm
deleted file mode 100755
index d3939b49c8369d15ed1257f0600815779f6e6cc1..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/CrossMatchDBAdaptor.pm
+++ /dev/null
@@ -1,283 +0,0 @@
-
-#
-# Ensembl module for Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor
-#
-# Cared for by Ewan Birney <birney@ebi.ac.uk>
-#
-# Copyright GRL and EBI
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor - DESCRIPTION of Object
-
-=head1 SYNOPSIS
-
-my $db=Bio::EnsEMBL::DBSQL::Obj->new(-dbname=>'july_dna',-host=>'ecs1c',-user=>'ensadmin');
-
-my $cross=Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor->new(-dbname=>'crossmatch',-host=>'ecs1c',-user=>'ensadmin');
-
-$db->_crossdb($cross);
-
-=head1 DESCRIPTION
-
-This Object is a database adapter for the crossmatch database, it loads the old and new databases, which are held in _new_db and _old_db. It also gets a SymmetricFeatureContainer object, where the methods for getting and returning crossmatches are.
-
-The crossdb can then be added to a standard db in its _crossdb method.
-
-=head1 CONTACT
-
-Ensembl - ensembl-dev@ebi.ac.uk
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
-
-=cut
-
-
-# Let the code begin...
-
-
-package Bio::EnsEMBL::DBSQL::CrossMatchDBAdaptor;
-use vars qw(@ISA);
-use strict;
-
-# Object preamble - inheriets from Bio::Root::RootI
-use DBI;
-use Bio::Root::RootI;
-use Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer;
-use Bio::EnsEMBL::DBLoader;
-
-@ISA = qw(Bio::Root::RootI);
-
-sub new {
- my($class,@args) = @_;
-
- my $self = {};
- bless $self,$class;
-
- my ($db,$host,$driver,$user,$password,$port) =
- $self->_rearrange([qw(DBNAME
- HOST
- DRIVER
- USER
- PASS
- PORT
- )],@args);
- $db || $self->throw("Database object must have a database name");
- $user || $self->throw("Database object must have a user");
-
- if( ! $driver ) {
- $driver = 'mysql';
- }
-
- if( ! $host ) {
- $host = 'localhost';
- }
- my $dsn = "DBI:$driver:database=$db;host=$host";
- my $dbh = DBI->connect("$dsn","$user",$password, {RaiseError => 1});
-
- $self->_db_handle($dbh);
-
- return $self;
-}
-
-
-=head2 new_dbobj
-
- Title : new_dbobj
- Usage : $crossdb->new_dbobj
- Function: reads the dblocation table to load the new db
- Example : $crossdb->new_dbobj()
- Returns : Bio::EnsEMBL::DBSQL::Obj
- Args : none
-
-
-=cut
-
-sub new_dbobj{
- my ($self) = @_;
-
- my $t = $self->_new_dbobj;
- if( defined $t ) { return $t; }
-
- # yank it out ;)
-
- my $sth = $self->prepare("select newdatabase from dblocation");
- $sth->execute;
- my ($loc) = $sth->fetchrow_array;
-
- #print STDERR "New database locator: $loc\n";
- my $db = Bio::EnsEMBL::DBLoader->new($loc);
-
- $self->_new_dbobj($db);
- $db->_crossdb($self);
- return $db;
-}
-
-
-=head2 old_dbobj
-
- Title : old_dbobj
- Usage : $crossdb->old_dbobj
- Function: reads the dblocation table to load the old db
- Example : $crossdb->old_dbobj()
- Returns : Bio::EnsEMBL::DBSQL::Obj
- Args : none
-
-
-=cut
-
-sub old_dbobj{
- my ($self) = @_;
-
- my $t = $self->_old_dbobj;
- if( defined $t ) { return $t; }
-
- # yank it out ;)
- my $sth = $self->prepare("select olddatabase from dblocation");
- $sth->execute;
- my ($loc) = $sth->fetchrow_array;
- #print STDERR "Old database locator: $loc\n";
- my $db = Bio::EnsEMBL::DBLoader->new($loc);
-
- $self->_old_dbobj($db);
-
- return $db;
-}
-
-=head2 get_SymmetricContigFeatureContainer
-
- Title : get_SymmetricContigFeatureContainer
- Usage : $crossdb->get_SymmetricContigFeatureContainer
- Function: Gets a Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer
- Example : $crossdb->get_SymmetricContigFeatureContainer
- Returns : Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer
- Args : none
-
-
-=cut
-
-sub get_SymmetricContigFeatureContainer{
- my ($self) = @_;
-
- return Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer->new($self);
-}
-
-=head2 get_clonelist
-
- Title : get_clonelist
- Usage : $crossdb->get_clonelist
- Function: Reads the clonelist table, to return list of clones with different
- versions between old and new
- Example : $crossdb->get_clonelist
- Returns : array of strings
- Args : none
-
-=cut
-
-sub get_clonelist{
- my ($self) = @_;
-
- my @clones;
- my $sth=$self->prepare("select clone from clonelist");
- $sth->execute;
- while (my $clone = $sth->fetchrow_array()) {
- push @clones,$clone;
- }
- return @clones;
-}
-
-=head2 _new_dbobj
-
- Title : _new_dbobj
- Usage : $obj->_new_dbobj($newval)
- Function: get/set for the new db adapter
- Returns : value of _new_dbobj
- Args : newvalue (optional)
-
-
-=cut
-
-sub _new_dbobj{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'_new_dbobj'} = $value;
- }
- return $obj->{'_new_dbobj'};
-
-}
-
-=head2 _old_dbobj
-
- Title : _old_dbobj
- Usage : $obj->_old_dbobj($newval)
- Function: get/set for the old db adapter
- Returns : value of _old_dbobj
- Args : newvalue (optional)
-
-
-=cut
-
-sub _old_dbobj{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'_old_dbobj'} = $value;
- }
- return $obj->{'_old_dbobj'};
-
-}
-
-=head2 prepare
-
- Title : prepare
- Usage : $sth = $dbobj->prepare($statement);
- Function: prepares a SQL statement on the DBI handle
- Example :$sth = $dbobj->prepare("select seq_start,seq_end from feature where analysis = \'example\' ");
- Returns : A DBI statement handle object
- Args : a SQL string
-
-=cut
-
-sub prepare {
- my ($self,$string) = @_;
-
- if( ! $string ) {
- $self->throw("Attempting to prepare an empty SQL query!");
- }
- if( !defined $self->_db_handle ) {
- $self->throw("Database object has lost its database handle! getting otta here!");
- }
-
- # should we try to verify the string?
-
- return $self->_db_handle->prepare($string);
-}
-
-=head2 _db_handle
-
- Title : _db_handle
- Usage : $obj->_db_handle($newval)
- Function: get/set for the db handle
- Example : $obj->_db_handle($newval)
- Returns : value of _db_handle
- Args : newvalue (optional)
-
-
-=cut
-
-sub _db_handle{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_db_handle'} = $value;
- }
- return $self->{'_db_handle'};
-
-}
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 4dcce3d6e41d20cffecdce9e0bf7a4845ba65fb2..55c99422d52f0966aadfeb0eac8caa6b489a01ec 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -319,48 +319,6 @@ sub password {
}
-=head2 get_Feature_Obj
-
- Title : get_Feature_Obj
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-=cut
-
-sub get_Feature_Obj {
- my( $self ) = @_;
-
- my( $feature_obj );
- unless ($feature_obj = $self->{'_feature_obj'}) {
- require Bio::EnsEMBL::DBSQL::Feature_Obj;
- $feature_obj = Bio::EnsEMBL::DBSQL::Feature_Obj->new($self);
- $self->{'_feature_obj'} = $feature_obj;
- }
-
- return $feature_obj;
-}
-
-=head2 feature_Obj
-
- Title : feature_Obj
- Usage : my $featureobj = $db->feature_Obj
- Function: Returns the feature object database handle
- Example :
- Returns : Bio::EnsEMBL::DB::Feature_ObjI
- Args :
-
-=cut
-
-sub feature_Obj {
- my $self = shift;
-
- #$self->warn("feature_Obj is deprecated: using get_Feature_Obj instead!");
- return $self->get_Feature_Obj(@_);
-}
-
=head2 get_MetaContainer
@@ -2989,4 +2947,47 @@ sub remove_ExternalAdaptor {
}
+=head1 Old Functions
+
+Functions which are completely deprecated
+
+=cut
+
+
+=head2 get_Feature_Obj
+
+ Title : get_Feature_Obj
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+=cut
+
+sub get_Feature_Obj {
+ my( $self ) = @_;
+
+ $self->throw("No more Feature Objs!");
+}
+
+=head2 feature_Obj
+
+ Title : feature_Obj
+ Usage : my $featureobj = $db->feature_Obj
+ Function: Returns the feature object database handle
+ Example :
+ Returns : Bio::EnsEMBL::DB::Feature_ObjI
+ Args :
+
+=cut
+
+sub feature_Obj {
+ my $self = shift;
+ $self->throw("No more Feature Objs!");
+
+}
+
+
+
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExternalWrapper.pm b/modules/Bio/EnsEMBL/DBSQL/ExternalWrapper.pm
deleted file mode 100644
index 49203ad2011dd44702331a24bd18f70833e4edef..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/ExternalWrapper.pm
+++ /dev/null
@@ -1,306 +0,0 @@
-
-#
-# Ensembl module for Bio::EnsEMBL::DBSQL::ExternalWrapper
-#
-# Cared for by Ewan Birney <birney@ebi.ac.uk>
-#
-# Copyright GRL and EBI
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::ExternalWrapper - Makes a standard Ensembl database a ExternalFeatureFactoryI implementing object
-
-=head1 SYNOPSIS
-
- # check out DB::ExternalFeatureFactoryI
-
-=head1 DESCRIPTION
-
-This class wraps a standard Ensembl database as if it is an
-ExternalFeatureFactory interface, allowing it to serve up Genes and
-(assumming someone gets to write this as well) features.
-
-The idea here is that this database will contain different data (eg,
-data on EMBL CDS from the original entry) which is updated at a different
-cycle from the main stuff.
-
-=head1 CONTACT
-
-Ensembl - ensembl-dev@ebi.ac.uk
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
-
-=cut
-
-
-# Let the code begin...
-
-
-package Bio::EnsEMBL::DBSQL::ExternalWrapper;
-use vars qw(@ISA);
-use strict;
-
-# Object preamble - inheriets from Bio::Root::RootI
-use Bio::EnsEMBL::Gene;
-use Bio::Root::RootI;
-use Bio::EnsEMBL::DB::ExternalFeatureFactoryI;
-
-@ISA = qw(Bio::EnsEMBL::DB::ExternalFeatureFactoryI Bio::Root::RootI);
-
-sub new {
- my($class,$dbobj) = @_;
-
-
- my $self = {};
- bless $self,$class;
-
- if( !defined $dbobj ) {
- $self->throw("No dbobj or not a dbobj [$dbobj]");
- }
-
- $self->dbobj($dbobj);
-
- return $self;
-}
-
-
-=head2 get_Ensembl_Genes_clone
-
- Title : get_Ensembl_Genes_clone
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_Ensembl_Genes_clone{
- my ($self,$cloneid) = @_;
- my $clone;
-
- my $dbobj = $self->dbobj;
-
- #print STDERR "Got dbobj $dbobj connected to ",$dbobj->dbname,"\n";
-
- eval {
- $clone = $self->dbobj->get_Clone($cloneid);
- };
-
- if( $@ ) {
- # return nothing
- return ();
- }
-
- my @genes=$clone->get_all_Genes();
- #foreach my $gene ( @genes ) {
- # print STDERR "got ",$gene->id,"\n";
- #}
-
- return $clone->get_all_Genes();
-}
-
-=head2 get_Ensembl_Genes_contig_list
-
- Title : get_Ensembl_Genes_contig_list
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_Ensembl_Genes_contig_list{
- my ($self,@contigs) = @_;
-
- if( scalar @contigs == 0 ) {
- return ();
- }
- #Hash of contigs by gene id
- my %gc;
-
- #Hash of array of gene objects by contig
- my %cg;
- my $list;
- my @genes;
- my @todocontigs;
- if (my $cgr = $self->cg) {
- #Get them from the cache
- #print STDERR "Getting external genes from the cache\n";
- my %cgh = %$cgr;
- foreach my $c (@contigs) {
- if ($cgh{$c}) {
- foreach my $g (@{$cgh{$c}}) {
- $g->refresh();
- }
- push (@genes,@{$cgh{$c}});
- }
- }
- return @genes;
- }
- else {
- foreach my $c (@contigs) {
- $cg{$c}=[];
- }
- push (@todocontigs,@contigs);
- }
-
- if( scalar @todocontigs == 0 ) {
- return @genes;
- }
- else {
- foreach my $c ( @todocontigs ) {
- $list .= "'$c',";
- }
- chop $list;
- $list = "($list)";
-
- my $sth = $self->dbobj->prepare("
- SELECT t.gene_id,c.id
- FROM transcript t,exon_transcript et,exon e,
- contig c
- WHERE c.id in $list
- AND c.internal_id = e.contig_id
- AND e.exon_id = et.exon_id
- AND t.transcript_id = et.transcript_id");
-
- $sth->execute();
- my @geneids;
-
- while( my ($id,$contig) = $sth->fetchrow_array ) {
- if (!exists $gc{$id}) {
- $gc{$id}=$contig;
- }
- }
-
- push(@geneids,keys(%gc));
-
- if( scalar(@geneids) == 0 ) {
- #print STDERR "No ids here...\n";
- return();
- }
-
- #print STDERR "Getting external genes normally\n";
- my $ga = $self->dbobj->get_GeneAdaptor();
- for my $gene_id ( @geneids ) {
- my $gene = $ga->fetch_by_dbID( $gene_id );
- push( @genes, $gene );
- }
-
- foreach my $gene (@genes) {
- if (my $contig = $gc{$gene->dbID}) {
- push(@{$cg{$contig}},$gene);
- }
- }
- $self->cg(\%cg);
-
- # print STDERR "Returning ".scalar(@genes)." $genes[0] genes...\n";
- return @genes;
- }
-}
-
-=head2 cg
-
- Title : cg
- Usage : $obj->cg($newval)
- Function: Getset for cg value
- Returns : value of cg
- Args : newvalue (optional)
-
-
-=cut
-
-sub cg{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'cg'} = $value;
- }
- return $obj->{'cg'};
-
-}
-
-=head2 get_Ensembl_SeqFeatures_contig
-
- Title : get_Ensembl_SeqFeatures_contig
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_Ensembl_SeqFeatures_contig{
- my ($self,$contigid) = @_;
- return;
-}
-
-
-
-=head2 get_Ensembl_SeqFeatures_clone
-
- Title : get_Ensembl_SeqFeatures_clone
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-
-
-sub get_Ensembl_SeqFeatures_clone{
- my ($self,$contigid) = @_;
- return;
-}
-
-
-
-
-
-
-
-
-
-
-=head2 dbobj
-
- Title : dbobj
- Usage : $obj->dbobj($newval)
- Function:
- Returns : value of dbobj
- Args : newvalue (optional)
-
-
-=cut
-
-sub dbobj{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'dbobj'} = $value;
- }
- return $obj->{'dbobj'};
-
-}
-
-
-
-
-
-
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/Feature_Obj.pm b/modules/Bio/EnsEMBL/DBSQL/Feature_Obj.pm
deleted file mode 100755
index cd25327e64367dfb95b47d37d3dd7938ef3255ba..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/Feature_Obj.pm
+++ /dev/null
@@ -1,849 +0,0 @@
-#
-# EnsEMBL module for Bio::EnsEMBL::DBSQL::Feature_Obj
-#
-# Cared for by Elia Stupka <elia@ebi.ac.uk>
-#
-# Copyright Elia Stupka
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::Feature_Obj - MySQL database adapter class for EnsEMBL Feature Objects
-
-=head1 SYNOPSIS
-
- use Bio::EnsEMBL::DBSQL::Obj;
- use Bio::EnsEMBL::DBSQL::Feature_Obj;
-
- $db = new Bio::EnsEMBL::DBSQL::Obj( -user => 'root', -db => 'pog' , -host => 'caldy' , -driver => 'mysql' );
- my $feature_obj=Bio::EnsEMBL::Feature_Obj->new($obj);
-
- #Check if a feature exists
- $feature_obj->exists();
-
-=head1 DESCRIPTION
-
-This is one of the objects contained in Bio:EnsEMBL::DBSQL::Obj, dealing with
-feature objects.
-
-The Obj object represents a database that is implemented somehow (you shouldn\'t
-care much as long as you can get the object).
-
-=head1 CONTACT
-
-Elia Stupka: elia@ebi.ac.uk
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object methods. Internal methods are
-usually preceded with a _
-
-=cut
-
-
-# Let the code begin...
-
-package Bio::EnsEMBL::DBSQL::Feature_Obj;
-
-use vars qw(@ISA);
-use strict;
-
-# Object preamble - inheriets from Bio::Root::Object
-
-use Bio::Root::RootI;
-#use Bio::EnsEMBL::DBSQL::Obj;
-use Bio::EnsEMBL::Gene;
-use Bio::EnsEMBL::Exon;
-use Bio::EnsEMBL::Transcript;
-use Bio::EnsEMBL::FeatureFactory;
-use DBI;
-use Bio::EnsEMBL::DBSQL::Utils;
-use Bio::EnsEMBL::DBSQL::DummyStatement;
-
-
-
-@ISA = qw(Bio::Root::RootI);
-
-# new() is inherited from Bio::Root::Object
-
-# _initialize is where the heavy stuff will happen when new is called
-
-sub new {
- my($class,$db_obj) = @_;
- my $self = {};
- bless $self,$class;
-
- $db_obj || $self->throw("Database Gene object must be passed a db obj!");
- $self->_db_obj($db_obj);
-
- return $self; # success - we hope!
-}
-
-=head2 delete
-
- Title : delete
- Usage :
- Function: deletes all features from a contig;
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub delete {
- my ($self,$contig) = @_;
-
- if (ref( $contig) && $contig->isa("Bio::EnsEMBL::DB::ContigI")) {
- $self->throw("You have to give a contig id, not a contig object!");
- }
-
- my $sth = $self->_db_obj->prepare("select fs.feature,fs.fset " .
- "from fset_feature as fs, " .
- " feature as f " .
- "where fs.feature = f.id " .
- "and f.contig = '$contig'");
-
- my $res = $sth->execute || $self->warn("Could not find features for contig $contig");
-
- my %fset;
-
- while (my $rowhash = $sth->fetchrow_hashref) {
- $fset{$rowhash->{fset}} = 1;
- }
-
- my @fset = keys %fset;
-
- if ($#fset >= 0) {
- my $fsstr = "";
-
- foreach my $fs (@fset) {
- $fsstr .= $fs . ",";
- }
-
- chop($fsstr);
-
-
-
- $sth = $self->_db_obj->prepare("delete from fset where id in ($fsstr)");
- $res = $sth->execute;
-
- $sth = $self->_db_obj->prepare("delete from fset_feature where fset in ($fsstr)");
- $res = $sth->execute;
- }
-
- #print(STDERR "Deleting features for contig $contig\n");
-
- $sth = $self->_db_obj->prepare("delete from feature where contig = '$contig'");
- $res = $sth->execute;
-
- #print(STDERR "Deleting repeat features for contig $contig\n");
-
- $sth = $self->_db_obj->prepare("delete from repeat_feature where contig = '$contig'");
- $res = $sth->execute;
-
-}
-
-=head2 write
-
- Title : write
- Usage : $obj->write($contig,@features)
- Function: Writes a feature on the genomic sequence of a contig into the database
- Example :
- Returns : nothing
- Args : Bio::EnsEMBL::SeqFeatureI
-
-
-=cut
-
-sub write {
- my ($self,$contig,@features) = @_;
-
- #
- # Yes - we need to rethink how we are writing features into the
- # database. This is a little obtuse and clunky now
- #
-
- $self->throw("$contig is not a Bio::EnsEMBL::DB::ContigI")
- unless (defined($contig) && $contig->isa("Bio::EnsEMBL::DB::ContigI"));
-
- my $contigid = $contig->id;
- my $analysis;
-
-
- # Put the repeats in a different table, and also things we need to write
- # as fsets.
- my @repeats;
- my @fset;
-
- FEATURE :
- foreach my $feature ( @features ) {
-
- if( ! $feature->isa('Bio::EnsEMBL::SeqFeatureI') ) {
- $self->throw("Feature $feature is not a feature!");
- }
-
- eval {
- $feature->validate();
- };
-
- if ($@) {
-
- next FEATURE;
- }
-
- if($feature->isa('Bio::EnsEMBL::RepeatI')) {
- push(@repeats,$feature);
- } elsif ( $feature->sub_SeqFeature ) {
- push(@fset,$feature);
- } else {
- if (!defined($feature->analysis)) {
- $self->throw("Feature " . $feature->seqname . " " . $feature->source_tag ." doesn't have analysis. Can't write to database");
- } else {
- $analysis = $feature->analysis;
- }
-
-
- my $analysisid = $self->write_Analysis($analysis);
-
- if ( $feature->isa('Bio::EnsEMBL::FeaturePair') ) {
- my $homol = $feature->feature2;
-#scp - hack to make p_value look like a float
- $feature->p_value(&exponent($feature->p_value));
- my $sth = $self->_db_obj->prepare(
- "insert into feature(id,contig,seq_start,seq_end,score,strand,name,analysis,hstart,hend,hid,perc_id,evalue,phase,end_phase) ".
- "values ('NULL',"
- .$contig->internal_id .","
- .$feature->start .","
- .$feature->end .","
- .$feature->score .","
- .$feature->strand .","
- ."'".$feature->source_tag."',"
- .$analysisid .","
- .$homol->start .","
- .$homol->end .","
- ."'".$homol->seqname ."',"
- .((defined $feature->percent_id) ? $feature->percent_id : 'NULL') .","
- .((defined $feature->p_value) ? ("\'".$feature->p_value."\'") : 'NULL') .","
- .((defined $feature->phase) ? $feature->phase : 'NULL') .","
- .((defined $feature->end_phase) ? $feature->end_phase : 'NULL') .")");
-
- $sth->execute();
-
-
- } else {
- my $sth = $self->_db_obj->prepare( "insert into feature(id,contig,seq_start,seq_end,score,strand,name,analysis,hstart,hend,hid,perc_id,evalue,phase,end_phase) ".
- "values (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)");
-
- $sth->execute('NULL',
- $contig->internal_id,
- $feature->start,
- $feature->end,
- $feature->score,
- $feature->strand,
- $feature->source_tag,
- $analysisid,
- -1,
- -1,
- "__NONE__",
- 'NULL',
- 'NULL',
- 'NULL',
- 'NULL' );
- }
- }
- }
-
- my $sth2 = $self->_db_obj->prepare("insert into repeat_feature(id,contig,seq_start,seq_end,score,strand,analysis,hstart,hend,hid) values(?,?,?,?,?,?,?,?,?,?)");
-
- foreach my $feature (@repeats) {
- if (!defined($feature->analysis)) {
- $self->throw("Feature " . $feature->seqname . " " . $feature->source_tag ." doesn't have analysis. Can't write to database");
- } else {
- $analysis = $feature->analysis;
- }
-
-
- my $analysisid = $self->write_Analysis($analysis);
- my $homol = $feature->feature2;
-
- $sth2->execute('NULL',
- $contig->internal_id,
- $feature->start,
- $feature->end,
- $feature->score,
- $feature->strand,
- $analysisid,
- $homol->start,
- $homol->end,
- $homol->seqname);
- }
-
-
- # Now the predictions
- # we can't block do these as we need to get out the id wrt to the features
- foreach my $feature ( @fset ) {
-# print STDERR "Adding in a fset feature ",$feature->gff_string,"\n";
-
- if (!defined($feature->analysis)) {
-
- $self->throw("Feature " . $feature->seqname . " " .
- $feature->source_tag .
- " doesn't have analysis. Can't write to database");
- } else {
- $analysis = $feature->analysis;
- }
-
- my $analysisid = $self->write_Analysis($analysis);
- my $score = $feature->score();
-
- if( !defined $score ) { $score = "-1000"; }
-
- my $sth3 = $self->_db_obj->prepare("insert into fset(id,score) values ('NULL',$score)");
- $sth3->execute();
-
- # get out this id. This looks really clunk I know. Any better ideas... ?
-
- my $sth4 = $self->_db_obj->prepare("select LAST_INSERT_ID()");
- $sth4->execute();
-
- my $arr = $sth4->fetchrow_arrayref();
- my $fset_id = $arr->[0];
-
- # now write each sub feature
- my $rank = 1;
-
- foreach my $sub ( $feature->sub_SeqFeature ) {
-#scp - hack to make p_value look like a float
- $feature->p_value(&exponent($feature->p_value));
- my $sth5 = $self->_db_obj->prepare("insert into feature "
- ."(id,contig,seq_start,seq_end,score,strand,analysis,name,hstart,hend,hid,evalue,perc_id,phase,end_phase) "
- ."values('NULL','"
- .$contig->internal_id ."',"
- .$sub->start .","
- .$sub->end . ","
- .$sub->score . ","
- .$sub->strand . ","
- .$analysisid . ","
- ."'".$sub->source_tag ."',"
- ."-1,-1,"
- ."'".($sub->primary_tag || "__NONE__")."',"
- . ((defined $sub->p_value) ? "\'".$sub->p_value."\'" : 'NULL') .","
- . ((defined $sub->percent_id) ? $sub->percent_id : 'NULL') .","
- . ((defined $sub->phase) ? $sub->phase : 'NULL') .","
- . ((defined $sub->end_phase) ? $sub->end_phase : 'NULL') .")");
-
- $sth5->execute();
- my $sth6 = $self->_db_obj->prepare("insert into fset_feature(fset,feature,rank) values ($fset_id,LAST_INSERT_ID(),$rank)");
- $sth6->execute();
- $rank++;
- }
- }
-
- return 1;
-}
-
-=head2 get_Protein_annseq
-
- Title : get_Protein_annseq
- Usage : get_Protein_annseq ($ENSP);
- Function: Creates an annseq object for a particular peptide, storing the peptide
- sequence in $annseq->primary_seq, and adding all the protein features as generic
- Seqfeatures
- Example :
- Returns : $annseq
- Args : $ENSP
-
-
-=cut
-
-sub get_Protein_annseq{
- my ($self,$ENSP) = @_;
-
- my $annseq = Bio::EnsEMBL::AnnSeq->new();
-
- my $sth = $self->_db_obj->prepare("select id from transcript where translation = '$ENSP'");
- my $res = $sth->execute();
- my $rowhash = $sth->fetchrow_hashref;
-
- my $gene_obj=Bio::EnsEMBL::DBSQL::Gene_Obj->new($self->_db_obj);
- my $transcript = $gene_obj->get_Transcript($rowhash->{'id'});
- my $translation = $gene_obj->get_Translation($ENSP);
-
- $transcript->translation($translation);
-
- my $seq = $transcript->translate();
- $annseq->primary_seq($seq);
-
- $sth = $self->_db_obj->prepare("select * from proteinfeature where translation = '$ENSP'");
- $res = $sth->execute();
-
- while( my $rowhash = $sth->fetchrow_hashref) {
- my $analysis = $rowhash->{'analysis'};
- my $sth2 = $self->_db_obj->prepare("select * from analysis where id = '$analysis'");
- my $res2 = $sth2->execute();
- my $rowhash2 = $sth2->fetchrow_hashref;
-
- my $feature = new Bio::SeqFeature::Generic ( -start => $rowhash->{'seq_start'},
- -end => $rowhash->{'seq_end'},
- -score => $rowhash->{'score'},
- -primary => $rowhash2->{'gff_feature'},
- -source => $rowhash2->{'gff_source'});
-
- $annseq->add_SeqFeature($feature);
- }
-
- return $annseq;
-}
-
-=head2 write_all_Protein_features
-
- Title : write_all_Protein_features
- Usage : $obj->write_all_Protein_features($ENSP)
- Function: writes all protein features of a particular peptide into the database
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub write_all_Protein_features {
- my ($self,$prot_annseq,$ENSP) = @_;
-
- my $c=0;
- foreach my $feature ($prot_annseq->all_SeqFeatures()) {
- my $sth = $self->_db_obj->prepare("insert into proteinfeature (id,seq_start, seq_end, score, analysis, translation) values (NULL,"
- .$feature->start().","
- .$feature->end().","
- .$feature->score().",'"
- .$c."','"
- .$ENSP."')");
- $sth->execute();
-
- my $sth2 = $self->_db_obj->prepare("insert into analysis (id,db,db_version,program,program_version,gff_source,gff_feature) values ('$c','testens',1,'elia_program',1,'"
- .$feature->source_tag()."','"
- .$feature->primary_tag()."')");
- $sth2->execute();
- $c++;
- }
-}
-
-=head2 write_Protein_feature
-
- Title : write_Protein_feature
- Usage : $obj->write_Protein_feature($ENSP, $feature)
- Function: writes a protein feature object of a particular peptide into the database
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub write_Protein_feature {
- my ($self,$ENSP,$feature) = @_;
-
- my $sth = $self->_db_obj->prepare("insert into proteinfeature (seq_start, seq_end, score, translation) values ("
- .$feature->start()." ,"
- .$feature->end()." ,'"
- .$feature->score()." ,'"
- .$ENSP."'
- )");
- $sth->execute();
-}
-
-=head2 get_Analysis
-
- Title : get_Analysis
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_Analysis {
- my ($self,$id) = @_;
- my $sth = $self->_db_obj->prepare("select db,db_version,program,program_version,gff_source,gff_feature,id from analysis where id = $id");
- my $rv = $sth->execute;
- my $rh = $sth->fetchrow_hashref;
-
- if ($sth->rows) {
- my $anal = Bio::EnsEMBL::FeatureFactory->new_analysis();
-
- if( defined $rh->{'db'} ) {
- $anal->db($rh->{'db'});
- }
- if( defined $rh->{'db_version'} ) {
- $anal->db_version($rh->{'db_version'});
- }
-
- $anal->program ($rh->{'program'});
- $anal->program_version($rh->{'program_version'});
- $anal->gff_source ($rh->{gff_source});
- $anal->gff_feature ($rh->{gff_feature});
- my $mid = $rh->{'id'};
-
- if( !$anal->isa('Bio::EnsEMBL::Ext::Analysis') ) {
- $anal->dbID("$mid");
- }
-
- return $anal;
- } else {
- $self->throw("Can't fetch analysis id $id\n");
- }
-
-}
-
-=head2 exists_Analysis
-
- Title : exists_Analysis
- Usage : $obj->exists_Analysis($anal)
- Function: Tests whether this feature already exists in the database
- Example :
- Returns : Analysis id if the entry exists
- Args : Bio::EnsEMBL::Analysis
-
-
-=cut
-
-sub exists_Analysis {
- my ($self,$anal) = @_;
-
-
- $self->throw("Object is not a Bio::EnsEMBL::AnalysisI") unless $anal->isa("Bio::EnsEMBL::AnalysisI");
- # If all the attributes of the analysis object are not set it's existence can't be tested
- $self->throw("program property of analysis object not defined") unless ($anal->program);
- $self->throw("program_version property of analysis object not defined") unless ($anal->program_version);
- $self->throw("gff_source property of analysis object not defined") unless ($anal->gff_source);
- $self->throw("gff_feature property of analysis object not defined") unless ($anal->gff_feature);
-
- my $query;
-
- # remove leading components of path from db and program
- # to prevent lines in 'analysis' table with explicit directories
- # quick fix only: this ought to be done somewhere like Analysis.pm, not here
- my $db = $anal->db;
- $db =~ s!.*/!!;
- $anal->db($db);
- my $prog = $anal->program;
- $prog =~ s!.*/!!;
- $anal->program($prog);
-
- if ($anal->has_database == 1) {
- $query = "select id from analysis where db = \"" . $anal->db . "\" and" .
- " db_version = \"" . $anal->db_version . "\" and " .
- " program = \"" . $anal->program . "\" and " .
- " program_version = \"" . $anal->program_version . "\" and " .
- " gff_source = \"" . $anal->gff_source . "\" and" .
- " gff_feature = \"" . $anal->gff_feature . "\"";
- } else {
- $query = "select id from analysis where " .
- " program = \"" . $anal->program . "\" and " .
- " program_version = \"" . $anal->program_version . "\" and " .
- " gff_source = \"" . $anal->gff_source . "\" and" .
- " gff_feature = \"" . $anal->gff_feature . "\"";
- }
-
- if( exists $self->_db_obj->_analysis_cache->{$query} ) {
- return $self->_db_obj->_analysis_cache->{$query};
- }
-
- my $sth = $self->_db_obj->prepare($query);
- my $rv = $sth->execute();
-
- if ($rv && $sth->rows > 0) {
- my $rowhash = $sth->fetchrow_hashref;
- my $anaid = $rowhash->{'id'};
- $self->_db_obj->_analysis_cache->{$query} = $anaid;
- return $anaid;
- } else {
- return 0;
- }
-}
-
-=head2 write_Analysis
-
- Title : write_Analysis
- Usage : $obj->write_Analysis($anal)
- Function: Writes analysis details to the database
- Checks first whether this analysis entry already exists
- Example :
- Returns : int
- Args : Bio::EnsEMBL::AnalysisI
-
-=cut
-
-sub write_Analysis {
- my ($self,$anal) = @_;
-
- $self->throw("Argument is not a Bio::EnsEMBL::AnalysisI") unless $anal->isa("Bio::EnsEMBL::AnalysisI");
- # If all the attributes of the analysis object are not set it shouldn't be written
- $self->throw("program property of analysis object not defined") unless ($anal->program);
- $self->throw("program_version property of analysis object not defined") unless ($anal->program_version);
- $self->throw("gff_source property of analysis object not defined") unless ($anal->gff_source);
- $self->throw("gff_feature property of analysis object not defined") unless ($anal->gff_feature);
-
- # First check whether this entry already exists.
- my $query;
- my $analysisid = $self->exists_Analysis($anal);
- return $analysisid if $analysisid;
-
-
- if ($anal->has_database == 1) {
- local $^W = 0;
- $query = "insert into analysis(id,db,db_version,program,program_version,gff_source,gff_feature) values (NULL,\"" .
- $anal->db . "\",\"" .
- $anal->db_version . "\",\"" .
- $anal->program . "\",\"" .
- $anal->program_version . "\",\"" .
- $anal->gff_source . "\",\"" .
- $anal->gff_feature . "\")";
- } else {
- $query = "insert into analysis(id,program,program_version,gff_source,gff_feature) values (NULL,\"" .
- $anal->program . "\",\"" .
- $anal->program_version . "\",\"" .
- $anal->gff_source . "\",\"" .
- $anal->gff_feature . "\")";
- }
-
- my $sth = $self->_db_obj->prepare($query);
- my $rv = $sth->execute;
-
-
- $sth = $self->_db_obj->prepare("select last_insert_id()");
- $rv = $sth->execute;
-
- if ($sth->rows == 1) {
- my $rowhash = $sth->fetchrow_hashref;
- return $rowhash->{'last_insert_id()'};
- } else {
- $self->throw("Wrong number of rows returned : " . $sth->rows . " : should be 1");
- }
-
-}
-
-=head2 find_GenomeHits
-
- Title : find_GenomeHits
- Usage : $obj->find_GenomeHits($hitid)
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-sub find_GenomeHits {
- my ($self,$arg) = @_;
-
- $self->throw("No hit id input") unless defined($arg);
-
- my $query = "select c.id, " .
- "f.seq_start, " .
- "f.seq_end, " .
- "f.score, " .
- "f.strand, " .
- "f.analysis, " .
- "f.name, " .
- "f.hstart, " .
- "f.hend, " .
- "f.hid " .
- "from feature as f,contig as c " .
- "where f.hid = '$arg' and " .
- "c.internal_id = f.contig";
-
- my $sth = $self->_db_obj->prepare($query);
- my $res = $sth->execute;
-
- my ($contig,$start,$end,$score,$strand,$analysisid,$name,$hstart,$hend,$hid);
-
-
- $sth->bind_columns(undef,\$contig,\$start,\$end,\$score,\$strand,\$analysisid,
- \$name,\$hstart,\$hend,\$hid);
-
-
- my %analhash; # Stores all the analysis objects
- my @features;
-
- while($sth->fetch) {
- my $out;
- my $analysis;
-
- if (!$analhash{$analysisid}) {
-
- $analysis = $self->get_Analysis($analysisid);
- $analhash{$analysisid} = $analysis;
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- if( !defined $name ) {
- $name = 'no_source';
- }
-
- $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();
- $out->set_all_fields($start,$end,$strand,$score,$name,'similarity',$contig,
- $hstart,$hend,1,$score,$name,'similarity',$hid);
-
- $out->analysis($analysis);
- $out->validate;
-
- push(@features,$out);
-
- }
-
- return @features;
-}
-
-
-
-=head2 get_PredictionFeature_by_id
-
- Title : get_PredictionFeature_by_id
- Usage : $obj->get_PredictionFeature_by_id($id)
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_PredictionFeature_by_id {
- my ($self,$genscan_id) = @_;
-
- unless ($genscan_id){$self->throw("I need a genscan id");}
-
- my %analhash;
-
- my $query = "select f.id,f.seq_start,f.seq_end,f.strand,f.score,f.analysis,fset.id,c.id " .
- "from feature f, fset ,fset_feature ff,contig c where ff.feature = f.id and fset.id = ff.fset ".
- " and c.internal_id=f.contig and ff.fset = $genscan_id and name = \'genscan\'";
-
- my $sth = $self->_db_obj->prepare($query);
-
- $sth->execute();
-
- my ($fid,$start,$end,$strand,$score,$analysisid,$fsetid,$contig);
-
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$score,\$analysisid,\$fsetid,\$contig);
-
- my $fset;
- my $analysis;
-
- $fset = new Bio::EnsEMBL::SeqFeature;
- $fset->source_tag('genscan');
- $fset->primary_tag('prediction');
- $fset->id($genscan_id);
-
- while( my $row = $sth->fetchrow_hashref ) {
- my $analysisid = $row->{analysis};
-
- if (!$analhash{$analysisid}) {
- $analysis = $self->get_Analysis($analysisid);
- $analhash{$analysisid} = $analysis;
- } else {
- $analysis = $analhash{$analysisid};
- }
- $fset->analysis($analysis);
- $fset->seqname($contig);
- $fset->raw_seqname($contig);
-
- my $out = new Bio::EnsEMBL::SeqFeature;
-
- $out->seqname ($contig);
- $out->start ($row->{seq_start});
- $out->end ($row->{seq_end});
- $out->strand ($row->{strand});
- $out->source_tag('genscan');
- $out->primary_tag('prediction');
-
- if( defined $score ) {
- $out->score($row->{score});
- }
-
- $out->analysis($analysis);
-
- # Final check that everything is ok.
- # MC THis isn't playing nicely with the c extensions
- #$out->validate();
- $fset->add_sub_SeqFeature($out,'EXPAND');
- $fset->strand($row->{strand});
- }
-
- return $fset;
-
-}
-
-
-
-
-=head2 get_PredictionFeature_as_Transcript
-
- Title : get_PredictionFeature_as_Transcript
- Usage : $obj->get_PredictionFeature_as_Transcript($id)
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-
-
-
-sub get_PredictionFeature_as_Transcript{
- my ($self,$genscan_id)=@_;
- unless ($genscan_id){$self->throw("I need a genscan id");}
-
- my $ft = $self->get_PredictionFeature_by_id($genscan_id);
- my $contig = $self->_db_obj->get_Contig($ft->seqname);
-
- # Due to f*cked up genscan phases we are reduced to guessing the phases
-# return &Bio::EnsEMBL::DBSQL::Utils::fset2transcript($ft,$contig);
- return Bio::EnsEMBL::DBSQL::Utils::fset2transcript_guess_phases($ft,$contig);
-}
-
-
-
-=head2 _db_obj
-
- Title : _db_obj
- Usage : $obj->_db_obj($newval)
- Function:
- Example :
- Returns : value of _db_obj
- Args : newvalue (optional)
-
-
-=cut
-
-sub _db_obj{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_db_obj'} = $value;
- }
- return $self->{'_db_obj'};
-
-}
-
-
-
-sub exponent {
- my ($number) = @_;
-
- my ($exp) = sprintf("%.3e", $number);
- return $exp;
-}
diff --git a/modules/Bio/EnsEMBL/DBSQL/Feature_ObjForeign.pm b/modules/Bio/EnsEMBL/DBSQL/Feature_ObjForeign.pm
deleted file mode 100644
index 9b7a1bce2f4d79366e6e084488ff5650f220444a..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/Feature_ObjForeign.pm
+++ /dev/null
@@ -1,852 +0,0 @@
-#
-# EnsEMBL module for Bio::EnsEMBL::DBSQL::Feature_ObjForeign
-#
-# Cared for by Elia Stupka <elia@ebi.ac.uk>, Philip lijnzaad@ebi.ac.uk
-#
-# Copyright EnsEMBL
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::Feature_ObjForeign, specialization of Feature_Obj that
-allows you to translate table names to other names. The intended use is
-for an database that reuses (readonly, not writing!) part of another
-database in order to save on speed (no loading of all the assembly related
-data) and disk usage.
-
-
-=head1 SYNOPSIS
-
- use Bio::EnsEMBL::DBSQL::Obj;
- use Bio::EnsEMBL::DBSQL::Feature_ObjForeign;
-
- $db = new Bio::EnsEMBL::DBSQL::Obj( -user => 'root', -db => 'pog' , -host => 'caldy' , -driver => 'mysql' );
- my $feature_obj =Bio::EnsEMBL::Feature_ObjForeign->new($obj);
-
- my $mapping = { feature => myfeature,
- static_golden_path => ens081.static_golden_path
- };
- my $feature_obj->table_name_tranlations $mapping;
-
- # From here on, all the application code first translates the table
- # names, then does the queries on possibly translated names.
-
-=head1 DESCRIPTION
-
-Bio::EnsEMBL::DBSQL::Feature_ObjForeign, specialization of Feature_Obj that
-allows you to translate table names to other names. The intended use is
-for an database that reuses (readonly, not writing!) part of another
-database in order to save on speed (no loading of all the assembly related
-data) and disk usage.
-
-=head1 CONTACT
-
-Elia Stupka: elia@ebi.ac.uk, Philip lijnzaad@ebi.ac.uk
-
-=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::DBSQL::Feature_ObjForeign;
-
-use vars qw(@ISA $AUTOLOAD);
-use strict;
-
-# Object preamble - inheriets from Bio::Root::Object
-
-use Bio::Root::RootI;
-#use Bio::EnsEMBL::DBSQL::Obj;
-
-use Bio::EnsEMBL::Ghost;
-use Bio::EnsEMBL::Gene;
-use Bio::EnsEMBL::Exon;
-use Bio::EnsEMBL::Transcript;
-use Bio::EnsEMBL::FeatureFactory;
-use DBI;
-use Bio::EnsEMBL::DBSQL::Utils;
-use Bio::EnsEMBL::DBSQL::DummyStatement;
-
-
-@ISA = qw(Bio::EnsEMBL::DBSQL::ObjForeign
- Bio::Root::RootI
- Bio::EnsEMBL::DBSQL::Feature_Obj
- );
-
-sub new { # comes from ObjForeign
- my ($class, @args) = @_;
- my $self= $class->SUPER::new(@_);
- bless $self, $class;
- $self;
-}
-
-=head2 delete
-
- Title : delete
- Usage :
- Function: deletes all features from a contig;
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub delete {
- my ($self,$contig) = @_;
-
- if (ref( $contig) && $contig->isa("Bio::EnsEMBL::DB::ContigI")) {
- $self->throw("You have to give a contig id, not a contig object!");
- }
-
-
- my $sth = $self->_db_obj->prepare("SELECT fs.feature,fs.fset " .
- "from ".$self->_lookup_table_name('fset_feature')." as fs, " .
- " ".$self->_lookup_table_name('feature')." as f " .
- "where fs.feature = f.id " .
- "and f.contig = '$contig'");
-
- my $res = $sth->execute || $self->warn("Could not find features for contig $contig");
-
- my %fset;
-
- while (my $rowhash = $sth->fetchrow_hashref) {
- $fset{$rowhash->{fset}} = 1;
- }
-
- my @fset = keys %fset;
-
- if ($#fset >= 0) {
- my $fsstr = "";
-
- foreach my $fs (@fset) {
- $fsstr .= $fs . ",";
- }
-
- chop($fsstr);
-
-
-
- $sth = $self->_db_obj->prepare("DELETE from ".$self->_lookup_table_name('fset')." where id in ($fsstr)");
- $res = $sth->execute;
-
- $sth = $self->_db_obj->prepare("DELETE from ".$self->_lookup_table_name('fset_feature')." where fset in ($fsstr)");
- $res = $sth->execute;
- }
-
- #print(STDERR "Deleting features for contig $contig\n");
-
- $sth = $self->_db_obj->prepare("DELETE from ".$self->_lookup_table_name('feature')." where contig = '$contig'");
- $res = $sth->execute;
-
- #print(STDERR "Deleting repeat features for contig $contig\n");
-
- $sth = $self->_db_obj->prepare("DELETE from ".$self->_lookup_table_name('repeat_feature')." where contig = '$contig'");
- $res = $sth->execute;
-
-}
-
-=head2 write
-
- Title : write
- Usage : $obj->write($contig,@features)
- Function: Writes a feature on the genomic sequence of a contig into the database
- Example :
- Returns : nothing
- Args : Bio::EnsEMBL::SeqFeatureI
-
-
-=cut
-
-sub write {
- my ($self,$contig,@features) = @_;
-
- #
- # Yes - we need to rethink how we are writing features into the
- # database. This is a little obtuse and clunky now
- #
-
- $self->throw("$contig is not a Bio::EnsEMBL::DB::ContigI")
- unless (defined($contig) && $contig->isa("Bio::EnsEMBL::DB::ContigI"));
-
- my $contigid = $contig->id;
- my $analysis;
-
-
- # Put the repeats in a different table, and also things we need to write
- # as fsets.
- my @repeats;
- my @fset;
-
- FEATURE :
- foreach my $feature ( @features ) {
-
- if( ! $feature->isa('Bio::EnsEMBL::SeqFeatureI') ) {
- $self->throw("Feature $feature is not a feature!");
- }
-
- eval {
- $feature->validate();
- };
-
- if ($@) {
-
- next FEATURE;
- }
-
- if($feature->isa('Bio::EnsEMBL::RepeatI')) {
- push(@repeats,$feature);
- } elsif ( $feature->sub_SeqFeature ) {
- push(@fset,$feature);
- } else {
- if (!defined($feature->analysis)) {
- $self->throw("Feature " . $feature->seqname . " " . $feature->source_tag ." doesn't have analysis. Can't write to database");
- } else {
- $analysis = $feature->analysis;
- }
-
-
- my $analysisid = $self->write_Analysis($analysis);
-
- if ( $feature->isa('Bio::EnsEMBL::FeaturePair') ) {
- my $homol = $feature->feature2;
- my $sth = $self->_db_obj->prepare(
- "INSERT into ".$self->_lookup_table_name('feature')."(id,contig,seq_start,seq_end,score,strand,name,analysis,hstart,hend,hid,perc_id,evalue,phase,end_phase) ".
- "values ('NULL',"
- .$contig->internal_id .","
- .$feature->start .","
- .$feature->end .","
- .$feature->score .","
- .$feature->strand .","
- ."'".$feature->source_tag."',"
- .$analysisid .","
- .$homol->start .","
- .$homol->end .","
- ."'".$homol->seqname ."',"
- .((defined $feature->percent_id) ? $feature->percent_id : 'NULL') .","
- .((defined $feature->p_value) ? &exponent($feature->p_value) : 'NULL') .","
- .((defined $feature->phase) ? $feature->phase : 'NULL') .","
- .((defined $feature->end_phase) ? $feature->end_phase : 'NULL') .")");
-
- $sth->execute();
-
-
- } else {
- my $sth = $self->_db_obj->prepare( "INSERT into ".$self->_lookup_table_name('feature')."(id,contig,seq_start,seq_end,score,strand,name,analysis,hstart,hend,hid,perc_id,evalue,phase,end_phase) ".
- "values (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)");
-
- $sth->execute('NULL',
- $contig->internal_id,
- $feature->start,
- $feature->end,
- $feature->score,
- $feature->strand,
- $feature->source_tag,
- $analysisid,
- -1,
- -1,
- "__NONE__",
- 'NULL',
- 'NULL',
- 'NULL',
- 'NULL' );
- }
- }
- }
-
- my $sth2 = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('repeat_feature')."(id,contig,seq_start,seq_end,score,strand,analysis,hstart,hend,hid) values(?,?,?,?,?,?,?,?,?,?)");
-
- foreach my $feature (@repeats) {
- if (!defined($feature->analysis)) {
- $self->throw("Feature " . $feature->seqname . " " . $feature->source_tag ." doesn't have analysis. Can't write to database");
- } else {
- $analysis = $feature->analysis;
- }
-
-
- my $analysisid = $self->write_Analysis($analysis);
- my $homol = $feature->feature2;
-
- $sth2->execute('NULL',
- $contig->internal_id,
- $feature->start,
- $feature->end,
- $feature->score,
- $feature->strand,
- $analysisid,
- $homol->start,
- $homol->end,
- $homol->seqname);
- }
-
-
- # Now the predictions
- # we can't block do these as we need to get out the id wrt to the features
- foreach my $feature ( @fset ) {
-# print STDERR "Adding in a fset feature ",$feature->gff_string,"\n";
-
- if (!defined($feature->analysis)) {
-
- $self->throw("Feature " . $feature->seqname . " " .
- $feature->source_tag .
- " doesn't have analysis. Can't write to database");
- } else {
- $analysis = $feature->analysis;
- }
-
- my $analysisid = $self->write_Analysis($analysis);
- my $score = $feature->score();
-
- if( !defined $score ) { $score = "-1000"; }
-
- my $sth3 = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('fset')."(id,score) values ('NULL',$score)");
- $sth3->execute();
-
- # get out this id. This looks really clunk I know. Any better ideas... ?
-
- my $sth4 = $self->_db_obj->prepare("SELECT LAST_INSERT_ID()");
- $sth4->execute();
-
- my $arr = $sth4->fetchrow_arrayref();
- my $fset_id = $arr->[0];
-
- # now write each sub feature
- my $rank = 1;
-
- foreach my $sub ( $feature->sub_SeqFeature ) {
- my $sth5 = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('feature')."(id,contig,seq_start,seq_end,score,strand,analysis,name,hstart,hend,hid,evalue,perc_id,phase,end_phase) "
- ."values('NULL','"
- .$contig->internal_id ."',"
- .$sub->start .","
- .$sub->end . ","
- .$sub->score . ","
- .$sub->strand . ","
- .$analysisid . ","
- ."'".$sub->source_tag ."',"
- ."-1,-1,"
- ."'".($sub->primary_tag || "__NONE__")."',"
- . ((defined $sub->p_value) ? &exponent($sub->p_value) : 'NULL') .","
- . ((defined $sub->percent_id) ? $sub->percent_id : 'NULL') .","
- . ((defined $sub->phase) ? $sub->phase : 'NULL') .","
- . ((defined $sub->end_phase) ? $sub->end_phase : 'NULL') .")");
-
- $sth5->execute();
- my $sth6 = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('fset_feature')."(fset,feature,rank) values ($fset_id,LAST_INSERT_ID(),$rank)");
- $sth6->execute();
- $rank++;
- }
- }
-
- return 1;
-}
-
-=head2 get_Protein_annseq
-
- Title : get_Protein_annseq
- Usage : get_Protein_annseq ($ENSP);
- Function: Creates an annseq object for a particular peptide, storing the peptide
- sequence in $annseq->primary_seq, and adding all the protein features as generic
- Seqfeatures
- Example :
- Returns : $annseq
- Args : $ENSP
-
-
-=cut
-
-sub get_Protein_annseq{
- my ($self,$ENSP) = @_;
-
- my $annseq = Bio::EnsEMBL::AnnSeq->new();
-
- my $sth = $self->_db_obj->prepare("SELECT id from ".$self->_lookup_table_name('transcript')." where translation = '$ENSP'");
- my $res = $sth->execute();
- my $rowhash = $sth->fetchrow_hashref;
-
- my $gene_obj=Bio::EnsEMBL::DBSQL::Gene_Obj->new($self->_db_obj);
- my $transcript = $gene_obj->get_Transcript($rowhash->{'id'});
- my $translation = $gene_obj->get_Translation($ENSP);
-
- $transcript->translation($translation);
-
- my $seq = $transcript->translate();
- $annseq->primary_seq($seq);
-
- $sth = $self->_db_obj->prepare("SELECT * from ".$self->_lookup_table_name('proteinfeature')." where translation = '$ENSP'");
- $res = $sth->execute();
-
- while( my $rowhash = $sth->fetchrow_hashref) {
- my $analysis = $rowhash->{'analysis'};
- my $sth2 = $self->_db_obj->prepare("SELECT * from ".$self->_lookup_table_name('analysis')." where id = '$analysis'");
- my $res2 = $sth2->execute();
- my $rowhash2 = $sth2->fetchrow_hashref;
-
- my $feature = new Bio::SeqFeature::Generic ( -start => $rowhash->{'seq_start'},
- -end => $rowhash->{'seq_end'},
- -score => $rowhash->{'score'},
- -primary => $rowhash2->{'gff_feature'},
- -source => $rowhash2->{'gff_source'});
-
- $annseq->add_SeqFeature($feature);
- }
-
- return $annseq;
-}
-
-=head2 write_all_Protein_features
-
- Title : write_all_Protein_features
- Usage : $obj->write_all_Protein_features($ENSP)
- Function: writes all protein features of a particular peptide into the database
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub write_all_Protein_features {
- my ($self,$prot_annseq,$ENSP) = @_;
-
- my $c=0;
- foreach my $feature ($prot_annseq->all_SeqFeatures()) {
- my $sth = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('proteinfeature')." (id,seq_start, seq_end, score, analysis, translation) values (NULL,"
- .$feature->start().","
- .$feature->end().","
- .$feature->score().",'"
- .$c."','"
- .$ENSP."')");
- $sth->execute();
-
- my $sth2 = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('analysis')." (id,db,db_version,program,program_version,gff_source,gff_feature) values ('$c','testens',1,'elia_program',1,'"
- .$feature->source_tag()."','"
- .$feature->primary_tag()."')");
- $sth2->execute();
- $c++;
- }
-}
-
-=head2 write_Protein_feature
-
- Title : write_Protein_feature
- Usage : $obj->write_Protein_feature($ENSP, $feature)
- Function: writes a protein feature object of a particular peptide into the database
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub write_Protein_feature {
- my ($self,$ENSP,$feature) = @_;
-
- my $sth = $self->_db_obj->prepare("INSERT into ".$self->_lookup_table_name('proteinfeature')." (seq_start, seq_end, score, translation) values ("
- .$feature->start()." ,"
- .$feature->end()." ,'"
- .$feature->score()." ,'"
- .$ENSP."'
- )");
- $sth->execute();
-}
-
-=head2 get_Analysis
-
- Title : get_Analysis
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_Analysis {
- my ($self,$id) = @_;
-
- my $sth = $self->_db_obj->prepare("SELECT db,db_version,program,program_version,gff_source,gff_feature,id from ".$self->_lookup_table_name('analysis')." where id = $id");
- my $rv = $sth->execute;
- my $rh = $sth->fetchrow_hashref;
-
- if ($sth->rows) {
- my $anal = Bio::EnsEMBL::FeatureFactory->new_analysis();
-
- if( defined $rh->{'db'} ) {
- $anal->db($rh->{'db'});
- }
- if( defined $rh->{'db_version'} ) {
- $anal->db_version($rh->{'db_version'});
- }
-
- $anal->program ($rh->{'program'});
- $anal->program_version($rh->{'program_version'});
- $anal->gff_source ($rh->{gff_source});
- $anal->gff_feature ($rh->{gff_feature});
- my $mid = $rh->{'id'};
-
- $anal->dbID("$mid");
- return $anal;
- } else {
- $self->throw("Can't fetch analysis id $id\n");
- }
-
-}
-
-=head2 exists_Analysis
-
- Title : exists_Analysis
- Usage : $obj->exists_Analysis($anal)
- Function: Tests whether this feature already exists in the database
- Example :
- Returns : Analysis id if the entry exists
- Args : Bio::EnsEMBL::Analysis
-
-
-=cut
-
-sub exists_Analysis {
- my ($self,$anal) = @_;
-
-
- $self->throw("Object is not a Bio::EnsEMBL::AnalysisI") unless $anal->isa("Bio::EnsEMBL::AnalysisI");
- # If all the attributes of the analysis object are not set it's existence can't be tested
- $self->throw("program property of analysis object not defined") unless ($anal->program);
- $self->throw("program_version property of analysis object not defined") unless ($anal->program_version);
- $self->throw("gff_source property of analysis object not defined") unless ($anal->gff_source);
- $self->throw("gff_feature property of analysis object not defined") unless ($anal->gff_feature);
-
- my $query;
-
- if ($anal->has_database == 1) {
- $query = "SELECT id from ".$self->_lookup_table_name('analysis')." where db = \"" . $anal->db . "\" and" .
- " db_version = \"" . $anal->db_version . "\" and " .
- " program = \"" . $anal->program . "\" and " .
- " program_version = \"" . $anal->program_version . "\" and " .
- " gff_source = \"" . $anal->gff_source . "\" and" .
- " gff_feature = \"" . $anal->gff_feature . "\"";
- } else {
- $query = "SELECT id from ".$self->_lookup_table_name('analysis')." where " .
- " program = \"" . $anal->program . "\" and " .
- " program_version = \"" . $anal->program_version . "\" and " .
- " gff_source = \"" . $anal->gff_source . "\" and" .
- " gff_feature = \"" . $anal->gff_feature . "\"";
- }
-
- if( exists $self->_db_obj->_analysis_cache->{$query} ) {
- return $self->_db_obj->_analysis_cache->{$query};
- }
-
- my $sth = $self->_db_obj->prepare($query);
- my $rv = $sth->execute();
-
- if ($rv && $sth->rows > 0) {
- my $rowhash = $sth->fetchrow_hashref;
- my $anaid = $rowhash->{'id'};
- $self->_db_obj->_analysis_cache->{$query} = $anaid;
- return $anaid;
- } else {
- return 0;
- }
-}
-
-=head2 write_Analysis
-
- Title : write_Analysis
- Usage : $obj->write_Analysis($anal)
- Function: Writes analysis details to the database
- Checks first whether this analysis entry already exists
- Example :
- Returns : int
- Args : Bio::EnsEMBL::AnalysisI
-
-=cut
-
-sub write_Analysis {
- my ($self,$anal) = @_;
-
- $self->throw("Argument is not a Bio::EnsEMBL::AnalysisI") unless $anal->isa("Bio::EnsEMBL::AnalysisI");
- # If all the attributes of the analysis object are not set it shouldn't be written
- $self->throw("program property of analysis object not defined") unless ($anal->program);
- $self->throw("program_version property of analysis object not defined") unless ($anal->program_version);
- $self->throw("gff_source property of analysis object not defined") unless ($anal->gff_source);
- $self->throw("gff_feature property of analysis object not defined") unless ($anal->gff_feature);
-
- # First check whether this entry already exists.
- my $query;
- my $analysisid = $self->exists_Analysis($anal);
- return $analysisid if $analysisid;
-
-
- if ($anal->has_database == 1) {
- local $^W = 0;
- $query = "INSERT into ".$self->_lookup_table_name('analysis')."(id,db,db_version,program,program_version,gff_source,gff_feature) values (NULL,\"" .
- $anal->db . "\",\"" .
- $anal->db_version . "\",\"" .
- $anal->program . "\",\"" .
- $anal->program_version . "\",\"" .
- $anal->gff_source . "\",\"" .
- $anal->gff_feature . "\")";
- } else {
- $query = "INSERT into ".$self->_lookup_table_name('analysis')."(id,program,program_version,gff_source,gff_feature) values (NULL,\"" .
- $anal->program . "\",\"" .
- $anal->program_version . "\",\"" .
- $anal->gff_source . "\",\"" .
- $anal->gff_feature . "\")";
- }
-
- my $sth = $self->_db_obj->prepare($query);
- my $rv = $sth->execute;
-
-
- $sth = $self->_db_obj->prepare("SELECT last_insert_id()");
- $rv = $sth->execute;
-
- if ($sth->rows == 1) {
- my $rowhash = $sth->fetchrow_hashref;
- return $rowhash->{'last_insert_id()'};
- } else {
- $self->throw("Wrong number of rows returned : " . $sth->rows . " : should be 1");
- }
-
-}
-
-=head2 find_GenomeHits
-
- Title : find_GenomeHits
- Usage : $obj->find_GenomeHits($hitid)
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-sub find_GenomeHits {
- my ($self,$arg) = @_;
-
- $self->throw("No hit id input") unless defined($arg);
-
- my $query = "SELECT c.id, " .
- "f.seq_start, " .
- "f.seq_end, " .
- "f.score, " .
- "f.strand, " .
- "f.analysis, " .
- "f.name, " .
- "f.hstart, " .
- "f.hend, " .
- "f.hid " .
- "from ".$self->_lookup_table_name('feature')." as f,".$self->_lookup_table_name('contig')." as c " .
- "where f.hid = '$arg' and " .
- "c.internal_id = f.contig";
-
- my $sth = $self->_db_obj->prepare($query);
- my $res = $sth->execute;
-
- my ($contig,$start,$end,$score,$strand,$analysisid,$name,$hstart,$hend,$hid);
-
-
- $sth->bind_columns(undef,\$contig,\$start,\$end,\$score,\$strand,\$analysisid,
- \$name,\$hstart,\$hend,\$hid);
-
-
- my %analhash; # Stores all the analysis objects
- my @features;
-
- while($sth->fetch) {
- my $out;
- my $analysis;
-
- if (!$analhash{$analysisid}) {
-
- $analysis = $self->get_Analysis($analysisid);
- $analhash{$analysisid} = $analysis;
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- if( !defined $name ) {
- $name = 'no_source';
- }
-
- $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();
- $out->set_all_fields($start,$end,$strand,$score,$name,'similarity',$contig,
- $hstart,$hend,1,$score,$name,'similarity',$hid);
-
- $out->analysis($analysis);
- $out->validate;
-
- push(@features,$out);
-
- }
-
- return @features;
-}
-
-
-
-=head2 get_PredictionFeature_by_id
-
- Title : get_PredictionFeature_by_id
- Usage : $obj->get_PredictionFeature_by_id($id)
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-
-
-
-
-sub get_PredictionFeature_by_id {
- my ($self,$genscan_id) = @_;
-
- unless ($genscan_id){$self->throw("I need a genscan id");}
-
- my $fsetid;
- my %analhash;
-
- my $query = "SELECT f.id,f.seq_start,f.seq_end,f.strand,f.score,f.analysis,fset.id,c.id " .
- "from ".$self->_lookup_table_name('feature')." f, ".$self->_lookup_table_name('fset')." fset,".$self->_lookup_table_name('fset_feature')." ff,".$self->_lookup_table_name('contig')." c where ff.feature = f.id and fset.id = ff.fset ".
- " and c.internal_id=f.contig and ff.fset ='$genscan_id' and name = 'genscan'";
-
-
- my $sth = $self->_db_obj->prepare($query);
-
- $sth->execute();
-
- my ($fid,$start,$end,$strand,$score,$analysisid,$contig);
-
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$score,\$analysisid,\$fsetid,\$contig);
-
- my $current_fset;
- if( $sth->fetch ) {
- my $out;
-
- my $analysis;
-
- if (!$analhash{$analysisid}) {
-
-
- $analysis = $self->get_Analysis($analysisid);
-
- $analhash{$analysisid} = $analysis;
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- $current_fset = new Bio::EnsEMBL::SeqFeature;
- $current_fset->source_tag('genscan');
- $current_fset->primary_tag('prediction');
- $current_fset->analysis($analysis);
- $current_fset->seqname($contig);
- $current_fset->id($fsetid);
-
-
- $out = new Bio::EnsEMBL::SeqFeature;
-
- $out->seqname ($contig);
- $out->start ($start);
- $out->end ($end);
- $out->strand ($strand);
-
- $out->source_tag('genscan');
- $out->primary_tag('prediction');
-
- if( defined $score ) {
- $out->score($score);
- }
-
- $out->analysis($analysis);
-
- # Final check that everything is ok.
-
- $out->validate();
- $current_fset->add_sub_SeqFeature($out,'EXPAND');
- $current_fset->strand($strand);
- }
-
- else { $self->throw("Fset $genscan_id does not exist in the database");}
-
-
-return $current_fset;
-
-}
-
-
-
-
-=head2 get_PredictionFeature_as_Transcript
-
- Title : get_PredictionFeature_as_Transcript
- Usage : $obj->get_PredictionFeature_as_Transcript($id)
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-
-
-
-sub get_PredictionFeature_as_Transcript{
- my ($self,$genscan_id)=@_;
- unless ($genscan_id){$self->throw("I need a genscan id");}
-
- my $ft=$self->get_PredictionFeature_by_id($genscan_id);
- my $contig=$self->_db_obj->get_Contig($ft->seqname);
-
- &Bio::EnsEMBL::DBSQL::Utils::fset2transcript($ft,$contig);
-
-
-}
-
-
-
-=head2 _db_obj
-
- Title : _db_obj
- Usage : $obj->_db_obj($newval)
- Function:
- Example :
- Returns : value of _db_obj
- Args : newvalue (optional)
-
-
-=cut
-
-sub _db_obj{
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'_db_obj'} = $value;
- }
- return $self->{'_db_obj'};
-
-}
-
-sub exponent {
- my ($number) = @_;
-
- my ($exp) = sprintf("%.3e", $number);
- return $exp;
-}
diff --git a/modules/Bio/EnsEMBL/DBSQL/ObjForeign.pm b/modules/Bio/EnsEMBL/DBSQL/ObjForeign.pm
deleted file mode 100644
index 9c3c6a977ee0aa498fb770d5d04da0be2c5ee582..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/ObjForeign.pm
+++ /dev/null
@@ -1,146 +0,0 @@
-# EnsEMBL module for Bio::EnsEMBL::DBSQL::Foreign
-#
-# Cared for Philip lijnzaad@ebi.ac.uk
-#
-# Copyright EnsEMBL
-#
-# You may distribute this module under the same terms as perl itself
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::ObjForeign
-
-
-=head1 SYNOPSIS
-
- use Bio::EnsEMBL::DBSQL::Obj;
- use Bio::EnsEMBL::DBSQL::Feature_ObjForeign;
-
- $db = new Bio::EnsEMBL::DBSQL::Obj( -user => 'root'
- , -db => 'pog'
- , -host => 'caldy'
- , -driver => 'mysql' );
-
- my $translations = { 'static_golden_path' => 'my_golden_path' ,
- 'exon' => 'ens075.exon'};
- my $feature_obj =
- Bio::EnsEMBL::Feature_ObjForeign->new(
- -dbobj => $db,
- -table_name_translations => $translations);
-
- # rest as with Feature_Obj.
-
-=head1 DESCRIPTION
-
-This class is like a utility class for mixing in to other Obj classes
-(e.g. Gene_Obj or Feature_Obj) resulting in an adaptor that translate
-table names to other names on the fly. The intended use is for an database
-that reuses part of another database in order to save on speed (no loading
-of all the assembly related data) and disk usage.
-
-This class is typically to be sub-classed.
-
-=head1 CONTACT
-
-Philip lijnzaad@ebi.ac.uk
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object methods. Internal
-methods are usually preceded with a _
-
-=cut
-
-# Let the code begin...
-
-package Bio::EnsEMBL::DBSQL::ObjForeign;
-
-use vars qw(@ISA);
-use strict;
-
-
-sub new {
- my ($class, @args) = @_;
- my $self= {};
- bless $self, $class;
-
- my ($db_obj, $table_name_translations, $read_db_obj)
- = $self->_rearrange([ qw( DBOBJ TABLE_NAME_TRANSLATIONS READ_DBOBJ) ]
- ,@args);
- $db_obj || $self->throw("I need a db obj ...");
- $self->_db_obj($db_obj);
- $read_db_obj = $db_obj unless $db_obj;
- $self->_read_db_obj($read_db_obj);
- # table_name_translations are optional
- $self->_table_name_translations($table_name_translations);
- $self->use_delayed_insert(1);
- return $self; # success - we hope!
-}
-
-sub _read_db_obj {
- my ($self, $value) = @_;
-
- if( defined $value) {
- my $needed = 'Bio::EnsEMBL::DBSQL::Obj';
- if ( ref($value) ne $needed ) {
- $self->throw("expecting a $needed");
- }
- $self->{'_read_db_obj'} = $value;
- }
- return $self->{'_read_db_obj'};
-}
-
-
-
-=head2 _table_name_tranlations
-
- Title : table_name_tranlations
- Usage :
- Function: sets/gets the hash used for looking up table names
- Example : $self->_table_name_tranlations
- { 'static_golden_path' => 'my_golden_path' , # same db
- 'exon' => 'ens075.exon' # different table
- }
- Returns :
- Args :
-
-
-=cut
-
-sub _table_name_translations {
- my ($self,$value) = @_;
- if( defined $value) {
- if ( ref($value) ne 'HASH') {
- $self->throw('expecting hash ref');
- }
- $self->{'_table_name_translations'} = $value;
- }
- return $self->{'_table_name_translations'};
-}
-
-=head2 _lookup_table_name
-
- Title : _lookup_table_name
- Usage :
- Function: translate name to other name
- Example :
- Returns : new name if there is a translation for this table name,
- the old name otherwise.
- Args : the table name.
-
-=cut
-
-sub _lookup_table_name {
- my ($self,$name) = @_;
-
- my $table = $self->_table_name_translations;
- my $newname = $table->{$name};
- if (defined $table && defined $newname ) {
- return $newname ;
- }
- return $name;
-}
-
-1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/RawContig.pm b/modules/Bio/EnsEMBL/DBSQL/RawContig.pm
deleted file mode 100755
index 4030890171cd2cc245ac7cbba3011709c791b77e..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/RawContig.pm
+++ /dev/null
@@ -1,2411 +0,0 @@
-#
-# BioPerl module for Contig
-#
-# Cared for by Ewan Birney <birney@sanger.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::DB::RawContig - Handle onto a database stored raw contiguous DNA
-
-=head1 SYNOPSIS
-
- # get a contig object somehow,eg from an DB::Obj
-
- @genes = $contig->get_all_Genes();
- @sf = $contig->get_all_RepeatFeatures();
- @sf = $contig->get_all_SimilarityFeatures();
-
- $contig->id();
- $contig->length();
- $primary_seq = $contig->primary_seq();
-
-=head1 DESCRIPTION
-
-A RawContig is physical piece of DNA coming out a sequencing project,
-ie a single product of an assembly process. A RawContig defines an atomic
-coordinate system on which features and genes are placed (remember that
-genes can cross between atomic coordinate systems).
-
-=head1 CONTACT
-
-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::DBSQL::RawContig;
-use vars qw(@ISA);
-use strict;
-
-# Object preamble - inherits from Bio::Root::Object
-
-use Bio::Root::RootI;
-
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::DBSQL::AnalysisAdaptor;
-use Bio::EnsEMBL::DBSQL::FeatureAdaptor;
-use Bio::EnsEMBL::DB::RawContigI;
-
-use Bio::EnsEMBL::Repeat;
-use Bio::EnsEMBL::ContigOverlap;
-use Bio::EnsEMBL::FeatureFactory;
-use Bio::EnsEMBL::Chromosome;
-use Bio::EnsEMBL::DBSQL::DBPrimarySeq;
-use Bio::PrimarySeq;
-
-@ISA = qw(Bio::EnsEMBL::DB::RawContigI Bio::Root::RootI);
-
-sub new {
- my( $pkg, @args ) = @_;
-
- my $self = bless {}, $pkg;
-
- my (
- $dbobj,
- $id,
- $perlonlysequences,
- $contig_overlap_source,
- $overlap_distance_cutoff,
- ) = $self->_rearrange([qw(
- DBOBJ
- ID
- PERLONLYSEQUENCES
- CONTIG_OVERLAP_SOURCE
- OVERLAP_DISTANCE_CUTOFF
- )], @args);
-
- $id || $self->throw("Cannot make contig db object without id");
- $dbobj || $self->throw("Cannot make contig db object without db object");
- if( !$dbobj->isa('Bio::EnsEMBL::DBSQL::Obj') && !$dbobj->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
- $self->throw("Cannot make contig db object with a $dbobj object");
- }
-
-
- $self->id($id);
- $self->dbobj($dbobj);
- $self->fetch();
- $self->perl_only_sequences($perlonlysequences);
- $self->overlap_distance_cutoff($overlap_distance_cutoff);
-
- return $self;
-}
-
-
-sub direct_new {
- my( $pkg, @args ) = @_;
- my $self = bless {}, $pkg;
-
- my (
- $dbobj,
- $id,
- $perlonlysequences,
- $overlap_distance_cutoff,
- $internal_id,
- $dna_id,
- $seq_version,
- $cloneid,
- $chr_start,
- $chr_end,
- $raw_start,
- $raw_end,
- $raw_ori,
- $offset,
- $contig_length
- ) = $self->_rearrange([qw(
- DBOBJ
- ID
- PERLONLYSEQUENCES
- OVERLAP_DISTANCE_CUTOFF
- INTERNAL_ID
- DNA_ID
- SEQ_VERSION
- CLONEID
- CHR_START
- CHR_END
- RAW_START
- RAW_END
- RAW_ORI
- OFFSET
- CONTIG_LENGTH
- )], @args);
-
- $id || $self->throw("Cannot make contig db object without id");
- $dbobj || $self->throw("Cannot make contig db object without db object");
-
- if( !$dbobj->isa('Bio::EnsEMBL::DBSQL::Obj') && !$dbobj->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
- $self->throw("Cannot make contig db object with a $dbobj object");
- }
-
- if( !$internal_id || !$dna_id || !defined($seq_version) || !$cloneid || !defined $chr_start || !defined $chr_end) {
- $self->throw("you don't have all the data to make a direct new [$internal_id,$dna_id,$seq_version,$cloneid,$chr_start,$chr_end]!");
- }
-
- $self->id($id);
- $self->dbobj($dbobj);
- $self->internal_id($internal_id);
- $self->dna_id($dna_id);
- $self->seq_version($seq_version);
- $self->cloneid ($cloneid);
- $self->perl_only_sequences($perlonlysequences);
- $self->overlap_distance_cutoff($overlap_distance_cutoff);
- $self->_chr_start($chr_start);
- $self->_chr_end($chr_end);
- $self->static_golden_start($raw_start);
- $self->static_golden_end($raw_end);
- $self->static_golden_ori($raw_ori);
- $self->embl_offset($offset);
- $self->length($contig_length);
-
- return $self;
-}
-
-
-=head2 fetch
-
- Title : fetch
- Usage : $contig->fetch($contig_id)
- Function: fetches the data necessary to build a Rawcontig object
- Example : $contig->fetch(1)
- Returns : Bio::EnsEMBL::DBSQL::RawContig object
- Args : $contig_id
-
-
-=cut
-
-sub fetch {
- my ($self) = @_;
-
- my $id=$self->id;
-
- my $query =
- " SELECT contig.internal_id
- , contig.dna
- , clone.embl_version
- , clone.id
- , contig.offset
- FROM contig
- , clone
- WHERE contig.clone = clone.internal_id
- AND contig.id = '$id'
- ";
-
- my $sth = $self->dbobj->prepare($query);
- my $res = $sth->execute();
-
- if (my $row = $sth->fetchrow_arrayref) {
- $self->internal_id($row->[0]);
- $self->dna_id ($row->[1]);
- $self->seq_version($row->[2]);
- $self->cloneid ($row->[3]);
- $self->embl_offset ($row->[4]);
- } else {
- $self->throw("Contig $id does not exist in the database or does not have DNA sequence");
- }
-
- return $self;
-}
-
-=head2 get_all_Genes
-
- Title : get_all_Genes
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_Genes{
- my ($self, $supporting) = @_;
- my @out;
- my $contig_id = $self->internal_id();
- my %got;
- # prepare the SQL statement
-
-
-my $query="
- SELECT t.gene_id
- FROM transcript t,
- exon_transcript et,
- exon e
- WHERE e.contig_id = '$contig_id'
- AND et.exon_id = e.exon_id
- AND t.transcript_id = et.transcript_id
- ";
-
-
- return $self->_gene_query($query,$supporting);
-}
-
-=head2 get_old_Genes
-
- Title : get_old_Genes
- Usage : my @mapped_Genes=$rc->get_old_Genes
- Function: Used to get out old Genes (not modifying coordinates)
- Returns : an array of Bio::EnsEMBL::Exon objects
- Args : none
-
-
-=cut
-
-sub get_old_Genes {
- my ($self,$mapref) = @_;
-
- my %map = %$mapref;
- #This method requires a connection to a crossmatch database
- if (!$self->_crossdb) { $self->throw("You need a crossmatch database to call get_old_Genes!");}
- my $crossdb = $self->_crossdb;
-
- #The crossdb should be holding onto old and new dbs, we need the old one here...
- my $old_db;
- eval {
- $old_db=$self->_crossdb->old_dbobj;
- };
- if ($@) {
- $self->throw("The crossmatch database has to hold the old dna database to be able to call get_old_Genes! $@");
- }
- my $oldcontig;
- my $oldid = $map{$self->id};
- eval {
- $oldcontig = $old_db->get_Contig($oldid);
- };
-
- #If the clone does not exist, these are really new Genes
- if ($@) {
- #print STDERR "Contig ".$oldid." doesn't exist in old db ".$old_db->dbname.", returning empty array...\n";
- return ();
- }
-
- my @genes=$oldcontig->get_all_Genes();
- my $size=scalar (@genes);
- #print STDERR "Returning $size old Genes as they are for contig ".$oldid."\n";
- return @genes;
-}
-
-=head2 get_all_Exons
-
- Title : get_all_Exons
- Usage :
- Function: returns all exons for this contig
- Example :
- Returns :
- Args :
-
-=cut
-
-sub get_all_Exons {
-
- my ($self)=@_;
-
-
- my $contig_id=$self->id;
-
-
- my $query="SELECT e.id, e.seq_start,e.seq_end,e.strand,e.phase,e.created,e.modified,e.version
- FROM exon e,contig c
- WHERE c.internal_id=e.contig and c.id ='$contig_id'";
-
- my $sth = $self->dbobj->prepare ($query);
- $sth->execute;
-
- my ($id,$start,$end,$strand,$phase,$created,$modified,$version);
- $sth->bind_columns (undef,\$id,\$start,\$end,\$strand,\$phase,\$created,\$modified,\$version);
-
- my @exons;
- while ($sth->fetch){
- my $exon=Bio::EnsEMBL::Exon->new;
- $exon->id($id);
- $exon->start($start);
- $exon->end($end);
- $exon->strand($strand);
- $exon->seqname($self->id);
- $exon->contig_id($self->id);
- $exon->phase($phase);
- $exon->created($created);
- $exon->modified($modified);
- $exon->version($version);
- $exon->sticky_rank(1);
-
- push @exons,$exon;
- }
- return @exons;
-}
-
-
-=head2 get_old_Exons
-
- Title : get_old_Exons
- Usage : my @mapped_exons=$rc->get_old_Exons
- Function: Used to get out exons in new coordinates
- Returns : an array of Bio::EnsEMBL::Exon objects
- Args : none
-
-
-=cut
-
-sub get_old_Exons {
- my ($self,$logfile,$maphref) = @_;
-
- my @unmapped;
-
- #This method requires a connection to a crossmatch database
- if (!$self->_crossdb) { $self->throw("You need a crossmatch database to call get_old_exons!");}
- my $crossdb = $self->_crossdb;
-
- my %map = %$maphref;
- #The crossdb should be holding onto old and new dbs, we need the old one here...
- my $old_db;
- eval {
- $old_db=$crossdb->old_dbobj;
- };
- if ($@) {
- $self->throw("The crossmatch database has to hold the old dna database to be able to call get_old_exons! $@");
- }
- my $oldclone;
- my $oldcontig;
- eval {
- $oldclone = $old_db->get_Clone($self->cloneid);
- };
-
- #If the clone does not exist, these are really new exons
- if ($@) {
- return ();
- }
-
- my $newclone= $self->dbobj->get_Clone($self->cloneid);
- #If the clones have the same version, the underlying dna hasn't changed,
- #therefore we just return the old exons...
-
- #FIXME - the above is not necessarily true - contigs may have changed
- #due to spliting on different boundaries and coordinates shifted accordingly
-
- if ($oldclone->embl_version == $newclone->embl_version) {
- my $oldcontig;
- my $oldid = $map{$self->id};
- eval {
- $oldcontig = $oldclone->get_Contig($oldid);
- };
- if ($@) {
- print STDERR "Clones with id ".$oldclone->id." have the same version in old and new db, but contig ".$self->id." is not there! (CLONE VERSION BUG)\n";
- return ();
- }
- my @exons=$oldcontig->get_all_Exons();
- foreach my $exon (@exons) {
- $exon->seqname($self->id);
- $exon->contig_id($self->id);
- }
- my $size=scalar (@exons);
- #print STDERR "Returning $size old exons as they are for contig ".$oldid." on clone ".$oldclone->id."\n";
- return @exons;
- }
- #We get out a SymmetricContigFeatureContainer from the crossdb and use it #to retrieve feature pairs for this contig, then sort them
- my $sfpc = $crossdb->get_SymmetricContigFeatureContainer;
- my @fp=$sfpc->get_FeaturePair_list_by_rawcontig_id($self->id,$newclone->embl_version);
- my @sorted_fp= sort { $a->start <=> $b->start} @fp;
-
- my %validoldcontigs;
- my %fphash;
- my @old_exons;
- foreach my $fp ( @sorted_fp ) {
- my $contigid = $fp->hseqname;
- my $oldcontig=$old_db->get_Contig($contigid);
- push @old_exons, $oldcontig->get_all_Exons;
- $validoldcontigs{$contigid} = $fp->hseqname;
- if( !exists $fphash{$fp->hseqname} ) {
- $fphash{$fp->hseqname} = [];
- }
- push(@{$fphash{$fp->hseqname}},$fp);
- }
- #We now need to get all the Genes for this clone on the old case
- # now perform the mapping
-
- my @mapped_exons;
- EXON:foreach my $exon (@old_exons) {
- my $mapped=0;
- foreach my $fp ( @{$fphash{$validoldcontigs{$exon->seqname}}} ) {
- if( $fp->hstart < $exon->start && $fp->hend > $exon->start ) {
- if( $fp->strand == $fp->hstrand ) {
- # straightforward mapping
- $exon->seqname($self->id);
- $exon->contig_id($self->id);
- $exon->start($fp->start + $exon->start - $fp->hstart);
- $exon->end($fp->start + $exon->end - $fp->hstart);
- } else {
- # Grrr strand hell.
- my $oldstart = $exon->start;
- my $oldend = $exon->end;
- $exon->seqname($self->id);
- $exon->contig_id($self->id);
- $exon->start($fp->hend - ($oldstart - $fp->hend));
- $exon->end ($fp->hend - ($oldend - $fp->hend));
- $exon->strand( -1 * $exon->strand);
- }
- $mapped=1;
- push (@mapped_exons,$exon);
- next EXON;
- }
- }
- if ($mapped == 0) {
- push (@unmapped,$exon->id);
- print $logfile "LOST EXON: ".$exon->id." (In get_old_Exons)\n";
- }
- }
- $self->unmapped_exons(@unmapped);
- return @mapped_exons;
-}
-
-
-=head2 get_Genes_by_Type
-
- Title : get_Genes_by_Type
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_Genes_by_Type{
- my ($self,$type,$supporting) = @_;
- my @out;
- my $contig_id = $self->internal_id();
- my %got;
- # prepare the SQL statement
-unless ($type){$self->throw("I need a type argument e.g. ensembl")};
-
-my $query="
- SELECT t.gene_id
- FROM transcript t,
- exon_transcript et,
- exon e, gene g
- WHERE e.contig_id = $contig_id
- AND et.exon_id = e.exon_id
- AND t.transcript_id = et.transcript_id
- AND t.gene_id = g.gene_id
- AND g.type = '$type'
- ";
-
-
- return $self->_gene_query($query,$supporting);
-}
-
-
-sub _gene_query{
-
- my ($self, $query,$supporting) = @_;
-
- my @out;
- my $contig_id = $self->internal_id();
- my %got;
- # prepare the SQL statement
- my $sth = $self->dbobj->prepare($query);
-
- my $res = $sth->execute();
- my $genea = $self->dbobj->get_GeneAdaptor();
-
- while (my $rowhash = $sth->fetchrow_hashref) {
-
- if( ! exists $got{$rowhash->{'gene_id'}}) {
- push(@out,$genea->fetch_by_dbID($rowhash->{'gene_id'}));
- $got{$rowhash->{'gene_id'}} = 1;
- }
- }
-
- if(defined ($supporting) && $supporting eq 'evidence'){
- my $exona = $self->dbobj->get_ExonAdaptor();
- foreach my $g(@out){
- foreach my $exon($g->get_all_Exons){
- $exona->fetch_evidence_by_Exon($exon);
- }
- }
- }
-
- if (@out) {
- return @out;
- }
- return;
-}
-
-
-
-=head2 has_genes
-
- Title : has_genes
- Usage :
- Function: returns 1 if there are genes, 0 otherwise.
- Example :
- Returns :
- Args :
-
-
-=cut
-
-
-
-
-sub has_genes{
- my ($self,@args) = @_;
- my $contig_id = $self->internal_id();
-
- my $seen =0;
- my $sth = $self->dbobj->prepare("select exon_id from exon where contig_id = '$contig_id' limit 1");
- $sth->execute();
-
- my $rowhash;
- while ( ($rowhash = $sth->fetchrow_hashref()) ) {
- $seen = 1;
- last;
- }
- return $seen;
-}
-
-=head2 primary_seq
-
- Title : primary_seq
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub primary_seq{
- my ($self,@args) = @_;
-
- if( $self->perl_only_sequences == 1 ) {
- return $self->perl_primary_seq();
- }
- return $self->db_primary_seq();
-
-}
-
-=head2 db_primary_seq
-
- Title : db_primary_seq
- Usage : $dbseq = $contig->db_primary_seq();
- Function: Gets a Bio::EnsEMBL::DBSQL::DBPrimarySeq object out from the contig
- Example :
- Returns : Bio::EnsEMBL::DBSQL::DBPrimarySeq object
- Args :
-
-
-=cut
-
-sub db_primary_seq {
- my ($self) = @_;
-
- my $dbseq = Bio::EnsEMBL::DBSQL::DBPrimarySeq->new(
- -dna => $self->dna_id,
- -db_handle => $self->dbobj->dnadb,
- );
-
- return $dbseq;
-}
-
-
-
-=head2 perl_primary_seq
-
- Title : seq
- Usage : $seq = $contig->perl_primary_seq();
- Function: Gets a Bio::PrimarySeqI object out from the contig
- Example :
- Returns : Bio::PrimarySeqI object
- Args :
-
-
-=cut
-
-sub perl_primary_seq {
- my ($self) = @_;
-
- if ( $self->_seq_cache() ) {
- return $self->_seq_cache();
- }
-
- my $dna_id = $self->dna_id()
- or $self->throw("No dna_id in RawContig ". $self->id);
- my $sth = $self->dbobj->dnadb->prepare(q{ SELECT sequence FROM dna WHERE id = ? });
- my $res = $sth->execute($dna_id);
-
- my($str) = $sth->fetchrow
- or $self->throw("No DNA sequence in RawContig " . $self->id . " for dna id " . $dna_id);
-
- # Shouldn't sequence integrity be checked on the way
- # into the datbase instead of here?
-# $str =~ /[^ABCDGHKMNRSTVWY]/ && $self->warn("Got some non standard DNA characters here! Yuk!");
-# $str =~ s/\s//g;
-# $str =~ s/[^ABCDGHKMNRSTVWY]/N/g;
-
- my $ret = Bio::PrimarySeq->new(
- -seq => $str,
- -display_id => $self->id, # eg: AC004092.00001
- -primary_id => $self->internal_id, # eg: 874
- -moltype => 'dna',
- );
- $self->_seq_cache($ret);
-
- return $ret;
-}
-
-=head2 _seq_cache
-
- Title : _seq_cache
- Usage : $obj->_seq_cache($newval)
- Function: Used to cache the primary seq object to avoid
- more than one trip to the database for the dna
- Returns : value of _seq_cache
- Args : newvalue (optional)
-
-
-=cut
-
-sub _seq_cache{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'_seq_cache'} = $value;
- }
- return $obj->{'_seq_cache'};
-
-}
-
-
-
-=head2 get_all_SeqFeatures
-
- Title : get_all_SeqFeatures
- Usage : foreach my $sf ( $contig->get_all_SeqFeatures
- Function: Gets all the sequence features on the whole contig
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_SeqFeatures {
- my ($self) = @_;
-
- my @out;
-
- push(@out,$self->get_all_SimilarityFeatures);
- push(@out,$self->get_all_RepeatFeatures);
- # push(@out,$self->get_all_PredictionFeatures);
-
- return @out;
-}
-
-
-=head2 get_all_SimilarityFeatures_above_score
-
- Title : get_all_SimilarityFeatures_above_score
- Usage : foreach my $sf ( $contig->get_all_SimilarityFeatures_above_score(analysis_type, score) )
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_SimilarityFeatures_above_score{
- my ($self, $analysis_type, $score) = @_;
-
- $self->throw("Must supply analysis_type parameter") unless $analysis_type;
- $self->throw("Must supply score parameter") unless $score;
-
- my @array;
-
- my $id = $self->internal_id();
- my $length = $self->length();
-
- if( $self->use_rawcontig_acc() ) {
- my $fplist = Bio::EnsEMBL::Ext::RawContigAcc::FeaturePairList_by_Score($id,$analysis_type,$score);
- @array = $fplist->each_FeaturePair;
- return @array;
- }
-
- my %analhash;
-
- #First of all, get all features that are part of a feature set with high enough score and have the right type
-
- my $statement = "SELECT feature.id, seq_start, seq_end, strand, feature.score, analysis, name, " .
- "hstart, hend, hid, evalue, perc_id, phase, end_phase, fset, rank, fset.score " .
- "FROM feature, fset_feature, fset, analysisprocess " .
- "WHERE feature.contig ='$id' " .
- "AND fset_feature.feature = feature.id " .
- "AND fset.id = fset_feature.fset " .
- "AND feature.score > '$score' " .
- "AND feature.analysis = analysisprocess.analysisId " .
- "AND analysisprocess.db = '$analysis_type' " .
- "ORDER BY fset";
-
- my $sth = $self->dbobj->prepare($statement);
- $sth->execute();
-
- my ($fid,$start,$end,$strand,$f_score,$analysisid,$name,$hstart,$hend,$hid,$evalue,$perc_id,$phase,$end_phase,$fset,$rank,$fset_score);
- my $seen = 0;
-
- # bind the columns
-
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$f_score,\$analysisid,\$name,\$hstart,\$hend,\$hid,\$evalue,\$perc_id,\$phase,\$end_phase,\$fset,\$rank,\$fset_score);
-
- my $out;
-
- my $fset_id_str = "";
-
- while($sth->fetch) {
-
- my $analysis;
-
- if (!$analhash{$analysisid}) {
- my $analysis_adp = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor($self->dbobj);
- $analysis = $analysis_adp->fetch_by_dbID($analysisid);
- $analhash{$analysisid} = $analysis;
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- if( !defined $name ) {
- $name = 'no_source';
- }
-
- #Build fset feature object if new fset found
- if ($fset != $seen) {
-# print(STDERR "Making new fset feature $fset\n");
- $out = new Bio::EnsEMBL::SeqFeature;
- $out->id($fset);
- $out->analysis($analysis);
- $out->seqname ($self->id);
- $out->score($fset_score);
- $out->source_tag($name);
- $out->primary_tag("FSET");
-
- $seen = $fset;
- push(@array,$out);
- }
- $fset_id_str = $fset_id_str . $fid . ",";
- #Build Feature Object
- my $feature = new Bio::EnsEMBL::SeqFeature;
- $feature->seqname ($self->id);
- $feature->start ($start);
- $feature->end ($end);
- $feature->strand ($strand);
- $feature->source_tag ($name);
- $feature->primary_tag('similarity');
- $feature->id ($fid);
- $feature->p_value ($evalue) if (defined $evalue);
- $feature->percent_id ($perc_id) if (defined $perc_id);
- $feature->phase ($phase) if (defined $phase);
- $feature->end_phase ($end_phase) if (defined $end_phase);
-
- if( defined $f_score ) {
- $feature->score($f_score);
- }
-
- $feature->analysis($analysis);
-
- # Final check that everything is ok.
- $feature->validate();
-
- #Add this feature to the fset
- $out->add_sub_SeqFeature($feature,'EXPAND');
-
- }
-
- #Then get the rest of the features, i.e. featurepairs and single features that are not part of a fset
- $fset_id_str =~ s/\,$//;
-
- if ($fset_id_str) {
- $statement = "SELECT feature.id, seq_start, seq_end, strand, score, analysis, name, hstart, hend, hid, evalue, perc_id, phase, end_phase " .
- "FROM feature, analysisprocess " .
- "WHERE feature.id not in (" . $fset_id_str . ") " .
- "AND feature.score > '$score' " .
- "AND feature.analysis = analysisprocess.analysisId " .
- "AND analysisprocess.db = '$analysis_type' " .
- "AND feature.contig = '$id' ";
-
- $sth = $self->dbobj->prepare($statement);
-
- } else {
- $statement = "SELECT feature.id, seq_start, seq_end, strand, score, analysis, name, hstart, hend, hid, evalue, perc_id, phase, end_phase " .
- "FROM feature, analysisprocess " .
- "WHERE feature.score > '$score' " .
- "AND feature.analysis = analysisprocess.analysisId " .
- "AND analysisprocess.db = '$analysis_type' " .
- "AND feature.contig = '$id' ";
-
- $sth = $self->dbobj->prepare($statement);
- }
-
- $sth->execute();
-
- # bind the columns
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$f_score,\$analysisid,\$name,\$hstart,\$hend,\$hid,\$evalue,\$perc_id,\$phase,\$end_phase);
-
- while($sth->fetch) {
- my $out;
- my $analysis;
-
- if (!$analhash{$analysisid}) {
-
- my $analysis_adp = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor($self->dbobj);
- $analysis = $analysis_adp->fetch_by_dbID($analysisid);
- $analhash{$analysisid} = $analysis;
-
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- if( !defined $name ) {
- $name = 'no_source';
- }
-
- if( $hid ne '__NONE__' ) {
- # is a paired feature
- # build EnsEMBL features and make the FeaturePair
-
- $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();
-
-
- $out->set_all_fields($start,$end,$strand,$f_score,$name,'similarity',$self->id,
- $hstart,$hend,1,$f_score,$name,'similarity',$hid);
-
- $out->analysis ($analysis);
- $out->id ($hid); # MC This is for Arek - but I don't
- # really know where this method has come from.
- } else {
- $out = new Bio::EnsEMBL::SeqFeature;
- $out->seqname ($self->id);
- $out->start ($start);
- $out->end ($end);
- $out->strand ($strand);
- $out->source_tag ($name);
- $out->primary_tag('similarity');
- $out->id ($fid);
- $out->p_value ($evalue) if (defined $evalue);
- $out->percent_id ($perc_id) if (defined $perc_id);
- $out->phase ($phase) if (defined $phase);
- $out->end_phase ($end_phase) if (defined $end_phase);
-
- if( defined $f_score ) {
- $out->score($f_score);
- }
- $out->analysis($analysis);
- }
- # Final check that everything is ok.
- $out->validate();
-
- push(@array,$out);
-
- }
-
- return @array;
-}
-
-
-
-=head2 get_all_SimilarityFeatures
-
- Title : get_all_SimilarityFeatures
- Usage : foreach my $sf ( $contig->get_all_SimilarityFeatures($start,$end) )
- Function: Gets all the sequence similarity features on the whole contig
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_SimilarityFeatures {
- my ($self) = @_;
-
- my @array;
- my @fps;
-
- my $id = $self->internal_id();
- my $length = $self->length();
-
- #Removed genscan addition, now Virtual Contig adds it using properly get_all_PredictionFeatures
-
- #my @genscan = $self->get_all_PredictionFeatures;
-
- #push(@array,@genscan);
- my %analhash;
-
- #Then get the rest of the features, i.e. featurepairs and single features that are not part of a fset
- my ($fid,$start,$end,$strand,$f_score,$analysisid,$name,$hstart,$hend,$hid,$evalue,$perc_id,$phase,$end_phase);
-
- my $sth = $self->dbobj->prepare("select id,seq_start,seq_end,strand,score,analysis,name,hstart,hend,hid, evalue, perc_id, phase, end_phase ".
- "from feature where contig = $id");
-
- $sth->execute();
-
- # bind the columns
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$f_score,\$analysisid,\$name,\$hstart,\$hend,\$hid,\$evalue,\$perc_id,\$phase,\$end_phase);
-
- FEAT: while($sth->fetch) {
- my $out;
- my $analysis;
-
- #print STDERR "\nID $fid, START $start, END $end, STRAND $strand, SCORE $f_score, EVAL $evalue, PHASE $phase, EPHASE $end_phase, ANAL $analysisid HID $hid\n";
-
- if (!$analhash{$analysisid}) {
-
- my $analysis_adp=Bio::EnsEMBL::DBSQL::AnalysisAdaptor->new($self->dbobj);
-
- eval {
- $analysis = $analysis_adp->fetch_by_dbID($analysisid);
- $analhash{$analysisid} = $analysis;
- };
- if ($@) {
- print STDERR "Error fetching analysis $analysisid. Skipping [$@]\n";
- next FEAT;
- }
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- if( !defined $name ) {
- $name = 'no_source';
- } elsif ($name eq "genscan" ||$name eq "fgenesh" ||$name eq "halfwise" ) {
- next FEAT;
- }
- if( $hid ne '__NONE__' ) {
- # is a paired feature
- # build EnsEMBL features and make the FeaturePair
- #print "making a feature pair\n";
- #print "name = ".$name." ID ".$hid."\n";
- $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();
-
-
- $out->set_all_fields($start,$end,$strand,$f_score,$name,'similarity',$self->id,
- $hstart,$hend,1,$f_score,$name,'similarity',$hid, $evalue, $perc_id, $phase, $end_phase);
-
- $out->analysis ($analysis);
- $out->id($fid);
- # see comment below
- #$out->id ($hid); # MC This is for Arek - but I don't
- # really know where this method has come from.
- } else {
- #print "making a single feature";
- #print "name = ".$name." ID ".$hid."\n";
- $out = new Bio::EnsEMBL::SeqFeature;
- $out->seqname ($self->id);
- $out->start ($start);
- $out->end ($end);
- $out->strand ($strand);
- $out->source_tag ($name);
- $out->primary_tag('similarity');
- $out->id ($fid);
- $out->p_value ($evalue) if (defined $evalue);
- $out->percent_id ($perc_id) if (defined $perc_id);
- $out->phase ($phase) if (defined $phase);
- $out->end_phase ($end_phase) if (defined $end_phase);
- $out->raw_seqname ($self->id);
-
- if( defined $f_score ) {
- $out->score($f_score);
- }
- $out->analysis($analysis);
- }
- # Final check that everything is ok.
- #print "gff string ".$out->gffstring."\n";
- $out->validate();
- if( $out->can('attach_seq') ) {
- $out->attach_seq($self->primary_seq);
- }
-
- push(@fps,$out);
-
- }
-
- push(@array,@fps);
-
- return @array;
-}
-
-=head2 get_all_RepeatFeatures
-
- Title : get_all_RepeatFeatures
- Usage : foreach my $sf ( $contig->get_all_RepeatFeatures )
- Function: Gets all the repeat features on a contig.
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_RepeatFeatures {
- my ($self) = @_;
-
- my @array;
- #print "getting all reapeat features\n";
- my $id = $self->internal_id();
- my $length = $self->length();
-
- my %analhash;
-
- # make the SQL query
- my $statement = "select id,seq_start,seq_end,strand,score,analysis,hstart,hend,hid " .
- "from repeat_feature where contig = '$id'";
-
- print "sql = ".$statement."\n";
- my $sth = $self->dbobj->prepare($statement);
-
- $sth->execute();
-
- my ($fid,$start,$end,$strand,$score,$analysisid,$hstart,$hend,$hid);
-
- # bind the columns
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$score,\$analysisid,\$hstart,\$hend,\$hid);
-
- while( $sth->fetch ) {
- my $out;
- my $analysis;
-
- if (!$analhash{$analysisid}) {
-
- my $analysis_adp = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor($self->dbobj);
- $analysis = $analysis_adp->fetch_by_dbID($analysisid);
- $analhash{$analysisid} = $analysis;
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
-
- if( $hid ne '__NONE__' ) {
- # is a paired feature
- # build EnsEMBL features and make the FeaturePair
-
- $out = Bio::EnsEMBL::FeatureFactory->new_repeat();
- $out->set_all_fields($start,$end,$strand,$score,'repeatmasker','repeat',$self->id,
- $hstart,$hend,1,$score,'repeatmasker','repeat',$hid);
-
- $out->analysis($analysis);
- $out->id($fid);
- } else {
- $self->warn("Repeat feature does not have a hid. bad news....");
- }
-
- $out->validate();
-
- push(@array,$out);
- }
-
- return @array;
-} # get_all_RepeatFeatures
-
-=head2 get_MarkerFeatures
-
- Title : get_MarkerFeatures
- Usage : @fp = $contig->get_MarkerFeatures;
- Function: Gets MarkerFeatures. MarkerFeatures can be asked for a Marker.
- Its assumed, that when you can get MarkerFeatures, then you can
- get the Map Code as well.
- Example : -
- Returns : -
- Args : -
-
-=cut
-
-sub get_MarkerFeatures {
- my ($self)=@_;
-
- my $id = $self->internal_id;
- my @markers;
-
- eval {
- require Bio::EnsEMBL::Map::MarkerFeature;
-
- my $statement="SELECT f.seq_start, f.seq_end, f.score, f.strand, f.name,
- f.hstart, f.hend, f.hid, f.analysis
- FROM feature f, analysis a
- WHERE f.contig='$id'
- AND f.analysis = a.id and a.db='mapprimer'";
-
- @markers=$self->_create_MarkerFeatures($statement);
-
- };
-
- if( $@ ) {
- print STDERR ("Problems retrieving map data. Most likely not connected to maps db\n$@\n" );
- }
-
- return @markers;
-} # get_MarkerFeatures
-
-
-=head2 get_landmark_MarkerFeatures
-
- Title : get_landmark_MarkerFeatures
- Usage : @fp = $contig->get_landmark_MarkerFeatures;
- Function: Gets MarkerFeatures with identifiers like D8S509.
- MarkerFeatures can be asked for a Marker.
- Its assumed, that when you can get MarkerFeatures, then you can
- get the Map Code as well.
- Example : -
- Returns : -
- Args : -
-
-=cut
-
-
-sub get_landmark_MarkerFeatures {
- my ($self)=@_;
-
-
- my $dbname=$self->dbobj->dbname;
- my $mapsdbname=$self->dbobj->mapdbname;
-
- my $id = $self->internal_id;
- my @markers;
-
-
- eval {
- require Bio::EnsEMBL::Map::MarkerFeature;
-
- my $statement="SELECT f.seq_start, f.seq_end, f.score, f.strand, f.name,
- f.hstart, f.hend, s.name, f.analysis
- FROM $dbname.feature f, $dbname.analysis a,
- $mapsdbname.MarkerSynonym s,$mapsdbname.Marker m
- WHERE f.contig='$id'
- AND f.analysis = a.id
- AND a.db='mapprimer'
- AND m.marker=s.marker
- AND f.hid=m.marker
- AND s.name regexp '^D[0-9,X,Y][0-9]?S'";
-
- @markers=$self->_create_MarkerFeatures($statement);
-
- };
-
- if( $@ ) {
- print STDERR ("Problems retrieving map data. Most likely not connected to maps db\n$@\n" );
- }
-
- return @markers;
-} # get_landmark_MarkerFeatures
-
-
-
-sub _create_MarkerFeatures
-{
-my ($self,$statement)=@_;
-
-my @result;
-my $analysis;
-my %analhash;
-
-
-my $sth = $self->dbobj->prepare($statement);
-$sth->execute;
-
-my ($start, $end, $score, $strand, $hstart,
- $name, $hend, $hid, $analysisid );
-
-
-$sth->bind_columns
- ( undef, \$start, \$end, \$score, \$strand, \$name,
- \$hstart, \$hend, \$hid, \$analysisid);
-
-
-while( $sth->fetch ) {
-
- my ( $out, $seqf1, $seqf2 );
-
- if (!$analhash{$analysisid}) {
-
- my $analysis_adp = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor($self->dbobj);
- $analysis = $analysis_adp->fetch_by_dbID($analysisid);
- $analhash{$analysisid} = $analysis;
-
- } else {
- $analysis = $analhash{$analysisid};
- }
-
- $seqf1 = Bio::EnsEMBL::SeqFeature->new();
- $seqf2 = Bio::EnsEMBL::SeqFeature->new();
- $out = Bio::EnsEMBL::Map::MarkerFeature->new
- ( -feature1 => $seqf1, -feature2 => $seqf2 );
- $out->set_all_fields
- ( $start,$end,$strand,$score,
- $name,'similarity',$self->id,
- $hstart,$hend,1,$score,$name,'similarity',$hid);
- $out->analysis($analysis);
- $out->mapdb( $self->dbobj->mapdb );
- $out->id ($hid);
-
- push( @result, $out );
-}
-
-return @result;
-
-} # _create_MarkerFeatures
-
-=head2 get_all_PredictionFeatures
-
- Title : get_all_PredictionFeatures
- Usage : foreach my $sf ( $contig->get_all_RepeatFeatures )
- Function: Gets all the repeat features on a contig.
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_PredictionFeatures {
- my ($self) = @_;
-
- my @array;
-
- my $id = $self->internal_id();
- my $length = $self->length();
- my $fsetid;
- my $previous;
- my %analhash;
-
- # make the SQL query
-
-
- my $query = "select f.id,f.seq_start,f.seq_end,f.strand,f.score,f.evalue,f.perc_id,f.phase,f.end_phase,f.analysis,f.hid,f.name ".
- "from feature f where contig = $id and name in ('genscan', 'fgenesh') order by name, hid";
-
-
- my $sth = $self->dbobj->prepare($query);
-
- $sth->execute();
-
- my ($fid,$start,$end,$strand,$score,$evalue,$perc_id,$phase,$end_phase,$analysisid,$hid, $name);
-
- # bind the columns
- $sth->bind_columns(undef,\$fid,\$start,\$end,\$strand,\$score,\$evalue,\$perc_id,\$phase,\$end_phase,\$analysisid,\$hid,\$name);
-
- $previous = -1;
- my $current_fset;
- my $fsetstart;
- my $count=1;
- my $prev;
-
- while( $sth->fetch ) {
- my $out;
-
- print STDERR "PHASE $phase\n";
-
- my $analysis;
-
- if (!$analhash{$analysisid}) {
-
- my $analysis_adp = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor($self->dbobj);
- $analysis = $analysis_adp->fetch_by_dbID($analysisid);
- $analhash{$analysisid} = $analysis;
-
-
- } else {
- $analysis = $analhash{$analysisid};
- }
- # Oh boyoboy. Yet another genscan hack to avoid duplicate genscans
- if (defined($prev) && $start == $prev->start && $end == $prev->end) {
- next;
- }
- #MC. This has been temporarily changed back to the old way of genscans
- if( $hid =~ /Initial/ || $hid =~ /Single Exon/ || $previous =~ /Single/ || $previous =~ /Terminal/ || $previous eq -1 ) {
- #if( $hid ne $previous || $previous eq -1 ) {
- $current_fset = new Bio::EnsEMBL::SeqFeature;
- $current_fset->source_tag($name);
- $current_fset->primary_tag('prediction');
- $current_fset->analysis($analysis);
- $current_fset->seqname($self->id);
- $current_fset->id($count);
- $current_fset->score(0.0);
- $count++;
- $current_fset->raw_seqname($self->id);
- $fsetstart = $start;
- push(@array,$current_fset);
- }
-
- $out = new Bio::EnsEMBL::SeqFeature;
-
- $out->seqname ($self->id);
- $out->raw_seqname($self->id);
-
- $out->start ($start);
- $out->end ($end);
- $out->strand ($strand);
- $out->score ($score) if (defined $score);
- $out->p_value ($evalue) if (defined $evalue);
- $out->percent_id($perc_id) if (defined $perc_id);
- $out->phase ($phase) if (defined $phase);
- $out->end_phase ($end_phase) if (defined $end_phase);
-
-
- my $query="select fset from fset_feature where feature=$fid";
- my $sth = $self->dbobj->prepare($query);
- $sth->execute();
-
-# $fsetid=$arr_ref->[0];
- my $fsetid = $self->internal_id . "." . $fsetstart;
- $out->id($fsetid); # to make genscan peptide work
- #print STDERR "\t\t===> get_pred_features fsetid: $fsetid\n";
- $out->source_tag($name);
- $out->primary_tag('prediction');
-
- if( defined $score ) {
- $out->score($score);
- }
-
- $out->analysis($analysis);
-
- # Final check that everything is ok.
-
- $out->validate();
-
- $current_fset->add_sub_SeqFeature($out,'EXPAND');
- $current_fset->strand($strand);
- $previous = $hid;
- $prev = $out;
-
- }
-
- return @array;
-}
-
-
-=head2 get_genscan_peptides
-
- Title : get_genscan_peptides
- Usage :
- Function: Returns genscan predictions as peptides
- Example :
- Returns :
- Args :
-
-
-=cut
-
-#have written this to use the new phase and end_phase tag in SeqFeature
-#Therefore this won't work with the older features, after all the old system was pretty ropey.
-sub get_genscan_peptides {
- my ($self) = @_;
- my @transcripts;
- foreach my $fset ($self->get_all_PredictionFeatures) {
- my $trans = &Bio::EnsEMBL::DBSQL::Utils::fset2transcript($fset,$self);
- push(@transcripts,$trans);
- }
-
- return @transcripts;
-}
-
-=head2 get_all_ExternalFeatures
-
- Title : get_all_ExternalFeatures
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_ExternalFeatures{
- my ($self) = @_;
-
- my @out;
- my $acc;
-
- $acc = $self->cloneid();
-
- my $embl_offset = $self->embl_offset();
-
- foreach my $extf ( $self->dbobj->_each_ExternalFeatureFactory ) {
-
- if( $extf->can('get_Ensembl_SeqFeatures_contig') ) {
-
- my @tmp = $extf->get_Ensembl_SeqFeatures_contig($self->internal_id,
- $self->seq_version,
- 1,
- $self->length,
- $self->id);
-
- push(@out,@tmp);
- }
- if( $extf->can('get_Ensembl_SeqFeatures_clone') ) {
-
- foreach my $sf ( $extf->get_Ensembl_SeqFeatures_clone($acc,$self->seq_version,$self->embl_offset,$self->embl_offset+$self->length()) ) {
-
- my $start = $sf->start - $embl_offset+1;
- my $end = $sf->end - $embl_offset+1;
- $sf->start($start);
- $sf->end($end);
- push(@out,$sf);
- }
- }
- }
- my $id = $self->id();
- foreach my $f ( @out ) {
- $f->seqname($id);
- }
-
- return @out;
-
-} # get_all_ExternalFeatures
-
-
-=head2 get_all_ExternalGenes
-
- Title : get_all_ExternalGenes
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub get_all_ExternalGenes {
- my ($self) = @_;
- my @out;
- my $acc;
-
- $acc = $self->cloneid();
- my $embl_offset = $self->embl_offset();
-
- foreach my $extf ( $self->dbobj->_each_ExternalFeatureFactory ) {
- if( $extf->can('get_Ensembl_Genes_clone') ) {
- my @genes = $extf->get_Ensembl_Genes_clone($acc);
- foreach my $gene (@genes){
- foreach my $exon ( $gene->all_Exon_objects ) {
- $exon->start($exon->start - $embl_offset+1);
- $exon->end($exon->end - $embl_offset+1);
- }
- push(@out,@genes);
- }
-
-
- }
- }
-
- return @out;
-}
-
-
-=head2 length
-
- Title : length
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub length{
- my ($self,$length) = @_;
-
- if( defined $length ) {
- $self->{'_length'} = $length;
- return $length;
- }
-
- my $id= $self->internal_id();
- $self->throw("Internal ID not set") unless $id;
- if (! defined ($self->{'_length'})) {
- my $sth = $self->dbobj->prepare("select length from contig where internal_id = \"$id\" ");
- $sth->execute();
-
- my $rowhash = $sth->fetchrow_hashref();
-
- $self->{'_length'} = $rowhash->{'length'};
- }
-
- return $self->{'_length'};
-}
-
-sub cloneid {
- my ($self,$arg) = @_;
-
- if (defined($arg)) {
- $self->{_cloneid} = $arg;
- }
-
- return $self->{_cloneid};
-}
-
-=head2 old_chromosome
-
- Title : chromosome
- Usage : $chr = $contig->chromosome( [$chromosome] )
- Function: get/set the chromosome of the contig.
- Example :
- Returns : the chromsome object
- Args :
-
-=cut
-
-sub old_chromosome {
- my ($self,$chromosome ) = @_;
- my $id= $self->internal_id();
-
- if( defined( $chromosome )) {
- $self->{_chromosome} = $chromosome;
- } else {
- if (! defined ($self->{_chromosome})) {
- my $sth = $self->dbobj->prepare("select chromosomeId from contig where internal_id = \"$id\" ");
- $sth->execute();
-
- my $rowhash = $sth->fetchrow_hashref();
- my $chrId = $rowhash->{'chromosomeId'};
- $self->{_chromosome} = Bio::EnsEMBL::Chromosome->get_by_id
- ( $chrId );
- }
- }
- return $self->{_chromosome};
-}
-
-=head2 seq_version
-
- Title : seq_version
- Usage : $obj->seq_version($newval)
- Function:
- Example :
- Returns : value of seq_version
- Args : newvalue (optional)
-
-
-=cut
-
-sub seq_version{
- my ($obj,$value) = @_;
- if( defined $value) {
- $obj->{'seq_version'} = $value;
- }
- return $obj->{'seq_version'};
-
-}
-
-=head2 embl_order
-
- Title : order
- Usage : $obj->embl_order
- Function:
- Returns :
- Args :
-
-
-=cut
-
-sub embl_order{
- my $self = shift;
- my $id = $self->id();
- my $sth = $self->dbobj->prepare("select corder from contig where id = \"$id\" ");
- $sth->execute();
- my $rowhash = $sth->fetchrow_hashref();
- return $rowhash->{'corder'};
-
-}
-
-
-
-
-=head2 embl_offset
-
- Title : embl_offset
- Usage :
- Returns :
- Args :
-
-
-=cut
-
-sub embl_offset{
- my ( $self, $arg ) = @_;
- my $id = $self->id();
- if( defined $arg ) {
- $self->{_embl_offset} = $arg;
- return;
- }
-
- if( defined $self->{_embl_offset} ) {
- return $self->{_embl_offset};
- } else {
- my $sth = $self->dbobj->prepare("select offset from contig where id = \"$id\" ");
- $sth->execute();
- my $rowhash = $sth->fetchrow_hashref();
- $self->{_embl_offset} = $rowhash->{'offset'};
- return $self->{_embl_offset};
- }
-}
-
-=head2 embl_accession
-
- Title : embl_accession
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub embl_accession{
- my $self = shift;
-
- return "AL000000";
-}
-
-
-=head2 id
-
- Title : id
- Usage : $obj->id($newval)
- Function:
- Example :
- Returns : value of id
- Args : newvalue (optional)
-
-
-=cut
-
-sub id {
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'id'} = $value;
- }
- return $self->{'id'};
-
-}
-
-=head2 internal_id
-
- Title : internal_id
- Usage : $obj->internal_id($newval)
- Function:
- Example :
- Returns : value of database internal id
- Args : newvalue (optional)
-
-=cut
-
-sub internal_id {
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'internal_id'} = $value;
- }
- return $self->{'internal_id'};
-
-}
-
-=head2 dna_id
-
- Title : dna_id
- Usage : $obj->dna_id($newval)
- Function: Get or set the id for this contig in the dna table
- Example :
- Returns : value of dna id
- Args : newvalue (optional)
-
-
-=cut
-
-sub dna_id {
- my ($self,$value) = @_;
- if( defined $value) {
- $self->{'dna_id'} = $value;
- }
- return $self->{'dna_id'};
-
-}
-
-
-=head2 seq_date
-
- Title : seq_date
- Usage : $contig->seq_date()
- Function: Gives the unix time value of the dna table created datetime field, which indicates
- the original time of the dna sequence data
- Example : $contig->seq_date()
- Returns : unix time
- Args : none
-
-
-=cut
-
-sub seq_date {
- my ($self) = @_;
-
- my $id = $self->internal_id();
- my $query = "select UNIX_TIMESTAMP(d.created) from dna as d,contig as c where c.internal_id = $id and c.dna = d.id";
- my $sth = $self->dbobj->dnadb->prepare($query);
- $sth->execute();
- my $rowhash = $sth->fetchrow_hashref();
- return $rowhash->{'UNIX_TIMESTAMP(d.created)'};
-}
-
-
-
-
-sub _db_obj {
- my ($self,@args) = @_;
- $self->warn("Someone is using a deprecated _db_obj call!");
- return $self->dbobj(@args);
-}
-
-=head2 dbobj
-
- Title : dbobj
- Usage :
- Function:
- Example :
- Returns : The Bio::EnsEMBL::DBSQL::ObjI object
- Args :
-
-
-=cut
-
-sub dbobj {
- my ($self,$arg) = @_;
-
- if (defined($arg)) {
- $self->throw("[$arg] is not a Bio::EnsEMBL::DBSQL::Obj") unless ($arg->isa("Bio::EnsEMBL::DBSQL::Obj") || $arg->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));
- $self->{'_dbobj'} = $arg;
- }
- return $self->{'_dbobj'};
-}
-
-=head2 crossdb
-
- Title : crossdb
- Usage :
- Function:
- Example :
- Returns : The Bio::EnsEMBL::DBSQL::CrossMatchAdaptor object
- Args :
-
-
-=cut
-
-sub _crossdb {
- my ($self,$arg) = @_;
-
- return $self->dbobj->_crossdb;
-}
-
-
-
-
-#
-# Static golden path tables
-#
-
-
-=head2 chromosome
-
- Title : chromosome
- Usage : $self->chromosome($newval)
- Function:
- Returns : value of chromosome
- Args :
-
-
-=cut
-
-sub chromosome{
- my $self = shift;
-
- if( defined $self->_chromosome) { return $self->_chromosome;}
-
- my $id = $self->internal_id;
- my $type = $self->dbobj->static_golden_path_type();
- my $sth = $self->dbobj->prepare("select chr_name from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute;
- my ($value) = $sth->fetchrow_array();
- if( !defined $value) { return undef; }
- $self->_chromosome($value);
- return $value;
-
-}
-
-=head2 _chromosome
-
- Title : chromosome
- Usage : $self->_chromosome($newval)
- Function:
- Returns : value of _chromosome
- Args : newvalue (optional)
-
-
-=cut
-
-sub _chromosome{
- my $self = shift;
- if( @_ ) {
- my $value = shift;
- $self->{'_chromosome'} = $value;
- }
- return $self->{'_chromosome'};
-
-}
-
-=head2 fpc_contig_name
-
- Title : fpc_contig_name
- Usage : $self->fpc_contig_name()
- Function:
- Returns : value of fpc_contig
- Args :
-
-
-=cut
-
-sub fpc_contig_name {
- my $self = shift;
-
- if( defined $self->_fpc_contig) { return $self->_fpc_contig;}
-
- my $id = $self->internal_id;
- my $type = $self->dbobj->static_golden_path_type();
- my $sth = $self->dbobj->prepare("select fpcctg_name from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute;
- my ($value) = $sth->fetchrow_array();
- if( !defined $value) { return undef; }
- $self->_fpc_contig($value);
- return $value;
-
-
-}
-
-=head2 _fpc_contig
-
- Title : fpc_contig
- Usage : $self->_fpc_contig($newval)
- Function:
- Returns : value of _fpc_contig
- Args : newvalue (optional)
-
-
-=cut
-
-sub _fpc_contig{
- my $self = shift;
- if( @_ ) {
- my $value = shift;
- $self->{'_fpc_contig'} = $value;
- }
- return $self->{'_fpc_contig'};
-
-}
-
-=head2 chr_start
-
- Title : chr_start
- Usage : $self->chr_start($newval)
- Function:
- Returns : value of chr_start
- Args :
-
-
-=cut
-
-sub chr_start{
- my $self = shift;
-
- if( defined $self->_chr_start) { return $self->_chr_start;}
-
- my $id = $self->internal_id;
- my $type = $self->dbobj->static_golden_path_type();
- my $sth = $self->dbobj->prepare("select chr_start from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute;
- my ($value) = $sth->fetchrow_array();
- if( !defined $value) { return undef; }
- $self->_chromosome($value);
- return $value;
-
-
-}
-
-=head2 _chr_start
-
- Title : chr_start
- Usage : $self->_chr_start($newval)
- Function:
- Returns : value of _chr_start
- Args : newvalue (optional)
-
-
-=cut
-
-sub _chr_start{
- my $self = shift;
- if( @_ ) {
- my $value = shift;
- $self->{'_chr_start'} = $value;
- }
- return $self->{'_chr_start'};
-
-}
-
-=head2 chr_end
-
- Title : chr_end
- Usage : $self->chr_end($newval)
- Function:
- Returns : value of chr_end
- Args :
-
-
-=cut
-
-sub chr_end{
- my $self = shift;
-
- if( defined $self->_chr_end) { return $self->_chr_end;}
-
- my $id = $self->internal_id;
- my $type = $self->dbobj->static_golden_path_type();
- my $sth = $self->dbobj->prepare("select chr_end from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute;
- my ($value) = $sth->fetchrow_array();
- if( !defined $value) { return undef; }
- $self->_chr_end($value);
- return $value;
-
-}
-
-=head2 _chr_end
-
- Title : chr_end
- Usage : $self->_chr_end($newval)
- Function:
- Returns : value of _chr_end
- Args : newvalue (optional)
-
-
-=cut
-
-sub _chr_end{
- my $self = shift;
- if( @_ ) {
- my $value = shift;
- $self->{'_chr_end'} = $value;
- }
- return $self->{'_chr_end'};
-
-}
-
-
-=head2 fpc_contig_start
-
- Title : fpc_contig_start
- Usage : $self->fpc_contig_start($newval)
- Function:
- Returns : value of fpc_contig_start
- Args :
-
-
-=cut
-
-sub fpc_contig_start {
- my $self = shift;
-
- if( defined $self->_fpc_contig_start) { return $self->_fpc_contig_start;}
-
- my $id = $self->internal_id;
- my $type = $self->dbobj->static_golden_path_type();
- my $sth = $self->dbobj->prepare("select fpcctg_start from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute;
- my ($value) = $sth->fetchrow_array();
- if( !defined $value) { return undef; }
- $self->_chromosome($value);
- return $value;
-
-
-}
-
-=head2 _fpc_contig_start
-
- Title : fpc_contig_start
- Usage : $self->_fpc_contig_start($newval)
- Function:
- Returns : value of _fpc_contig_start
- Args : newvalue (optional)
-
-
-=cut
-
-sub _fpc_contig_start{
- my $self = shift;
- if( @_ ) {
- my $value = shift;
- $self->{'_fpc_contig_start'} = $value;
- }
- return $self->{'_fpc_contig_start'};
-
-}
-
-=head2 fpc_contig_end
-
- Title : fpc_contig_end
- Usage : $self->fpc_contig_end($newval)
- Function:
- Returns : value of fpc_contig_end
- Args :
-
-
-=cut
-
-sub fpc_contig_end{
- my $self = shift;
-
- if( defined $self->_fpc_contig_end) { return $self->_fpc_contig_end;}
-
- my $id = $self->internal_id;
- my $type = $self->dbobj->static_golden_path_type();
- my $sth = $self->dbobj->prepare("select fpcctg_end from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute;
- my ($value) = $sth->fetchrow_array();
- if( !defined $value) { return undef; }
- $self->_fpc_contig_end($value);
- return $value;
-
-}
-
-=head2 _fpc_contig_end
-
- Title : fpc_contig_end
- Usage : $self->_fpc_contig_end($newval)
- Function:
- Returns : value of _fpc_contig_end
- Args : newvalue (optional)
-
-
-=cut
-
-sub _fpc_contig_end{
- my $self = shift;
- if( @_ ) {
- my $value = shift;
- $self->{'_fpc_contig_end'} = $value;
- }
- return $self->{'_fpc_contig_end'};
-
-}
-
-
-
-=head2 static_golden_start
-
- Title : static_golden_start
- Usage : $self->static_golden_start($newval)
- Function:
- Returns : value of static_golden_start (in RawContig coordinates)
- Args :
-
-
-=cut
-
-sub static_golden_start{
- my ($self,$static_golden_start) = @_;
-
- if( defined $static_golden_start ) {
- $self->{'_static_golden_start'} = $static_golden_start;
- return $static_golden_start;
- }
-
- my $id= $self->internal_id();
- $self->throw("Internal ID not set") unless $id;
-
- my $type = $self->dbobj->static_golden_path_type();
- if (! defined ($self->{'_static_golden_start'})) {
- my $sth = $self->dbobj->prepare("select raw_start from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute();
-
- my $rowhash = $sth->fetchrow_hashref();
-
- $self->{'_static_golden_start'} = $rowhash->{'raw_start'};
- }
- return $self->{'_static_golden_start'};
-}
-
-=head2 static_golden_end
-
- Title : static_golden_end
- Usage : $self->static_golden_end($newval)
- Function:
- Returns : value of static_golden_end (in RawContig coordinates)
- Args :
-
-
-=cut
-
-sub static_golden_end{
- my ($self,$static_golden_end) = @_;
-
- if( defined $static_golden_end ) {
- $self->{'_static_golden_end'} = $static_golden_end;
- return $static_golden_end;
- }
-
- my $id= $self->internal_id();
- $self->throw("Internal ID not set") unless $id;
-
- my $type = $self->dbobj->static_golden_path_type();
- if (! defined ($self->{'_static_golden_end'})) {
- my $sth = $self->dbobj->prepare("select raw_end from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute();
-
- my $rowhash = $sth->fetchrow_hashref();
-
- $self->{'_static_golden_end'} = $rowhash->{'raw_end'};
- }
- return $self->{'_static_golden_end'};
-}
-
-=head2 static_golden_ori
-
- Title : static_golden_ori
- Usage : $self->static_golden_ori($newval)
- Function:
- Returns : value of static_golden_ori
- Args :
-
-
-=cut
-
-sub static_golden_ori{
- my ($self,$static_golden_ori) = @_;
-
- if( defined $static_golden_ori ) {
- $self->{'_static_golden_ori'} = $static_golden_ori;
- return $static_golden_ori;
- }
-
- my $id= $self->internal_id();
- $self->throw("Internal ID not set") unless $id;
-
- my $type = $self->dbobj->static_golden_path_type();
- if (! defined ($self->{'_static_golden_ori'})) {
- my $sth = $self->dbobj->prepare("select raw_ori from static_golden_path where raw_id = $id and type = '$type'");
- $sth->execute();
-
- my $rowhash = $sth->fetchrow_hashref();
-
- $self->{'_static_golden_ori'} = $rowhash->{'raw_ori'};
- }
- return $self->{'_static_golden_ori'};
-}
-
-
-=head2 static_golden_type
-
- Title : static_golden_type
- Usage : $self->static_golden_type($newval)
- Function:
- Returns : value of static_golden_type
- Args :
-
-
-=cut
-
-sub static_golden_type{
- my $self = shift;
-
- return $self->dbobj->static_golden_path_type();
-
-}
-
-
-=head2 is_static_golden
-
- Title : is_static_golden
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub is_static_golden{
- my ($self,@args) = @_;
-
- if( defined $self->fpc_contig_name ) {
- return 1;
- }
-
-}
-
-
-=head2 perl_only_sequences
-
- Title : perl_only_sequences
- Usage : $obj->perl_only_sequences($newval)
- Function:
- Returns : value of perl_only_sequences
- Args : newvalue (optional)
-
-
-=cut
-
-sub perl_only_sequences{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'perl_only_sequences'} = $value;
- }
- return $obj->{'perl_only_sequences'};
-
-}
-
-=head2 use_rawcontig_acc
-
- Title : use_rawcontig_acc
- Usage : $obj->use_rawcontig_acc($newval)
- Function:
- Returns : value of use_rawcontig_acc
- Args : newvalue (optional)
-
-
-=cut
-
-sub use_rawcontig_acc{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'use_rawcontig_acc'} = $value;
- }
- return $obj->{'use_rawcontig_acc'};
-
-}
-
-=head2 overlap_distance_cutoff
-
- Title : overlap_distance_cutoff
- Usage : my $cutoff = $contig->overlap_distance_cutoff()
- Function: Gets or sets an integer which is used when building
- VirtualContigs. If the distance in a contig overlap
- is greater than the cutoff, then the overlap will
- not be returned.
- Returns : value of overlap_distance_cutoff
- Args : positive integer
-
-
-=cut
-
-
-sub overlap_distance_cutoff {
- my( $self, $cutoff ) = @_;
-
- if (defined $cutoff) {
- if( $cutoff !~ /^\d+$/ && $cutoff != -1 ) {
- $self->throw("'$cutoff' is not an positive integer");
- }
- $self->{'_overlap_distance_cutoff'} = $cutoff;
- }
- return $self->{'_overlap_distance_cutoff'};
-}
-
-
-sub is_golden {
- my $self = shift;
-
- if( defined $self->get_left_overlap || defined $self->get_right_overlap ) {
- return 1;
- }
- return 0;
-}
-
-
-=head2 unmapped_exons
-
- Title : unmapped_exons
- Usage : $obj->unmapped_exons($newval)
- Function: Getset for unmapped_exons value
- Returns : value of unmapped_exons
- Args : newvalue (optional)
-
-
-=cut
-
-sub unmapped_exons{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'unmapped_exons'} = $value;
- }
- return $obj->{'unmapped_exons'};
-
-}
-
-
-=head2 SeqI implementing functions
-
-=head2 species
-
- Title : species
- Usage :
- Function:
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub species{
- my ($self,@args) = @_;
-
- return undef;
-}
-
-
-# AS: on the way to contexts
-# we need temporarily subseq
-sub subseq {
- my ( $self, $start, $end ) = @_;
- my $length = $end-$start+1;
- my $id = $self->dna_id();
- my $sth = $self->dbobj->dnadb->prepare("
- SELECT SUBSTRING(sequence,$start,$length)
- FROM dna
- WHERE id = $id
- ");
- $sth->execute();
- my ($value) = $sth->fetchrow_array();
- return $value;
-}
-
-
-
-1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/SymmetricContigFeatureContainer.pm b/modules/Bio/EnsEMBL/DBSQL/SymmetricContigFeatureContainer.pm
deleted file mode 100755
index 6f30dcbbfb232e3a175cca3ba6d38a9b1b57d097..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/DBSQL/SymmetricContigFeatureContainer.pm
+++ /dev/null
@@ -1,147 +0,0 @@
-
-#
-# Ensembl module for Bio::EnsEMBL::DBSQL::SymmetricContigFeatureContainer
-#
-# 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::DBSQL::SymmetricContigFeatureContainer - Binds to SymmetricContigFeature table
-
-=head1 SYNOPSIS
-
-Give standard usage here
-
-=head1 DESCRIPTION
-
-This module is a container for symmetric contig feature pairs, i.e. pairs of features between contigs that have identical sequence in two versions of a database. The pairs are stored symmetrically, i.e. each feature on each contig is stored in the contig_feature table, and each pair is stored with an id in a separate table.
-
-The method which fetches teh feature pairs breaks the symmetry by asking for all the feature pairs with a certain version of the clone (on which the contig is sitting). The crosmmatching at the moment relies on the sv version of the clones.
-
-=head1 AUTHOR - Ewan Birney
-
-This module is part of the Ensembl project http://www.ensembl.org
-
-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::DBSQL::SymmetricContigFeatureContainer;
-use vars qw(@ISA);
-use strict;
-
-# Object preamble - inherits from Bio::Root::RootI
-
-
-use Bio::EnsEMBL::DBSQL::BaseAdaptor;
-use Bio::EnsEMBL::FeatureFactory;
-
-@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
-
-=head2 get_FeaturePair_list_by_rawcontig_id
-
- Title : get_FeaturePair_list_by_rawcontig_id
- Usage : $scfc->get_FeaturePair_list_by_rawcontig_id($rid,15)
- Function: gets all the feature pairs for a specific rawcontig id
- and clone version
- Example : $scfc->get_FeaturePair_list_by_rawcontig_id('AC000043.12',5)
- Returns : array of Bio::EnsEMBL::FeaturePair
- Args : id of the rawcontig,sv version of the clone it is on
-
-
-=cut
-
-sub get_FeaturePair_list_by_rawcontig_id{
- my ($self,$id,$version) = @_;
-
- if( !defined $id ) {
- $self->throw("Must have a raw contig id");
- }
- if( !defined $version ) {
- $self->throw("Must have a raw contig version");
- }
-
- my $sth = $self->prepare("select a.seq_start,a.seq_end,a.strand,b.seq_start,b.seq_end,b.strand,b.rawcontigid,p.score from symmetric_contig_feature a, symmetric_contig_pair_hit p,symmetric_contig_feature b where a.symchid = p.symchid and p.symchid = b.symchid and a.symcfid != b.symcfid and a.rawcontigid = '$id' and a.rawversion=$version");
-
-
- $sth->execute || $self->throw("Unable to retrieve versions!");
- my @out;
-
- while( my $aref = $sth->fetchrow_arrayref ) {
- my ($start,$end,$strand,$hstart,$hend,$hstrand,$hname,$score) = @{$aref};
- my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();
- $out->set_all_fields($start,$end,$strand,$score,$id,'symmetric',$id,
- $hstart,$hend,$hstrand,$score,$hname,'symmetric',$hname);
- push(@out,$out);
- }
-
- return @out;
-}
-
-
-=head2 write_FeaturePair_List
-
- Title : write_FeaturePair_List
- Usage : $scfc->write_FeaturePair_List(@fp)
- Function: Writes an array of feature pairs to the db
- Example : $scfc0>write_FeaturePair_List(@fp)
- Returns : nothing
- Args : array of Bio::EnsEMBL::FeaturePair
-
-
-=cut
-
-sub write_FeaturePair_List{
- my ($self,@fp) = @_;
-
- foreach my $fp ( @fp ) {
- my $score = $fp->score;
- my $sth = $self->prepare("INSERT INTO symmetric_contig_pair_hit (symchid,score) VALUES (NULL,$score)");
- $sth->execute;
- $sth = $self->prepare("select LAST_INSERT_ID()");
- $sth->execute;
- my ($hitid) = $sth->fetchrow_array;
-
- my $seqname = $fp->feature1->seqname;
- print STDERR "Parsing $seqname\n";
- $seqname =~ /(\w+)\.(\d+)\.(\S+)/ || $self->throw("Feature pair name does not conform to acc.version.number sequence");
- my $version = $2;
- my $contigid = "$1.$3";
- print STDERR "Got $contigid\n";
- my $clone=$1;
- $sth = $self->prepare("INSERT INTO symmetric_contig_feature (symcfid,symchid,rawcontigid,rawversion,clone,seq_start,seq_end,strand) VALUES (NULL,$hitid,'".$contigid."',".$version.",'".$clone."',".$fp->feature1->start.",".$fp->feature1->end.",".$fp->feature1->strand.")");
- $sth->execute;
-
- $seqname = $fp->feature2->seqname;
- print STDERR "And $seqname\n";
- $seqname =~ /(\w+)\.(\d+)\.(\S+)/ || $self->throw("Feature pair name does not conform to acc.version.number sequence");
- $version = $2;
- $contigid = "$1.$3";
- print STDERR "Got $contigid\n";
- $clone=$1;
- $sth = $self->prepare("INSERT INTO symmetric_contig_feature (symcfid,symchid,rawcontigid,rawversion,clone,seq_start,seq_end,strand) VALUES (NULL,$hitid,'".$contigid."',".$version.",'".$clone."',".$fp->feature2->start.",".$fp->feature2->end.",".$fp->feature2->strand.")");
- $sth->execute;
- }
-
-}
-
-
-1;
-
-
diff --git a/modules/Bio/EnsEMBL/RawContig.pm b/modules/Bio/EnsEMBL/RawContig.pm
index d3a1f57f84340f3d179e2021a7dd26f314b9c52f..bb35922e6d6e1a4b81982d753a817f92b8f49135 100644
--- a/modules/Bio/EnsEMBL/RawContig.pm
+++ b/modules/Bio/EnsEMBL/RawContig.pm
@@ -78,6 +78,9 @@ sub new {
( $international_name );
}
+
+
+
# things to take over from DBSQL/RawContig ?
# fetch - done in DBSQL/RawContigAdaptor
# get_all_Genes - should be in GeneAdaptor