Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm @ 0:1f6dce3d34e0
Uploaded
| author | mahtabm |
|---|---|
| date | Thu, 11 Apr 2013 02:01:53 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,532 @@ +=head1 LICENSE + + Copyright (c) 1999-2012 The European Bioinformatics Institute and + Genome Research Limited. All rights reserved. + + This software is distributed under a modified Apache license. + For license details, please see + + http://www.ensembl.org/info/about/code_licence.html + +=head1 CONTACT + + Please email comments or questions to the public Ensembl + developers list at <dev@ensembl.org>. + + Questions may also be sent to the Ensembl help desk at + <helpdesk@ensembl.org>. + +=cut + +=head1 NAME + +Bio::EnsEMBL::DBSQL::SlicingEventAdaptor - Database adaptor for the retrieval and +storage of SplicingEvent objects + +=head1 SYNOPSIS + + use Bio::EnsEMBL::Registry; + + Bio::EnsEMBL::Registry->load_registry_from_db( + -host => 'ensembldb.ensembl.org', + -user => 'anonymous', + ); + + $se_adaptor = + Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingEvent" ); + + $se = $se_adaptor->fetch_by_dbID(12); + + $slice_adaptor = + Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" ); + + $slice = + $slice_adaptor->fetch_by_region( 'chromosome', '1', 1, 1000000 ); + + @ase = @{ $se_adaptor->fetch_all_by_Slice($slice) }; + +=head1 DESCRIPTION + +This is a database aware adaptor for the retrieval and storage ofSlicingEvents +objects. + +=head1 METHODS + +=cut +package Bio::EnsEMBL::DBSQL::SplicingEventAdaptor; + +use strict; + +use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning ); +use Bio::EnsEMBL::DBSQL::SliceAdaptor; +use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor; +use Bio::EnsEMBL::DBSQL::DBAdaptor; +use Bio::EnsEMBL::SplicingEvent; + +use vars '@ISA'; +@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor); + + +=head2 list_dbIDs + + Example : @gene_ids = @{$gene_adaptor->list_dbIDs()}; + Description: Gets an array of internal ids for all genes in the current db + Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region. + Returntype : Listref of Ints + Exceptions : none + Caller : general + Status : Stable + +=cut + +sub list_dbIDs { + my ($self,$ordered) = @_; + + return $self->_list_dbIDs("splicing_event", undef, $ordered); +} + + +=head2 fetch_all_by_Slice + + Arg [1] : Bio::EnsEMBL::Slice $slice + The slice to fetch genes on. + Arg [2] : type of Transcript event + Arg [3] : (optional) boolean $load_features + If true, transcript will be loaded immediately rather + than lazy loaded later. +=cut + +sub fetch_all_by_Slice { + my ( $self, $slice, $type, $load_features ) = @_; + + my $constraint = ''; + + if ( defined($type) ) { + $constraint .= sprintf( " AND at.code = %s", + $self->dbc()->db_handle()->quote($type) ); + } + + my $tes = + $self->SUPER::fetch_all_by_Slice_constraint( $slice, $constraint ); + + # Is there any use in having a splice event without the pairs and + # features?? + + if ( !$load_features || scalar( @{$tes} ) < 2 ) { + return $tes; + } + + # Load pairs and features. + foreach my $te ( @{$tes} ) { + $te->get_all_Features(); + $te->get_all_Pairs(); + } + + return $tes; +} ## end sub fetch_all_by_Slice + + +sub fetch_all_by_Gene { + my ( $self, $gene ) = @_; + + my $sth = $self->dbc->prepare( + q( +SELECT se.splicing_event_id, + se.seq_region_id, + se.seq_region_start, + se.seq_region_end, + se.seq_region_strand, + se.name, + at.code +FROM splicing_event se + JOIN attrib_type at USING (attrib_type_id) +WHERE se.gene_id =) . $gene->dbID() ); + + $sth->execute(); + + my ( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, $type ); + + $sth->bind_columns( + \( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, + $type ) ); + + my @splicing_events; + + my $sa = $self->db()->get_SliceAdaptor(); + + while ( $sth->fetch() ) { + my $slice = + $sa->fetch_by_seq_region_id( $seq_region_id, + $seq_region_start, + $seq_region_end, + $seq_region_strand ); + + push( @splicing_events, + $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', { + 'start' => $seq_region_start, + 'end' => $seq_region_end, + 'strand' => $seq_region_strand, + 'adaptor' => $self, + 'slice' => $slice, + 'dbID' => $splicing_event_id, + 'name' => $name, + 'gene_id' => $gene->dbID(), + 'type' => $type } ) ); + } + + foreach my $te (@splicing_events) { + $te->get_all_Features(); + $te->get_all_Pairs(); + } + + return \@splicing_events; +} ## end sub fetch_all_by_Gene + +sub fetch_all_by_Exon { + my ( $self, $exon ) = @_; + + my $sth = $self->dbc()->prepare( + q( +SELECT DISTINCT splicing_event_id +FROM splicing_event_feature +WHERE exon_id =) . $exon->dbID() ); + + $sth->execute(); + + my $se_id; + $sth->bind_col( 1, \$se_id ); + + my @list; + while ( $sth->fetch() ) { + push( @list, $se_id ); + } + + $sth = $self->dbc->prepare( + q( +SELECT se.splicing_event_id, + se.seq_region_id, + se.seq_region_start, + se.seq_region_end, + se.seq_region_strand, + se.name, + at.code, + se.gene_id +FROM splicing_event se + JOIN attrib_type at USING (attrib_type_id) +WHERE se.splicing_event_id in ) . '(' . join( ',', @list ) . ')' ); + + $sth->execute(); + + my ( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, $type, $gene_id ); + + $sth->bind_columns( + \( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, + $type, $gene_id ) ); + + my @splicing_events; + + my $sa = $self->db->get_SliceAdaptor(); + + while ( $sth->fetch ) { + my $slice = + $sa->fetch_by_seq_region_id( $seq_region_id, + $seq_region_start, + $seq_region_end, + $seq_region_strand ); + + push( @splicing_events, + $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', { + 'start' => $seq_region_start, + 'end' => $seq_region_end, + 'strand' => $seq_region_strand, + 'adaptor' => $self, + 'slice' => $slice, + 'dbID' => $splicing_event_id, + 'name' => $name, + 'gene_id' => $gene_id, + 'type' => $type } ) ); + } + + foreach my $te (@splicing_events) { + $te->get_all_Features(); + $te->get_all_Pairs(); + } + + return \@splicing_events; +} ## end sub fetch_all_by_Exon + +sub fetch_all_by_Transcript { + my ( $self, $transcript ) = @_; + + my $sth = $self->dbc->prepare( + q( +SELECT DISTINCT splicing_event_id +FROM splicing_event_feature +WHERE transcript_id =) . $transcript->dbID() ); + + $sth->execute(); + + my $se_id; + $sth->bind_col( 1, \$se_id ); + + my @list; + while ( $sth->fetch() ) { + push( @list, $se_id ); + } + + $sth = $self->dbc->prepare( + q( +SELECT se.splicing_event_id, + se.seq_region_id, + se.seq_region_start, + se.seq_region_end, + se.seq_region_strand, + se.name, + at.code, + se.gene_id +FROM splicing_event se + JOIN attrib_type at USING (attrib_type_id) +WHERE se.splicing_event_id in ) . '(' . join( ',', @list ) . ')' ); + + $sth->execute(); + + my ( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, $type, $gene_id ); + + $sth->bind_columns( + \( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, + $type, $gene_id ) ); + + my @splicing_events; + + my $sa = $self->db()->get_SliceAdaptor(); + + while ( $sth->fetch() ) { + my $slice = + $sa->fetch_by_seq_region_id( $seq_region_id, + $seq_region_start, + $seq_region_end, + $seq_region_strand ); + + push( @splicing_events, + $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', { + 'start' => $seq_region_start, + 'end' => $seq_region_end, + 'strand' => $seq_region_strand, + 'adaptor' => $self, + 'slice' => $slice, + 'dbID' => $splicing_event_id, + 'name' => $name, + 'gene_id' => $gene_id, + 'type' => $type } ) ); + } + + foreach my $te (@splicing_events) { + $te->get_all_Features(); + $te->get_all_Pairs(); + } + + return \@splicing_events; +} ## end sub fetch_all_by_Transcript + +# _tables +# Arg [1] : none +# Description: PROTECTED implementation of superclass abstract method. +# Returns the names, aliases of the tables to use for queries. +# Returntype : list of listrefs of strings +# Exceptions : none +# Caller : internal +# Status : At Risk + +sub _tables { + return ( [ 'splicing_event', 'se' ], [ 'attrib_type', 'at' ] ); +} + +# _columns +# Arg [1] : none +# Example : none +# Description: PROTECTED implementation of superclass abstract method. +# Returns a list of columns to use for queries. +# Returntype : list of strings +# Exceptions : none +# Caller : internal +# Status : At Risk + +sub _columns { + return ( 'se.splicing_event_id', 'se.seq_region_id', + 'se.seq_region_start', 'se.seq_region_end', + 'se.seq_region_strand', 'se.name', + 'se.gene_id', 'at.code' ); +} + +sub _left_join { + return ( [ 'attrib_type', 'at.attrib_type_id = se.attrib_type_id' ] ); +} + +sub _objs_from_sth { + my ( $self, $sth, $mapper, $dest_slice ) = @_; + + my ( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, $gene_id, $type ); + + $sth->bind_columns( + \( $splicing_event_id, $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand, $name, + $gene_id, $type ) ); + + my $sa = $self->db()->get_SliceAdaptor(); + + my @splicing_events; + my %slice_hash; + my %sr_name_hash; + my %sr_cs_hash; + + my $asm_cs; + my $cmp_cs; + my $asm_cs_vers; + my $asm_cs_name; + my $cmp_cs_vers; + my $cmp_cs_name; + + if ( defined($mapper) ) { + $asm_cs = $mapper->assembled_CoordSystem(); + $cmp_cs = $mapper->component_CoordSystem(); + $asm_cs_name = $asm_cs->name(); + $asm_cs_vers = $asm_cs->version(); + $cmp_cs_name = $cmp_cs->name(); + $cmp_cs_vers = $cmp_cs->version(); + } + + my $dest_slice_start; + my $dest_slice_end; + my $dest_slice_strand; + my $dest_slice_length; + my $dest_slice_cs; + my $dest_slice_sr_name; + my $dest_slice_sr_id; + my $asma; + + if ( defined($dest_slice) ) { + $dest_slice_start = $dest_slice->start(); + $dest_slice_end = $dest_slice->end(); + $dest_slice_strand = $dest_slice->strand(); + $dest_slice_length = $dest_slice->length(); + $dest_slice_cs = $dest_slice->coord_system(); + $dest_slice_sr_name = $dest_slice->seq_region_name(); + $dest_slice_sr_id = $dest_slice->get_seq_region_id(); + $asma = $self->db->get_AssemblyMapperAdaptor(); + } + +FEATURE: + while ( $sth->fetch() ) { + # Need to get the internal_seq_region, if present. + $seq_region_id = $self->get_seq_region_id_internal($seq_region_id); + + my $slice = $slice_hash{ "ID:" . $seq_region_id }; + my $dest_mapper = $mapper; + + if ( !$slice ) { + $slice = $sa->fetch_by_seq_region_id($seq_region_id); + $slice_hash{ "ID:" . $seq_region_id } = $slice; + $sr_name_hash{$seq_region_id} = $slice->seq_region_name(); + $sr_cs_hash{$seq_region_id} = $slice->coord_system(); + } + + # Obtain a mapper if none was defined, but a dest_seq_region was. + if ( !defined($dest_mapper) + && defined($dest_slice) + && !$dest_slice_cs->equals( $slice->coord_system ) ) + { + $dest_mapper = + $asma->fetch_by_CoordSystems( $dest_slice_cs, + $slice->coord_system ); + $asm_cs = $dest_mapper->assembled_CoordSystem(); + $cmp_cs = $dest_mapper->component_CoordSystem(); + $asm_cs_name = $asm_cs->name(); + $asm_cs_vers = $asm_cs->version(); + $cmp_cs_name = $cmp_cs->name(); + $cmp_cs_vers = $cmp_cs->version(); + } + + my $sr_name = $sr_name_hash{$seq_region_id}; + my $sr_cs = $sr_cs_hash{$seq_region_id}; + + # Remap the feature coordinates to another coord system if a mapper + # was provided. + if ( defined($dest_mapper) ) { + + if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) { + ( $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand ) + = + $dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end, + $seq_region_strand, $sr_cs, 1, $dest_slice); + + } else { + + ( $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand ) + = $dest_mapper->fastmap( $sr_name, $seq_region_start, + $seq_region_end, $seq_region_strand, + $sr_cs ); + } + + # Skip features that map to gaps or coord system boundaries. + if ( !defined($seq_region_id) ) { next FEATURE } + + # Get a slice in the coord system we just mapped to. + $slice = $slice_hash{ "ID:" . $seq_region_id } ||= + $sa->fetch_by_seq_region_id($seq_region_id); + } + + # If a destination slice was provided convert the coords. If the + # dest_slice starts at 1 and is foward strand, nothing needs doing. + if ( defined($dest_slice) ) { + if ( $dest_slice_start != 1 || $dest_slice_strand != 1 ) { + if ( $dest_slice_strand == 1 ) { + $seq_region_start = $seq_region_start - $dest_slice_start + 1; + $seq_region_end = $seq_region_end - $dest_slice_start + 1; + } else { + my $tmp_seq_region_start = $seq_region_start; + $seq_region_start = $dest_slice_end - $seq_region_end + 1; + $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1; + $seq_region_strand = -$seq_region_strand; + } + } + + # Throw away features off the end of the requested slice. + if ( $seq_region_end < 1 + || $seq_region_start > $dest_slice_length + || ( $dest_slice_sr_id != $seq_region_id ) ) + { + next FEATURE; + } + + $slice = $dest_slice; + } + + # Finally, create the new splicing_event. + push( @splicing_events, + $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', { + 'start' => $seq_region_start, + 'end' => $seq_region_end, + 'strand' => $seq_region_strand, + 'adaptor' => $self, + 'slice' => $slice, + 'dbID' => $splicing_event_id, + 'name' => $name, + 'gene_id' => $gene_id, + 'type' => $type } ) ); + + } ## end while ( $sth->fetch() ) + + return \@splicing_events; +} ## end sub _objs_from_sth + + +1;