Mercurial > repos > mahtabm > ensembl
view variant_effect_predictor/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm @ 3:d30fa12e4cc5 default tip
Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Mon, 13 Jan 2014 10:38:30 -0500 |
| parents | 1f6dce3d34e0 |
| children |
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=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::TranscriptAdaptor - An adaptor which performs database interaction relating to the storage and retrieval of Transcripts =head1 SYNOPSIS use Bio::EnsEMBL::Registry; Bio::EnsEMBL::Registry->load_registry_from_db( -host => 'ensembldb.ensembl.org', -user => 'anonymous' ); $transcript_adaptor = Bio::EnsEMBL::Registry->get_adaptor( 'Human', 'Core', 'Transcript' ); $transcript = $transcript_adaptor->fetch_by_dbID(1234); $transcript = $transcript_adaptor->fetch_by_stable_id('ENST00000201961'); $slice = $slice_adaptor->fetch_by_region( 'Chromosome', '3', 1, 1000000 ); @transcripts = @{ $transcript_adaptor->fetch_all_by_Slice($slice) }; ($transcript) = @{ $transcript_adaptor->fetch_all_by_external_name('NP_065811.1') }; =head1 DESCRIPTION This adaptor provides a means to retrieve and store information related to Transcripts. Primarily this involves the retrieval or storage of Bio::EnsEMBL::Transcript objects from a database. See Bio::EnsEMBL::Transcript for details of the Transcript class. =cut package Bio::EnsEMBL::DBSQL::TranscriptAdaptor; use strict; use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor; use Bio::EnsEMBL::Gene; use Bio::EnsEMBL::Exon; use Bio::EnsEMBL::Transcript; use Bio::EnsEMBL::Translation; use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning ); use vars qw(@ISA); @ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor ); # _tables # # Description: PROTECTED implementation of superclass abstract method. # Returns the names, aliases of the tables to use for queries. # Returntype : list of listrefs of strings # Exceptions : none # Caller : internal # Status : Stable sub _tables { return ( [ 'transcript', 't' ], [ 'xref', 'x' ], [ 'external_db', 'exdb' ] ); } #_columns # # Description: PROTECTED implementation of superclass abstract method. # Returns a list of columns to use for queries. # Returntype : list of strings # Exceptions : none # Caller : internal # Status : Stable sub _columns { my ($self) = @_; my $created_date = $self->db()->dbc()->from_date_to_seconds("created_date"); my $modified_date = $self->db()->dbc()->from_date_to_seconds("modified_date"); return ( 't.transcript_id', 't.seq_region_id', 't.seq_region_start', 't.seq_region_end', 't.seq_region_strand', 't.analysis_id', 't.gene_id', 't.is_current', 't.stable_id', 't.version', $created_date, $modified_date, 't.description', 't.biotype', 't.status', 'exdb.db_name', 'exdb.status', 'exdb.db_display_name', 'x.xref_id', 'x.display_label', 'x.dbprimary_acc', 'x.version', 'x.description', 'x.info_type', 'x.info_text' ); } sub _left_join { return ( [ 'xref', "x.xref_id = t.display_xref_id" ], [ 'external_db', "exdb.external_db_id = x.external_db_id" ] ); } =head2 fetch_by_stable_id Arg [1] : String $stable_id The stable id of the transcript to retrieve Example : my $tr = $tr_adaptor->fetch_by_stable_id('ENST00000309301'); Description: Retrieves a transcript via its stable id. Returntype : Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable =cut sub fetch_by_stable_id { my ($self, $stable_id) = @_; my $constraint = "t.stable_id = ? AND t.is_current = 1"; $self->bind_param_generic_fetch($stable_id,SQL_VARCHAR); my ($transcript) = @{ $self->generic_fetch($constraint) }; return $transcript; } sub fetch_all { my ($self) = @_; my $constraint = 't.biotype != "LRG_gene" and t.is_current = 1'; my @trans = @{ $self->generic_fetch($constraint) }; return \@trans ; } =head2 fetch_all_versions_by_stable_id Arg [1] : String $stable_id The stable ID of the transcript to retrieve Example : my $tr = $tr_adaptor->fetch_all_version_by_stable_id ('ENST00000309301'); Description : Similar to fetch_by_stable_id, but retrieves all versions of a transcript stored in the database. Returntype : listref of Bio::EnsEMBL::Transcript objects Exceptions : if we cant get the gene in given coord system Caller : general Status : At Risk =cut sub fetch_all_versions_by_stable_id { my ($self, $stable_id) = @_; my $constraint = "t.stable_id = ?"; $self->bind_param_generic_fetch($stable_id,SQL_VARCHAR); return $self->generic_fetch($constraint); } =head2 fetch_by_translation_stable_id Arg [1] : String $transl_stable_id The stable identifier of the translation of the transcript to retrieve Example : my $tr = $tr_adaptor->fetch_by_translation_stable_id ('ENSP00000311007'); Description: Retrieves a Transcript object using the stable identifier of its translation. Returntype : Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable =cut sub fetch_by_translation_stable_id { my ($self, $transl_stable_id ) = @_; my $sth = $self->prepare(qq( SELECT t.transcript_id FROM translation tl, transcript t WHERE tl.stable_id = ? AND tl.transcript_id = t.transcript_id AND t.is_current = 1 )); $sth->bind_param(1, $transl_stable_id, SQL_VARCHAR); $sth->execute(); my ($id) = $sth->fetchrow_array; $sth->finish; if ($id){ return $self->fetch_by_dbID($id); } else { return undef; } } =head2 fetch_by_translation_id Arg [1] : Int $id The internal identifier of the translation whose transcript is to be retrieved Example : my $tr = $tr_adaptor->fetch_by_translation_id($transl->dbID); Description: Given the internal identifier of a translation this method retrieves the transcript associated with that translation. If the transcript cannot be found undef is returned instead. Returntype : Bio::EnsEMBL::Transcript or undef Exceptions : none Caller : general Status : Stable =cut sub fetch_by_translation_id { my ( $self, $p_dbID ) = @_; if ( !defined($p_dbID) ) { throw("dbID argument is required"); } my $sth = $self->prepare( "SELECT transcript_id " . "FROM translation " . "WHERE translation_id = ?" ); $sth->bind_param( 1, $p_dbID, SQL_INTEGER ); $sth->execute(); my ($dbID) = $sth->fetchrow_array(); $sth->finish(); if ($dbID) { return $self->fetch_by_dbID($dbID); } return undef; } =head2 fetch_all_by_Gene Arg [1] : Bio::EnsEMBL::Gene $gene The gene to fetch transcripts of Example : my $gene = $gene_adaptor->fetch_by_stable_id('ENSG0000123'); my @transcripts = { $tr_adaptor->fetch_all_by_Gene($gene) }; Description: Retrieves Transcript objects for given gene. Puts Genes slice in each Transcript. Returntype : Listref of Bio::EnsEMBL::Transcript objects Exceptions : none Caller : Gene->get_all_Transcripts() Status : Stable =cut sub fetch_all_by_Gene { my ( $self, $gene ) = @_; my $constraint = "t.gene_id = " . $gene->dbID(); # Use the fetch_all_by_Slice_constraint method because it handles the # difficult Haps/PARs and coordinate remapping. # Get a slice that entirely overlaps the gene. This is because we # want all transcripts to be retrieved, not just ones overlapping # the slice the gene is on (the gene may only partially overlap the # slice). For speed reasons, only use a different slice if necessary # though. my $gslice = $gene->slice(); if ( !defined($gslice) ) { throw("Gene must have attached slice to retrieve transcripts."); } my $slice; if ( $gene->start() < 1 || $gene->end() > $gslice->length() ) { if ( $gslice->is_circular() ) { $slice = $gslice; } else { $slice = $self->db->get_SliceAdaptor->fetch_by_Feature($gene); } } else { $slice = $gslice; } my $transcripts = $self->fetch_all_by_Slice_constraint( $slice, $constraint ); if ( $slice != $gslice ) { my @out; foreach my $tr ( @{$transcripts} ) { push( @out, $tr->transfer($gslice) ); } $transcripts = \@out; } my $canonical_t = $gene->canonical_transcript(); foreach my $t ( @{$transcripts} ) { if ( $t->equals($canonical_t) ) { $t->is_canonical(1); last; } } return $transcripts; } ## end sub fetch_all_by_Gene =head2 fetch_all_by_Slice Arg [1] : Bio::EnsEMBL::Slice $slice The slice to fetch transcripts on Arg [2] : (optional) Boolean $load_exons If true, exons will be loaded immediately rather than lazy loaded later Arg [3] : (optional) String $logic_name The logic name of the type of features to obtain ARG [4] : (optional) String $constraint An extra contraint. Example : my @transcripts = @{ $tr_adaptor->fetch_all_by_Slice($slice) }; Description: Overrides superclass method to optionally load exons immediately rather than lazy-loading them later. This is more efficient when there are a lot of transcripts whose exons are going to be used. Returntype : Listref of Bio::EnsEMBL::Transcript objects Exceptions : thrown if exon cannot be placed on transcript slice Caller : Slice::get_all_Transcripts Status : Stable =cut sub fetch_all_by_Slice { my ( $self, $slice, $load_exons, $logic_name, $constraint ) = @_; my $transcripts; if ( defined($constraint) && $constraint ne '' ) { $transcripts = $self->SUPER::fetch_all_by_Slice_constraint( $slice, 't.is_current = 1 AND ' . $constraint, $logic_name ); } else { $transcripts = $self->SUPER::fetch_all_by_Slice_constraint( $slice, 't.is_current = 1', $logic_name ); } # if there are 0 or 1 transcripts still do lazy-loading if ( !$load_exons || @$transcripts < 2 ) { return $transcripts; } # preload all of the exons now, instead of lazy loading later # faster than 1 query per transcript # first check if the exons are already preloaded # @todo FIXME: Should test all exons. if ( exists( $transcripts->[0]->{'_trans_exon_array'} ) ) { return $transcripts; } # get extent of region spanned by transcripts my ( $min_start, $max_end ); foreach my $tr (@$transcripts) { if ( !defined($min_start) || $tr->seq_region_start() < $min_start ) { $min_start = $tr->seq_region_start(); } if ( !defined($max_end) || $tr->seq_region_end() > $max_end ) { $max_end = $tr->seq_region_end(); } } my $ext_slice; if ( $min_start >= $slice->start() && $max_end <= $slice->end() ) { $ext_slice = $slice; } else { my $sa = $self->db()->get_SliceAdaptor(); $ext_slice = $sa->fetch_by_region( $slice->coord_system->name(), $slice->seq_region_name(), $min_start, $max_end, $slice->strand(), $slice->coord_system->version() ); } # associate exon identifiers with transcripts my %tr_hash = map { $_->dbID => $_ } @{$transcripts}; my $tr_id_str = join( ',', keys(%tr_hash) ); my $sth = $self->prepare( "SELECT transcript_id, exon_id, rank " . "FROM exon_transcript " . "WHERE transcript_id IN ($tr_id_str)" ); $sth->execute(); my ( $tr_id, $ex_id, $rank ); $sth->bind_columns( \( $tr_id, $ex_id, $rank ) ); my %ex_tr_hash; while ( $sth->fetch() ) { $ex_tr_hash{$ex_id} ||= []; push( @{ $ex_tr_hash{$ex_id} }, [ $tr_hash{$tr_id}, $rank ] ); } my $ea = $self->db()->get_ExonAdaptor(); my $exons = $ea->fetch_all_by_Slice_constraint( $ext_slice, sprintf( "e.exon_id IN (%s)", join( ',', sort { $a <=> $b } keys(%ex_tr_hash) ) ) ); # move exons onto transcript slice, and add them to transcripts foreach my $ex ( @{$exons} ) { my $new_ex; if ( $slice != $ext_slice ) { $new_ex = $ex->transfer($slice); if ( !defined($new_ex) ) { throw("Unexpected. " . "Exon could not be transfered onto Transcript slice." ); } } else { $new_ex = $ex; } foreach my $row ( @{ $ex_tr_hash{ $new_ex->dbID() } } ) { my ( $tr, $rank ) = @{$row}; $tr->add_Exon( $new_ex, $rank ); } } my $tla = $self->db()->get_TranslationAdaptor(); # load all of the translations at once $tla->fetch_all_by_Transcript_list($transcripts); return $transcripts; } ## end sub fetch_all_by_Slice =head2 fetch_all_by_external_name Arg [1] : String $external_name An external identifier of the transcript to be obtained Arg [2] : (optional) String $external_db_name The name of the external database from which the identifier originates. Arg [3] : Boolean override. Force SQL regex matching for users who really do want to find all 'NM%' Example : my @transcripts = @{ $tr_adaptor->fetch_all_by_external_name( 'NP_065811.1') }; my @more_transcripts = @{$tr_adaptor->fetch_all_by_external_name( 'NP_0658__._')}; Description: Retrieves all transcripts which are associated with an external identifier such as a GO term, Swissprot identifer, etc. Usually there will only be a single transcript returned in the list reference, but not always. Transcripts are returned in their native coordinate system, i.e. the coordinate system in which they are stored in the database. If they are required in another coordinate system the Transcript::transfer or Transcript::transform method can be used to convert them. If no transcripts with the external identifier are found, a reference to an empty list is returned. SQL wildcards % and _ are supported in the $external_name but their use is somewhat restricted for performance reasons. Users that really do want % and _ in the first three characters should use argument 3 to prevent optimisations Returntype : listref of Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable =cut sub fetch_all_by_external_name { my ( $self, $external_name, $external_db_name, $override) = @_; my $entryAdaptor = $self->db->get_DBEntryAdaptor(); my @ids = $entryAdaptor->list_transcript_ids_by_extids( $external_name, $external_db_name, $override ); return $self->fetch_all_by_dbID_list( \@ids ); } =head2 fetch_all_by_GOTerm Arg [1] : Bio::EnsEMBL::OntologyTerm The GO term for which transcripts should be fetched. Example: @transcripts = @{ $transcript_adaptor->fetch_all_by_GOTerm( $go_adaptor->fetch_by_accession('GO:0030326') ) }; Description : Retrieves a list of transcripts that are associated with the given GO term, or with any of its descendent GO terms. The transcripts returned are in their native coordinate system, i.e. in the coordinate system in which they are stored in the database. If another coordinate system is required then the Transcript::transfer or Transcript::transform method can be used. Return type : listref of Bio::EnsEMBL::Transcript Exceptions : Throws of argument is not a GO term Caller : general Status : Stable =cut sub fetch_all_by_GOTerm { my ( $self, $term ) = @_; assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' ); if ( $term->ontology() ne 'GO' ) { throw('Argument is not a GO term'); } my $entryAdaptor = $self->db->get_DBEntryAdaptor(); my %unique_dbIDs; foreach my $accession ( map { $_->accession() } ( $term, @{ $term->descendants() } ) ) { my @ids = $entryAdaptor->list_transcript_ids_by_extids( $accession, 'GO' ); foreach my $dbID (@ids) { $unique_dbIDs{$dbID} = 1 } } my @result = @{ $self->fetch_all_by_dbID_list( [ sort { $a <=> $b } keys(%unique_dbIDs) ] ) }; return \@result; } ## end sub fetch_all_by_GOTerm =head2 fetch_all_by_GOTerm_accession Arg [1] : String The GO term accession for which genes should be fetched. Example : @genes = @{ $gene_adaptor->fetch_all_by_GOTerm_accession( 'GO:0030326') }; Description : Retrieves a list of genes that are associated with the given GO term, or with any of its descendent GO terms. The genes returned are in their native coordinate system, i.e. in the coordinate system in which they are stored in the database. If another coordinate system is required then the Gene::transfer or Gene::transform method can be used. Return type : listref of Bio::EnsEMBL::Gene Exceptions : Throws of argument is not a GO term accession Caller : general Status : Stable =cut sub fetch_all_by_GOTerm_accession { my ( $self, $accession ) = @_; if ( $accession !~ /^GO:/ ) { throw('Argument is not a GO term accession'); } my $goAdaptor = Bio::EnsEMBL::Registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' ); my $term = $goAdaptor->fetch_by_accession($accession); return $self->fetch_all_by_GOTerm($term); } =head2 fetch_by_display_label Arg [1] : String $label - display label of transcript to fetch Example : my $tr = $tr_adaptor->fetch_by_display_label("BRCA2"); Description: Returns the transcript which has the given display label or undef if there is none. If there are more than 1, only the first is reported. Returntype : Bio::EnsEMBL::Transcript Exceptions : none Caller : general Status : Stable =cut sub fetch_by_display_label { my $self = shift; my $label = shift; my $constraint = "x.display_label = ? AND t.is_current = 1"; $self->bind_param_generic_fetch($label,SQL_VARCHAR); my ($transcript) = @{ $self->generic_fetch($constraint) }; return $transcript; } =head2 fetch_all_by_exon_stable_id Arg [1] : String $stable_id The stable id of an exon in a transcript Example : my $tr = $tr_adaptor->fetch_all_by_exon_stable_id ('ENSE00000309301'); Description: Retrieves a list of transcripts via an exon stable id. Returntype : Listref of Bio::EnsEMBL::Transcript objects Exceptions : none Caller : general Status : Stable =cut sub fetch_all_by_exon_stable_id { my ($self, $stable_id) = @_; my @trans ; my $sth = $self->prepare(qq( SELECT t.transcript_id FROM exon_transcript et, exon e, transcript t WHERE e.exon_id = et.exon_id AND et.transcript_id = t.transcript_id AND e.stable_id = ? AND t.is_current = 1 )); $sth->bind_param(1, $stable_id, SQL_VARCHAR); $sth->execute(); while( my $id = $sth->fetchrow_array ) { my $transcript = $self->fetch_by_dbID($id); push(@trans, $transcript) if $transcript; } if (!@trans) { return undef; } return \@trans; } =head2 fetch_all_by_biotype Arg [1] : String $biotype listref of $biotypes The biotype of the gene to retrieve. You can also have a reference to a list of biotypes in the event of needing several. Example : $transcript = $transcript_adaptor->fetch_all_by_biotype('pseudogene'); $transcript = $transcript_adaptor->fetch_all_by_biotype(['protein_coding','ambiguous_orf']); Description: Retrieves an array reference of transcript objects from the database via its biotype or biotypes. The transcript will be retrieved in its native coordinate system (i.e. in the coordinate system it is stored in the database). It may be converted to a different coordinate system through a call to transform() or transfer(). If the transcript is not found undef is returned instead. Returntype : listref of Bio::EnsEMBL::Transcript Exceptions : if we cant get the transcript in given coord system Caller : general Status : Stable =cut sub fetch_all_by_biotype { my ($self, $biotype) = @_; if (!defined $biotype){ throw("Biotype or listref of biotypes expected"); } my $constraint; if (ref($biotype) eq 'ARRAY'){ $constraint = "t.biotype IN ("; foreach my $b (@{$biotype}){ $constraint .= "?,"; $self->bind_param_generic_fetch($b,SQL_VARCHAR); } chop($constraint); #remove last , from expression $constraint .= ") and t.is_current = 1"; } else{ $constraint = "t.biotype = ? and t.is_current = 1"; $self->bind_param_generic_fetch($biotype,SQL_VARCHAR); } my @transcripts = @{ $self->generic_fetch($constraint) }; return \@transcripts ; } =head2 store Arg [1] : Bio::EnsEMBL::Transcript $transcript The transcript to be written to the database Arg [2] : Int $gene_dbID The identifier of the gene that this transcript is associated with Arg [3] : DEPRECATED (optional) Int $analysis_id The analysis_id to use when storing this gene. This is for backward compatibility only and used to fall back to the gene analysis_id if no analysis object is attached to the transcript (which you should do for new code). Example : $transID = $tr_adaptor->store($transcript, $gene->dbID); Description: Stores a transcript in the database and returns the new internal identifier for the stored transcript. Returntype : Int Exceptions : none Caller : general Status : Stable =cut sub store { my ( $self, $transcript, $gene_dbID, $analysis_id ) = @_; if ( !ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript') ) { throw("$transcript is not a EnsEMBL transcript - not storing"); } my $db = $self->db(); if ( $transcript->is_stored($db) ) { return $transcript->dbID(); } # Force lazy-loading of exons and ensure coords are correct. $transcript->recalculate_coordinates(); my $is_current = ( defined( $transcript->is_current() ) ? $transcript->is_current() : 1 ); # store analysis my $analysis = $transcript->analysis(); my $new_analysis_id; if ($analysis) { if ( $analysis->is_stored($db) ) { $new_analysis_id = $analysis->dbID; } else { $new_analysis_id = $db->get_AnalysisAdaptor->store($analysis); } } elsif ($analysis_id) { # Fall back to analysis passed in (usually from gene) if analysis # wasn't set explicitely for the transcript. This is deprectated # though. warning( "You should explicitely attach " . "an analysis object to the Transcript. " . "Will fall back to Gene analysis, " . "but this behaviour is deprecated." ); $new_analysis_id = $analysis_id; } else { throw("Need an analysis_id to store the Transcript."); } # # Store exons - this needs to be done before the possible transfer # of the transcript to another slice (in _prestore()). Transfering # results in copies being made of the exons and we need to preserve # the object identity of the exons so that they are not stored twice # by different transcripts. # my $exons = $transcript->get_all_Exons(); my $exonAdaptor = $db->get_ExonAdaptor(); foreach my $exon ( @{$exons} ) { $exonAdaptor->store($exon); } my $original_translation = $transcript->translation(); my $original = $transcript; my $seq_region_id; ( $transcript, $seq_region_id ) = $self->_pre_store($transcript); # First store the transcript without a display xref. The display xref # needs to be set after xrefs are stored which needs to happen after # transcript is stored. # # Store transcript # my $store_transcript_sql = qq( INSERT INTO transcript SET gene_id = ?, analysis_id = ?, seq_region_id = ?, seq_region_start = ?, seq_region_end = ?, seq_region_strand = ?, biotype = ?, status = ?, description = ?, is_current = ?, canonical_translation_id = ? ); if ( defined( $transcript->stable_id() ) ) { my $created = $self->db->dbc->from_seconds_to_date($transcript->created_date()); my $modified = $self->db->dbc->from_seconds_to_date($transcript->modified_date()); $store_transcript_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified; } my $tst = $self->prepare($store_transcript_sql); $tst->bind_param( 1, $gene_dbID, SQL_INTEGER ); $tst->bind_param( 2, $new_analysis_id, SQL_INTEGER ); $tst->bind_param( 3, $seq_region_id, SQL_INTEGER ); $tst->bind_param( 4, $transcript->start(), SQL_INTEGER ); $tst->bind_param( 5, $transcript->end(), SQL_INTEGER ); $tst->bind_param( 6, $transcript->strand(), SQL_TINYINT ); $tst->bind_param( 7, $transcript->biotype(), SQL_VARCHAR ); $tst->bind_param( 8, $transcript->status(), SQL_VARCHAR ); $tst->bind_param( 9, $transcript->description(), SQL_LONGVARCHAR ); $tst->bind_param( 10, $is_current, SQL_TINYINT ); # If the transcript has a translation, this is updated later: $tst->bind_param( 11, undef, SQL_INTEGER ); if ( defined( $transcript->stable_id() ) ) { $tst->bind_param( 12, $transcript->stable_id(), SQL_VARCHAR ); my $version = ($transcript->version()) ? $transcript->version() : 1; $tst->bind_param( 13, $version, SQL_INTEGER ); } $tst->execute(); $tst->finish(); my $transc_dbID = $tst->{'mysql_insertid'}; # # Store translation # my $alt_translations = $transcript->get_all_alternative_translations(); my $translation = $transcript->translation(); if ( defined($translation) ) { # Make sure that the start and end exon are set correctly. my $start_exon = $translation->start_Exon(); my $end_exon = $translation->end_Exon(); if ( !defined($start_exon) ) { throw("Translation does not define a start exon."); } if ( !defined($end_exon) ) { throw("Translation does not defined an end exon."); } # If the dbID is not set, this means the exon must have been a # different object in memory than the the exons of the transcript. # Try to find the matching exon in all of the exons we just stored. if ( !defined( $start_exon->dbID() ) ) { my $key = $start_exon->hashkey(); ($start_exon) = grep { $_->hashkey() eq $key } @$exons; if ( defined($start_exon) ) { $translation->start_Exon($start_exon); } else { throw( "Translation's start_Exon does not appear " . "to be one of the exons in " . "its associated Transcript" ); } } if ( !defined( $end_exon->dbID() ) ) { my $key = $end_exon->hashkey(); ($end_exon) = grep { $_->hashkey() eq $key } @$exons; if ( defined($end_exon) ) { $translation->end_Exon($end_exon); } else { throw( "Translation's end_Exon does not appear " . "to be one of the exons in " . "its associated Transcript." ); } } my $old_dbid = $translation->dbID(); $db->get_TranslationAdaptor()->store( $translation, $transc_dbID ); # Need to update the canonical_translation_id for this transcript. my $sth = $self->prepare( q( UPDATE transcript SET canonical_translation_id = ? WHERE transcript_id = ?) ); $sth->bind_param( 1, $translation->dbID(), SQL_INTEGER ); $sth->bind_param( 2, $transc_dbID, SQL_INTEGER ); $sth->execute(); # Set values of the original translation, we may have copied it when # we transformed the transcript. $original_translation->dbID( $translation->dbID() ); $original_translation->adaptor( $translation->adaptor() ); } ## end if ( defined($translation...)) # # Store the alternative translations, if there are any. # if ( defined($alt_translations) && scalar( @{$alt_translations} ) > 0 ) { foreach my $alt_translation ( @{$alt_translations} ) { my $start_exon = $alt_translation->start_Exon(); my $end_exon = $alt_translation->end_Exon(); if ( !defined($start_exon) ) { throw("Translation does not define a start exon."); } elsif ( !defined($end_exon) ) { throw("Translation does not defined an end exon."); } if ( !defined( $start_exon->dbID() ) ) { my $key = $start_exon->hashkey(); ($start_exon) = grep { $_->hashkey() eq $key } @{$exons}; if ( defined($start_exon) ) { $alt_translation->start_Exon($start_exon); } else { throw( "Translation's start_Exon does not appear " . "to be one of the exon in" . "its associated Transcript" ); } } elsif ( !defined( $end_exon->dbID() ) ) { my $key = $end_exon->hashkey(); ($end_exon) = grep { $_->hashkey() eq $key } @$exons; if ( defined($end_exon) ) { $translation->end_Exon($end_exon); } else { throw( "Translation's end_Exon does not appear " . "to be one of the exons in " . "its associated Transcript." ); } } $db->get_TranslationAdaptor() ->store( $alt_translation, $transc_dbID ); } ## end foreach my $alt_translation... } ## end if ( defined($alt_translations...)) # # Store the xrefs/object xref mapping. # my $dbEntryAdaptor = $db->get_DBEntryAdaptor(); foreach my $dbe ( @{ $transcript->get_all_DBEntries() } ) { $dbEntryAdaptor->store( $dbe, $transc_dbID, "Transcript", 1 ); } # # Update transcript to point to display xref if it is set. # if ( my $dxref = $transcript->display_xref() ) { my $dxref_id; if ( $dxref->is_stored($db) ) { $dxref_id = $dxref->dbID(); } else { $dxref_id = $dbEntryAdaptor->exists($dxref); } if ( defined($dxref_id) ) { my $sth = $self->prepare( "UPDATE transcript " . "SET display_xref_id = ? " . "WHERE transcript_id = ?" ); $sth->bind_param( 1, $dxref_id, SQL_INTEGER ); $sth->bind_param( 2, $transc_dbID, SQL_INTEGER ); $sth->execute(); $dxref->dbID($dxref_id); $dxref->adaptor($dbEntryAdaptor); $sth->finish(); } else { warning(sprintf( "Display_xref %s:%s is not stored in database.\n" . "Not storing relationship to this transcript.", $dxref->dbname(), $dxref->display_id() ) ); $dxref->dbID(undef); $dxref->adaptor(undef); } } ## end if ( my $dxref = $transcript...) # # Link transcript to exons in exon_transcript table # my $etst = $self->prepare( "INSERT INTO exon_transcript (exon_id,transcript_id,rank) " . "VALUES (?,?,?)" ); my $rank = 1; foreach my $exon ( @{ $transcript->get_all_Exons } ) { $etst->bind_param( 1, $exon->dbID, SQL_INTEGER ); $etst->bind_param( 2, $transc_dbID, SQL_INTEGER ); $etst->bind_param( 3, $rank, SQL_INTEGER ); $etst->execute(); $rank++; } $etst->finish(); # Now the supporting evidence my $tsf_adaptor = $db->get_TranscriptSupportingFeatureAdaptor(); $tsf_adaptor->store( $transc_dbID, $transcript->get_all_supporting_features() ); # store transcript attributes if there are any my $attr_adaptor = $db->get_AttributeAdaptor(); $attr_adaptor->store_on_Transcript( $transc_dbID, $transcript->get_all_Attributes() ); # store the IntronSupportingEvidence features my $ise_adaptor = $db->get_IntronSupportingEvidenceAdaptor(); my $intron_supporting_evidence = $transcript->get_all_IntronSupportingEvidence(); foreach my $ise (@{$intron_supporting_evidence}) { $ise_adaptor->store($ise); $ise_adaptor->store_transcript_linkage($ise, $transcript, $transc_dbID); } # Update the original transcript object - not the transfered copy that # we might have created. $original->dbID($transc_dbID); $original->adaptor($self); return $transc_dbID; } ## end sub store =head2 get_Interpro_by_transid Arg [1] : String $trans_stable_id The stable if of the transcript to obtain Example : @i = $tr_adaptor->get_Interpro_by_transid($trans->stable_id()); Description: Gets interpro accession numbers by transcript stable id. A hack really - we should have a much more structured system than this. Returntype : listref of strings (Interpro_acc:description) Exceptions : none Caller : domainview? , GeneView Status : Stable =cut sub get_Interpro_by_transid { my ($self,$trans_stable_id) = @_; my $sth = $self->prepare(qq( SELECT STRAIGHT_JOIN i.interpro_ac, x.description FROM transcript t, translation tl, protein_feature pf, interpro i, xref x WHERE t.stable_id = ? AND tl.transcript_id = t.transcript_id AND tl.translation_id = pf.translation_id AND i.id = pf.hit_name AND i.interpro_ac = x.dbprimary_acc AND t.is_current = 1 )); $sth->bind_param(1, $trans_stable_id, SQL_VARCHAR); $sth->execute(); my @out; my %h; while( (my $arr = $sth->fetchrow_arrayref()) ) { if( $h{$arr->[0]} ) { next; } $h{$arr->[0]}=1; my $string = $arr->[0] .":".$arr->[1]; push(@out,$string); } return \@out; } =head2 is_Transcript_canonical() Arg [1] : Bio::EnsEMBL::Transcript $transcript The transcript to query with Example : $tr_adaptor->is_Transcript_canonical($transcript); Description : Returns a boolean if the given transcript is considered canonical with respect to a gene Returntype : Boolean Exceptions : None Caller : Bio::EnsEMBL::Transcript Status : Beta =cut sub is_Transcript_canonical { my ($self, $transcript) = @_; return $self->dbc()->sql_helper()->execute_single_result( -SQL => 'select count(*) from gene where canonical_transcript_id =?', -PARAMS => [$transcript->dbID()] ); } =head2 remove Arg [1] : Bio::EnsEMBL::Transcript $transcript The transcript to remove from the database Example : $tr_adaptor->remove($transcript); Description: Removes a transcript completely from the database, and all associated information. This method is usually called by the GeneAdaptor::remove method because this method will not preform the removal of genes which are associated with this transcript. Do not call this method directly unless you know there are no genes associated with the transcript! Returntype : none Exceptions : throw on incorrect arguments warning if transcript is not in this database Caller : GeneAdaptor::remove Status : Stable =cut sub remove { my $self = shift; my $transcript = shift; if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) { throw("Bio::EnsEMBL::Transcript argument expected"); } # sanity check: make sure nobody tries to slip past a prediction transcript # which inherits from transcript but actually uses different tables if($transcript->isa('Bio::EnsEMBL::PredictionTranscript')) { throw("TranscriptAdaptor can only remove Transcripts " . "not PredictionTranscripts"); } if ( !$transcript->is_stored($self->db()) ) { warning("Cannot remove transcript ". $transcript->dbID .". Is not stored ". "in this database."); return; } # remove the supporting features of this transcript my $prot_adp = $self->db->get_ProteinAlignFeatureAdaptor; my $dna_adp = $self->db->get_DnaAlignFeatureAdaptor; my $sfsth = $self->prepare("SELECT feature_type, feature_id " . "FROM transcript_supporting_feature " . "WHERE transcript_id = ?"); $sfsth->bind_param(1, $transcript->dbID, SQL_INTEGER); $sfsth->execute(); # statements to check for shared align_features my $sth1 = $self->prepare("SELECT count(*) FROM supporting_feature " . "WHERE feature_type = ? AND feature_id = ?"); my $sth2 = $self->prepare("SELECT count(*) " . "FROM transcript_supporting_feature " . "WHERE feature_type = ? AND feature_id = ?"); SUPPORTING_FEATURE: while(my ($type, $feature_id) = $sfsth->fetchrow()){ # only remove align_feature if this is the last reference to it $sth1->bind_param(1, $type, SQL_VARCHAR); $sth1->bind_param(2, $feature_id, SQL_INTEGER); $sth1->execute; $sth2->bind_param(1, $type, SQL_VARCHAR); $sth2->bind_param(2, $feature_id, SQL_INTEGER); $sth2->execute; my ($count1) = $sth1->fetchrow; my ($count2) = $sth2->fetchrow; if ($count1 + $count2 > 1) { #warn "transcript: shared feature, not removing $type|$feature_id\n"; next SUPPORTING_FEATURE; } #warn "transcript: removing $type|$feature_id\n"; if($type eq 'protein_align_feature'){ my $f = $prot_adp->fetch_by_dbID($feature_id); $prot_adp->remove($f); } elsif($type eq 'dna_align_feature'){ my $f = $dna_adp->fetch_by_dbID($feature_id); $dna_adp->remove($f); } else { warning("Unknown supporting feature type $type. Not removing feature."); } } $sfsth->finish(); $sth1->finish(); $sth2->finish(); # delete the association to supporting features $sfsth = $self->prepare("DELETE FROM transcript_supporting_feature WHERE transcript_id = ?"); $sfsth->bind_param(1, $transcript->dbID, SQL_INTEGER); $sfsth->execute(); $sfsth->finish(); # delete the associated IntronSupportingEvidence and if the ISE had no more # linked transcripts remove it my $ise_adaptor = $self->db->get_IntronSupportingEvidenceAdaptor(); foreach my $ise (@{$transcript->get_all_IntronSupportingEvidence()}) { $ise_adaptor->remove_transcript_linkage($ise, $transcript); if(! $ise->has_linked_transcripts()) { $ise_adaptor->remove($ise); } } # remove all xref linkages to this transcript my $dbeAdaptor = $self->db->get_DBEntryAdaptor(); foreach my $dbe (@{$transcript->get_all_DBEntries}) { $dbeAdaptor->remove_from_object($dbe, $transcript, 'Transcript'); } # remove the attributes associated with this transcript my $attrib_adp = $self->db->get_AttributeAdaptor; $attrib_adp->remove_from_Transcript($transcript); # remove the translation associated with this transcript my $translationAdaptor = $self->db->get_TranslationAdaptor(); if( defined($transcript->translation()) ) { $translationAdaptor->remove( $transcript->translation ); } # remove exon associations to this transcript my $exonAdaptor = $self->db->get_ExonAdaptor(); foreach my $exon ( @{$transcript->get_all_Exons()} ) { # get the number of transcript references to this exon # only remove the exon if this is the last transcript to # reference it my $sth = $self->prepare( "SELECT count(*) FROM exon_transcript WHERE exon_id = ?" ); $sth->bind_param(1, $exon->dbID, SQL_INTEGER); $sth->execute(); my ($count) = $sth->fetchrow_array(); $sth->finish(); if($count == 1){ $exonAdaptor->remove( $exon ); } } my $sth = $self->prepare( "DELETE FROM exon_transcript WHERE transcript_id = ?" ); $sth->bind_param(1, $transcript->dbID, SQL_INTEGER); $sth->execute(); $sth->finish(); $sth = $self->prepare( "DELETE FROM transcript WHERE transcript_id = ?" ); $sth->bind_param(1, $transcript->dbID, SQL_INTEGER); $sth->execute(); $sth->finish(); $transcript->dbID(undef); $transcript->adaptor(undef); return; } =head2 update Arg [1] : Bio::EnsEMBL::Transcript $transcript The transcript to update Example : $tr_adaptor->update($transcript); Description: Updates a transcript in the database. Returntype : None Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript. warn if the method is called on a transcript that does not exist in the database. Should warn if trying to update the number of attached exons, but this is a far more complex process and is not yet implemented. Caller : general Status : Stable =cut sub update { my ( $self, $transcript ) = @_; if ( !defined($transcript) || !ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript') ) { throw("Must update a transcript object, not a $transcript"); } my $update_transcript_sql = qq( UPDATE transcript SET analysis_id = ?, display_xref_id = ?, description = ?, biotype = ?, status = ?, is_current = ?, canonical_translation_id = ? WHERE transcript_id = ? ); my $display_xref = $transcript->display_xref(); my $display_xref_id; if ( defined($display_xref) && $display_xref->dbID() ) { $display_xref_id = $display_xref->dbID(); } else { $display_xref_id = undef; } my $sth = $self->prepare($update_transcript_sql); $sth->bind_param( 1, $transcript->analysis()->dbID(), SQL_INTEGER ); $sth->bind_param( 2, $display_xref_id, SQL_INTEGER ); $sth->bind_param( 3, $transcript->description(), SQL_LONGVARCHAR ); $sth->bind_param( 4, $transcript->biotype(), SQL_VARCHAR ); $sth->bind_param( 5, $transcript->status(), SQL_VARCHAR ); $sth->bind_param( 6, $transcript->is_current(), SQL_TINYINT ); $sth->bind_param( 7, ( defined( $transcript->translation() ) ? $transcript->translation()->dbID() : undef ), SQL_INTEGER ); $sth->bind_param( 8, $transcript->dbID(), SQL_INTEGER ); $sth->execute(); } ## end sub update =head2 list_dbIDs Example : @transcript_ids = @{ $t_adaptor->list_dbIDs }; Description: Gets a list of internal ids for all transcripts in the db. Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region. Returntype : Listref of Ints Exceptions : none Caller : general Status : Stable =cut sub list_dbIDs { my ($self, $ordered) = @_; return $self->_list_dbIDs("transcript",undef, $ordered); } =head2 list_stable_ids Example : @stable_trans_ids = @{ $transcript_adaptor->list_stable_ids }; Description: Gets a list of stable ids for all transcripts in the current database. Returntype : Listref of Strings Exceptions : none Caller : general Status : Stable =cut sub list_stable_ids { my ($self) = @_; return $self->_list_dbIDs("transcript", "stable_id"); } #_objs_from_sth # Arg [1] : StatementHandle $sth # Arg [2] : Bio::EnsEMBL::AssemblyMapper $mapper # Arg [3] : Bio::EnsEMBL::Slice $dest_slice # Description: PROTECTED implementation of abstract superclass method. # Responsible for the creation of Transcripts. # Returntype : Listref of Bio::EnsEMBL::Transcripts in target coord system # Exceptions : none # Caller : internal # Status : Stable sub _objs_from_sth { my ($self, $sth, $mapper, $dest_slice) = @_; # # This code is ugly because an attempt has been made to remove as many # function calls as possible for speed purposes. Thus many caches and # a fair bit of gymnastics is used. # my $sa = $self->db()->get_SliceAdaptor(); my $aa = $self->db->get_AnalysisAdaptor(); my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor(); my @transcripts; my %analysis_hash; my %slice_hash; my %sr_name_hash; my %sr_cs_hash; my ( $transcript_id, $seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $analysis_id, $gene_id, $is_current, $stable_id, $version, $created_date, $modified_date, $description, $biotype, $status, $external_db, $external_status, $external_db_name, $xref_id, $xref_display_label, $xref_primary_acc, $xref_version, $xref_description, $xref_info_type, $xref_info_text ); $sth->bind_columns( \( $transcript_id, $seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $analysis_id, $gene_id, $is_current, $stable_id, $version, $created_date, $modified_date, $description, $biotype, $status, $external_db, $external_status, $external_db_name, $xref_id, $xref_display_label, $xref_primary_acc, $xref_version, $xref_description, $xref_info_type, $xref_info_text ) ); my $asm_cs; my $cmp_cs; my $asm_cs_vers; my $asm_cs_name; my $cmp_cs_vers; my $cmp_cs_name; if($mapper) { $asm_cs = $mapper->assembled_CoordSystem(); $cmp_cs = $mapper->component_CoordSystem(); $asm_cs_name = $asm_cs->name(); $asm_cs_vers = $asm_cs->version(); $cmp_cs_name = $cmp_cs->name(); $cmp_cs_vers = $cmp_cs->version(); } my $dest_slice_start; my $dest_slice_end; my $dest_slice_strand; my $dest_slice_length; my $dest_slice_cs; my $dest_slice_sr_name; my $dest_slice_sr_id; my $asma; if($dest_slice) { $dest_slice_start = $dest_slice->start(); $dest_slice_end = $dest_slice->end(); $dest_slice_strand = $dest_slice->strand(); $dest_slice_length = $dest_slice->length(); $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()) { #get the analysis object my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id); #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} = $slice->coord_system(); } #obtain a mapper if none was defined, but a dest_seq_region was if(!$dest_mapper && $dest_slice && !$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($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, $sr_cs ); } #skip features that map to gaps or coord system boundaries next FEATURE if(!defined($seq_region_id)); #get a slice in the coord system we just mapped to if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) { $slice = $slice_hash{"ID:".$seq_region_id} ||= $sa->fetch_by_seq_region_id($seq_region_id); } else { $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 (defined($dest_slice)) { 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; if ( $dest_slice->is_circular ) { if ( $seq_region_start > $seq_region_end ) { # Looking at a feature overlapping the chromsome origin. if ( $seq_region_end > $dest_slice_start ) { # Looking at the region in the beginning of the chromosome $seq_region_start -= $dest_slice->seq_region_length(); } if ( $seq_region_end < 0 ) { $seq_region_end += $dest_slice->seq_region_length(); } } else { if ( $dest_slice_start > $dest_slice_end && $seq_region_end < 0 ) { # Looking at the region overlapping the chromosome # origin and a feature which is at the beginning of the # chromosome. $seq_region_start += $dest_slice->seq_region_length(); $seq_region_end += $dest_slice->seq_region_length(); } } } } else { if ( $dest_slice->is_circular() && $seq_region_start > $seq_region_end ) { if ( $seq_region_end > $dest_slice_start ) { # Looking at the region in the beginning of the chromosome. $seq_region_start = $dest_slice_end - $seq_region_end + 1; $seq_region_end = $seq_region_end - $dest_slice->seq_region_length() - $dest_slice_start + 1; } else { my $tmp_seq_region_start = $seq_region_start; $seq_region_start = $dest_slice_end - $seq_region_end - $dest_slice->seq_region_length() + 1; $seq_region_end = $dest_slice_end - $tmp_seq_region_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; } ## end else [ if ( $dest_slice_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 ne $seq_region_id ) ) { next FEATURE; } $slice = $dest_slice; } my $display_xref; if ($xref_id) { $display_xref = Bio::EnsEMBL::DBEntry->new_fast( { 'dbID' => $xref_id, 'display_id' => $xref_display_label, 'primary_id' => $xref_primary_acc, 'version' => $xref_version, 'description' => $xref_description, 'info_type' => $xref_info_type, 'info_text' => $xref_info_text, 'adaptor' => $dbEntryAdaptor, 'db_display_name' => $external_db_name, 'dbname' => $external_db } ); } # Finally, create the new Transcript. push( @transcripts, $self->_create_feature_fast( 'Bio::EnsEMBL::Transcript', { 'analysis' => $analysis, 'start' => $seq_region_start, 'end' => $seq_region_end, 'strand' => $seq_region_strand, 'adaptor' => $self, 'slice' => $slice, 'dbID' => $transcript_id, 'stable_id' => $stable_id, 'version' => $version, 'created_date' => $created_date || undef, 'modified_date' => $modified_date || undef, 'external_name' => $xref_display_label, 'external_db' => $external_db, 'external_status' => $external_status, 'external_display_name' => $external_db_name, 'display_xref' => $display_xref, 'description' => $description, 'biotype' => $biotype, 'status' => $status, 'is_current' => $is_current, 'edits_enabled' => 1 } ) ); } return \@transcripts; } =head2 fetch_all_by_exon_supporting_evidence Arg [1] : String $hit_name Name of supporting feature Arg [2] : String $feature_type one of "dna_align_feature" or "protein_align_feature" Arg [3] : (optional) Bio::Ensembl::Analysis Example : $tr = $tr_adaptor->fetch_all_by_exon_supporting_evidence ('XYZ', 'dna_align_feature'); Description: Gets all the transcripts with exons which have a specified hit on a particular type of feature. Optionally filter by analysis. Returntype : Listref of Bio::EnsEMBL::Transcript objects Exceptions : If feature_type is not of correct type. Caller : general Status : Stable =cut sub fetch_all_by_exon_supporting_evidence { my ($self, $hit_name, $feature_type, $analysis) = @_; if($feature_type !~ /(dna)|(protein)_align_feature/) { throw("feature type must be dna_align_feature or protein_align_feature"); } my $anal_from = ""; $anal_from = ", analysis a " if ($analysis); my $anal_where = ""; $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis); my $sql = qq( SELECT DISTINCT(t.transcript_id) FROM transcript t, exon_transcript et, supporting_feature sf, $feature_type f $anal_from WHERE t.transcript_id = et.transcript_id AND t.is_current = 1 AND et.exon_id = sf.exon_id AND sf.feature_id = f.${feature_type}_id AND sf.feature_type = ? AND f.hit_name=? $anal_where ); my $sth = $self->prepare($sql); $sth->bind_param(1, $feature_type, SQL_VARCHAR); $sth->bind_param(2, $hit_name, SQL_VARCHAR); $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis); $sth->execute(); my @transcripts; while( my $id = $sth->fetchrow_array ) { my $transcript = $self->fetch_by_dbID( $id ); push(@transcripts, $transcript) if $transcript; } return \@transcripts; } =head2 fetch_all_by_transcript_supporting_evidence Arg [1] : String $hit_name Name of supporting feature Arg [2] : String $feature_type one of "dna_align_feature" or "protein_align_feature" Arg [3] : (optional) Bio::Ensembl::Analysis Example : $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence('XYZ', 'dna_align_feature'); Description: Gets all the transcripts with evidence from a specified hit_name on a particular type of feature, stored in the transcript_supporting_feature table. Optionally filter by analysis. For hits stored in the supporting_feature table (linked to exons) use fetch_all_by_exon_supporting_evidence instead. Returntype : Listref of Bio::EnsEMBL::Transcript objects Exceptions : If feature_type is not of correct type. Caller : general Status : Stable =cut sub fetch_all_by_transcript_supporting_evidence { my ($self, $hit_name, $feature_type, $analysis) = @_; if($feature_type !~ /(dna)|(protein)_align_feature/) { throw("feature type must be dna_align_feature or protein_align_feature"); } my $anal_from = ""; $anal_from = ", analysis a " if ($analysis); my $anal_where = ""; $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis); my $sql = qq( SELECT DISTINCT(t.transcript_id) FROM transcript t, transcript_supporting_feature sf, $feature_type f $anal_from WHERE t.transcript_id = sf.transcript_id AND t.is_current = 1 AND sf.feature_id = f.${feature_type}_id AND sf.feature_type = ? AND f.hit_name=? $anal_where ); my $sth = $self->prepare($sql); $sth->bind_param(1, $feature_type, SQL_VARCHAR); $sth->bind_param(2, $hit_name, SQL_VARCHAR); $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis); $sth->execute(); my @transcripts; while( my $id = $sth->fetchrow_array ) { my $transcript = $self->fetch_by_dbID( $id ); push(@transcripts, $transcript) if $transcript; } return \@transcripts; } ########################## # # # DEPRECATED METHODS # # # ########################## =head2 get_display_xref Description: DEPRECATED. Use $transcript->display_xref() instead. =cut sub get_display_xref { my ($self, $transcript) = @_; deprecate("display_xref should be retreived from Transcript object directly."); if ( !defined $transcript ) { throw("Must call with a Transcript object"); } my $sth = $self->prepare(qq( SELECT e.db_name, x.display_label, e.db_external_name, x.xref_id FROM transcript t, xref x, external_db e WHERE t.transcript_id = ? AND t.display_xref_id = x.xref_id AND x.external_db_id = e.external_db_id )); $sth->bind_param(1, $transcript->dbID, SQL_INTEGER); $sth->execute(); my ($db_name, $display_label, $xref_id, $display_db_name ) = $sth->fetchrow_array(); if ( !defined $xref_id ) { return undef; } my $db_entry = Bio::EnsEMBL::DBEntry->new( -dbid => $xref_id, -adaptor => $self->db->get_DBEntryAdaptor(), -dbname => $db_name, -display_id => $display_label -db_display_name => $display_db_name ); return $db_entry; } =head2 get_stable_entry_info Description: DEPRECATED. Use $transcript->stable_id() instead. =cut sub get_stable_entry_info { my ($self, $transcript) = @_; deprecate("Stable ids should be loaded directly now"); unless ( defined $transcript && ref $transcript && $transcript->isa('Bio::EnsEMBL::Transcript') ) { throw("Needs a Transcript object, not a $transcript"); } my $sth = $self->prepare(qq( SELECT stable_id, version FROM transcript WHERE transcript_id = ? )); $sth->bind_param(1, $transcript->dbID, SQL_INTEGER); $sth->execute(); my @array = $sth->fetchrow_array(); $transcript->{'_stable_id'} = $array[0]; $transcript->{'_version'} = $array[1]; return 1; } =head2 fetch_all_by_DBEntry Description: DEPRECATED. Use fetch_all_by_external_name() instead. =cut sub fetch_all_by_DBEntry { my $self = shift; deprecate('Use fetch_all_by_external_name instead.'); return $self->fetch_all_by_external_name(@_); } 1;