Raw content of Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor =head1 LICENSE Copyright (c) 1999-2009 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 /info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at <ensembl-dev@ebi.ac.uk>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. =cut =head1 NAME Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor - Adaptor for ProteinAlignFeatures =head1 SYNOPSIS $pafa = $registry->get_adaptor( 'Human', 'Core', 'ProteinAlignFeature' ); my @features = @{ $pafa->fetch_all_by_Slice($slice) }; $pafa->store(@features); =head1 METHODS =cut package Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor; use vars qw(@ISA); use strict; use Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor; use Bio::EnsEMBL::DnaPepAlignFeature; use Bio::EnsEMBL::Utils::Exception qw(throw warning); @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor); =head2 store Arg [1] : list of Bio::EnsEMBL::DnaPepAlignFeature @feats Example : $protein_align_feature_adaptor->store(@feats); Description: stores a list of ProteinAlignFeatures in the database Returntype : none Exceptions : throw if any of the provided features cannot be stored which may occur if: * The feature does not have an associated Slice * The feature does not have an associated analysis * The Slice the feature is associated with is on a seq_region unknown to this database A warning is given if: * The feature has already been stored in this db Caller : Pipeline Status : Stable =cut sub store{ my ($self, @feats) = @_; throw("Must call store with features") if( scalar(@feats) == 0 ); my @tabs = $self->_tables; my ($tablename) = @{$tabs[0]}; my $db = $self->db(); my $slice_adaptor = $db->get_SliceAdaptor(); my $analysis_adaptor = $db->get_AnalysisAdaptor(); my $sth = $self->prepare( "INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_start, hit_end, hit_name, cigar_line, analysis_id, score, evalue, perc_ident, external_db_id, hcoverage) VALUES (?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?)"); FEATURE: foreach my $feat ( @feats ) { if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaPepAlignFeature") ) { throw("feature must be a Bio::EnsEMBL::DnaPepAlignFeature," . " not a [".ref($feat)."]."); } if($feat->is_stored($db)) { warning("PepDnaAlignFeature [".$feat->dbID."] is already stored" . " in this database."); next FEATURE; } #sanity check the hstart and hend my $hstart = $feat->hstart(); my $hend = $feat->hend(); $self->_check_start_end_strand($hstart,$hend,1); my $cigar_string = $feat->cigar_string(); if(!$cigar_string) { $cigar_string = $feat->length() . 'M'; warning("DnaPepAlignFeature does not define a cigar_string.\n" . "Assuming ungapped block with cigar_string=$cigar_string\n"); } my $hseqname = $feat->hseqname(); if(!$hseqname) { throw("DnaPepAlignFeature must define an hseqname."); } if(!defined($feat->analysis)) { throw("An analysis must be attached to the features to be stored."); } #store the analysis if it has not been stored yet if(!$feat->analysis->is_stored($db)) { $analysis_adaptor->store($feat->analysis()); } my $slice = $feat->slice(); if(!defined($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) { throw("A slice must be attached to the features to be stored."); } my $original = $feat; my $seq_region_id; ($feat, $seq_region_id) = $self->_pre_store($feat); $sth->bind_param(1,$seq_region_id,SQL_INTEGER); $sth->bind_param(2,$feat->start,SQL_INTEGER); $sth->bind_param(3,$feat->end,SQL_INTEGER); $sth->bind_param(4,$feat->strand,SQL_TINYINT); $sth->bind_param(5,$feat->hstart,SQL_INTEGER); $sth->bind_param(6,$feat->hend,SQL_INTEGER); $sth->bind_param(7,$feat->hseqname,SQL_VARCHAR); $sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR); $sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER); $sth->bind_param(10,$feat->score,SQL_DOUBLE); $sth->bind_param(11,$feat->p_value,SQL_DOUBLE); $sth->bind_param(12,$feat->percent_id,SQL_REAL); $sth->bind_param(13,$feat->external_db_id,SQL_INTEGER); $sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE); $sth->execute(); $original->dbID($sth->{'mysql_insertid'}); $original->adaptor($self); } $sth->finish(); } =head2 _objs_from_sth Arg [1] : DBI statement handle $sth an exectuted DBI statement handle generated by selecting the columns specified by _columns() from the table specified by _table() Example : @dna_dna_align_feats = $self->_obj_from_hashref Description: PROTECTED implementation of superclass abstract method. Creates DnaDnaAlignFeature objects from a DBI hashref Returntype : listref of Bio::EnsEMBL::ProteinAlignFeatures Exceptions : none Caller : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch Status : Stable =cut sub _objs_from_sth { my ($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 = $self->db->get_AnalysisAdaptor(); my @features; my %analysis_hash; my %slice_hash; my %sr_name_hash; my %sr_cs_hash; my ($protein_align_feature_id, $seq_region_id, $seq_region_start, $seq_region_end, $analysis_id, $seq_region_strand, $hit_start, $hit_end, $hit_name, $cigar_line, $evalue, $perc_ident, $score, $external_db_id, $hcoverage, $external_db_name, $external_display_db_name ); $sth->bind_columns(\$protein_align_feature_id, \$seq_region_id, \$seq_region_start,\$seq_region_end, \$analysis_id, \$seq_region_strand, \$hit_start,\$hit_end, \$hit_name, \$cigar_line, \$evalue, \$perc_ident, \$score, \$external_db_id, \$hcoverage, \$external_db_name, \$external_display_db_name ); 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_sr_name; my $dest_slice_sr_id; if($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_sr_name = $dest_slice->seq_region_name(); $dest_slice_sr_id = $dest_slice->get_seq_region_id(); } FEATURE: while($sth->fetch()) { #get the analysis object my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id); #get the slice object my $slice = $slice_hash{"ID:".$seq_region_id}; 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(); } 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($mapper) { ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) = $mapper->fastmap($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} ||= # $sa->fetch_by_seq_region_id($asm_cs_name, $sr_name, undef, undef, undef, # $asm_cs_vers); # } } # # If a destination slice was provided convert the coords # If the dest_slice starts at 1 and is foward strand, nothing needs doing # if($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; $seq_region_strand *= -1; } } #throw away features off the end of the requested slice if($seq_region_end < 1 || $seq_region_start > $dest_slice_length || ( $dest_slice_sr_id ne $seq_region_id )) { next FEATURE; } $slice = $dest_slice; } # Finally, create the new ProteinAlignFeature. push( @features, $self->_create_feature_fast( 'Bio::EnsEMBL::DnaPepAlignFeature', { 'slice' => $slice, 'start' => $seq_region_start, 'end' => $seq_region_end, 'strand' => $seq_region_strand, 'hseqname' => $hit_name, 'hstart' => $hit_start, 'hend' => $hit_end, 'hstrand' => 1, # dna_pep_align features # are always hstrand 1 'score' => $score, 'p_value' => $evalue, 'percent_id' => $perc_ident, 'cigar_string' => $cigar_line, 'analysis' => $analysis, 'adaptor' => $self, 'dbID' => $protein_align_feature_id, 'external_db_id' => $external_db_id, 'hcoverage' => $hcoverage, 'dbname' => $external_db_name, 'db_display_name' => $external_display_db_name } ) ); } return \@features; } sub _tables { my $self = shift; return (['protein_align_feature', 'paf'], ['external_db','exdb']); } sub _columns { my $self = shift; #warning _objs_from_hashref method depends on ordering of this list return qw( paf.protein_align_feature_id paf.seq_region_id paf.seq_region_start paf.seq_region_end paf.analysis_id paf.seq_region_strand paf.hit_start paf.hit_end paf.hit_name paf.cigar_line paf.evalue paf.perc_ident paf.score paf.external_db_id paf.hcoverage exdb.db_name exdb.db_display_name); } sub _left_join{ return (['external_db',"exdb.external_db_id = paf.external_db_id"]); } =head2 list_dbIDs Arg [1] : none Example : @feature_ids = @{$protein_align_feature_adaptor->list_dbIDs()}; Description: Gets an array of internal ids for all protein align features 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 : ? Status : Stable =cut sub list_dbIDs { my ($self,$ordered) = @_; return $self->_list_dbIDs("protein_align_feature", undef, $ordered); } 1;