Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
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| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,406 @@ +=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::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") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) { + 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) { + + if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) { + ( $seq_region_id, $seq_region_start, + $seq_region_end, $seq_region_strand ) + = + $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 ) + = + $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;