Bio::EnsEMBL::DBSQL DnaAlignFeatureAdaptor
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvsRaw content
Summary
Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor - Adaptor for DnaAlignFeatures
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor
Bio::EnsEMBL::DnaDnaAlignFeature
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Data::Dumper
Inherit
Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor
Synopsis
  $dafa = $registry->get_adaptor( 'Human', 'Core', 'DnaAlignFeature' );
my @features = @{ $dafa->fetch_all_by_Slice($slice) }; $dafa->store(@features);
Description
This is an adaptor responsible for the retrieval and storage of
DnaDnaAlignFeatures from the database. This adaptor inherits most of its
functionality from the BaseAlignFeatureAdaptor and BaseFeatureAdaptor
superclasses.
Methods
_columnsDescriptionCode
_left_join
No description
Code
_objs_from_sthDescriptionCode
_tablesDescriptionCode
list_dbIDsDescriptionCode
save
No description
Code
storeDescriptionCode
Methods description
_columnscode    nextTop
  Args       : none
Example : @columns = $self->_columns
Description: PROTECTED implementation of abstract superclass method.
Returns a list of columns that are needed for object creation.
Returntype : list of strings
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
Status : Stable
_objs_from_sthcodeprevnextTop
  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::DnaDnaAlignFeatures
Exceptions : none
Caller : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
Status : Stable
_tablescodeprevnextTop
  Args       : none
Example : @tabs = $self->_tables
Description: PROTECTED implementation of the abstract method inherited from
BaseFeatureAdaptor. Returns list of [tablename, alias] pairs
Returntype : list of listrefs of strings
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
Status : Stable
list_dbIDscodeprevnextTop
  Arg [1]    : none
Example : @feature_ids = @{$dna_align_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all dna align features in
the current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller : ?
Status : Stable
storecodeprevnextTop
  Arg [1]    : list of Bio::EnsEMBL::DnaAlignFeatures @feats
the features to store in the database
Example : $dna_align_feature_adaptor->store(@features);
Description: Stores a list of DnaAlignFeatures 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 associate 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
Methods code
_columnsdescriptionprevnextTop
sub _columns {
  my $self = shift;

  #warning, implementation of _objs_from_sth method depends on order of list
return qw(daf.dna_align_feature_id daf.seq_region_id daf.analysis_id daf.seq_region_start daf.seq_region_end daf.seq_region_strand daf.hit_start daf.hit_end daf.hit_name daf.hit_strand daf.cigar_line daf.evalue daf.perc_ident daf.score daf.external_db_id daf.hcoverage daf.external_data daf.pair_dna_align_feature_id exdb.db_name exdb.db_display_name);
}
_left_joindescriptionprevnextTop
sub _left_join {
    return (['external_db',"exdb.external_db_id = daf.external_db_id"]);
}
_objs_from_sthdescriptionprevnextTop
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.
#
# in case of userdata we need the features on the dest_slice
# in case of get_all_supporting_features dest_slice is not provided ..
my $sa = $dest_slice ? $dest_slice->adaptor() : $self->db()->get_SliceAdaptor(); my $aa = $self->db->get_AnalysisAdaptor(); my @features; my %analysis_hash; my %slice_hash; my %sr_name_hash; my %sr_cs_hash; my($dna_align_feature_id, $seq_region_id, $analysis_id, $seq_region_start, $seq_region_end, $seq_region_strand, $hit_start, $hit_end, $hit_name, $hit_strand, $cigar_line, $evalue, $perc_ident, $score, $external_db_id, $hcoverage, $extra_data, $pair_dna_align_feature_id, $external_db_name, $external_display_db_name); $sth->bind_columns(\$ dna_align_feature_id,\$ seq_region_id,\$ analysis_id,\$ seq_region_start,\$ seq_region_end,\$ seq_region_strand,\$ hit_start,\$ hit_end,\$ hit_name,\$ hit_strand,\$ cigar_line,\$ evalue,\$ perc_ident,\$ score,\$ external_db_id,\$ hcoverage,\$ extra_data,\$ pair_dna_align_feature_id,\$ 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 $dest_slice_seq_region_id; if($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_seq_region_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} ||= $sa->fetch_by_seq_region_id($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($dest_slice) { if($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_seq_region_id ne $seq_region_id )) { next FEATURE; } } $slice = $dest_slice; } # Finally, create the new DnaAlignFeature.
push( @features, $self->_create_feature_fast( 'Bio::EnsEMBL::DnaDnaAlignFeature', { 'slice' => $slice, 'start' => $seq_region_start, 'end' => $seq_region_end, 'strand' => $seq_region_strand, 'hseqname' => $hit_name, 'hstart' => $hit_start, 'hend' => $hit_end, 'hstrand' => $hit_strand, 'score' => $score, 'p_value' => $evalue, 'percent_id' => $perc_ident, 'cigar_string' => $cigar_line, 'analysis' => $analysis, 'adaptor' => $self, 'dbID' => $dna_align_feature_id, 'external_db_id' => $external_db_id, 'hcoverage' => $hcoverage, 'extra_data' => $extra_data ? $self->get_dumped_data($extra_data) : '', 'dbname' => $external_db_name, 'db_display_name' => $external_display_db_name, 'pair_dna_align_feature_id' => $pair_dna_align_feature_id } ) ); } return\@ features;
}
_tablesdescriptionprevnextTop
sub _tables {
  my $self = shift;

  return (['dna_align_feature', 'daf'],['external_db','exdb']);
}
list_dbIDsdescriptionprevnextTop
sub list_dbIDs {
   my ($self, $ordered) = @_;

   return $self->_list_dbIDs("dna_align_feature",undef, $ordered);
}

1;
}
savedescriptionprevnextTop
sub save {
  my ($self, $features) = @_;

  my @feats = @$features;
  throw("Must call store with features") if( scalar(@feats) == 0 );

  my @tabs = $self->_tables;
  my ($tablename) = @{$tabs[0]};

  my $db = $self->db();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();

  my $sql = qq{INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_start, hit_end, hit_strand, hit_name, cigar_line, analysis_id, score, evalue, perc_ident, external_db_id, hcoverage, pair_dna_align_feature_id, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};

  my %analyses = ();

  my $sth = $self->prepare($sql);
     
 FEATURE: foreach my $feat ( @feats ) {
    if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
      throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature,"
            . " not a [".ref($feat)."].");
    }

    if($feat->is_stored($db)) {
      warning("DnaDnaAlignFeature [".$feat->dbID."] is already stored" .
              " in this database.");
      next FEATURE;
    }

    my $hstart  = $feat->hstart || 0; # defined $feat->hstart  ? $feat->hstart : $feat->start ;
my $hend = $feat->hend || 0; # defined $feat->hend ? $feat->hend : $feat->end;
my $hstrand = $feat->hstrand|| 0; # defined $feat->hstrand ? $feat->hstrand : $feat->strand;
if( $hstart && $hend ) { if($hend < $hstart) { throw("Invalid Feature start/end [$hstart/$hend]. Start must be less than or equal to end."); } } my $cigar_string = $feat->cigar_string(); if(!$cigar_string) { $cigar_string = $feat->length() . 'M'; warning("DnaDnaAlignFeature does not define a cigar_string.\n" . "Assuming ungapped block with cigar_line=$cigar_string ."); } my $hseqname = $feat->hseqname(); if(!$hseqname) { throw("DnaDnaAlignFeature 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()); } $analyses{ $feat->analysis->dbID }++; my $original = $feat; my $seq_region_id; ($feat, $seq_region_id) = $self->_pre_store_userdata($feat); my $extra_data = $feat->extra_data ? $self->dump_data($feat->extra_data) : ''; $sth->bind_param(1,$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); $sth->bind_param(5,$hstart,SQL_INTEGER); $sth->bind_param(6,$hend,SQL_INTEGER); $sth->bind_param(7,$hstrand,SQL_TINYINT); $sth->bind_param(8,$hseqname,SQL_VARCHAR); $sth->bind_param(9,$cigar_string,SQL_LONGVARCHAR); $sth->bind_param(10,$feat->analysis->dbID,SQL_INTEGER); $sth->bind_param(11,$feat->score,SQL_DOUBLE); # $sth->bind_param(11,$feat->score); # if the above statement does not work it means you need to upgrade DBD::mysql, meantime you can replace it with this line
$sth->bind_param(12,$feat->p_value,SQL_DOUBLE); $sth->bind_param(13,$feat->percent_id,SQL_FLOAT); $sth->bind_param(14,$feat->external_db_id,SQL_INTEGER); $sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE); $sth->bind_param(16,$feat->pair_dna_align_feature_id,SQL_INTEGER); $sth->bind_param(17,$extra_data,SQL_LONGVARCHAR); $sth->execute(); $original->dbID($sth->{'mysql_insertid'}); $original->adaptor($self); } $sth->finish(); ## js5 hack to update meta_coord table...
if( keys %analyses ) { my $sth = $self->prepare( 'select sr.coord_system_id, max(daf.seq_region_end-daf.seq_region_start) from seq_region as sr, dna_align_feature as daf where daf.seq_region_id=sr.seq_region_id and analysis_id in ('.join(',',keys %analyses).') group by coord_system_id' ); $sth->execute; foreach( @{ $sth->fetchall_arrayref } ) { my $sth2 = $self->prepare( qq(insert ignore into meta_coord values("dna_align_feature",$_->[0],$_->[1])) ); $sth2->execute; $sth2->finish; $sth2 = $self->prepare( qq(update meta_coord set max_length = $_->[1] where coord_system_id = $_->[0] and table_name="dna_align_feature" and max_length < $_->[1]) ); $sth2->execute; $sth2->finish; } $sth->finish; }
}
storedescriptionprevnextTop
sub store {
  my ($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 $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_strand, hit_name, cigar_line,
                             analysis_id, score, evalue, perc_ident, external_db_id, 
                             hcoverage, pair_dna_align_feature_id)
     VALUES (?,?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?, ?)");

 FEATURE: foreach my $feat ( @feats ) {
    if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
      throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature,"
            . " not a [".ref($feat)."].");
    }

    if($feat->is_stored($db)) {
      warning("DnaDnaAlignFeature [".$feat->dbID."] is already stored" .
              " in this database.");
      next FEATURE;
    }

    my $hstart = $feat->hstart();
    my $hend   = $feat->hend();
    my $hstrand = $feat->hstrand();
    $self->_check_start_end_strand($hstart,$hend, $hstrand);

    my $cigar_string = $feat->cigar_string();
    if(!$cigar_string) {
      $cigar_string = $feat->length() . 'M';
      warning("DnaDnaAlignFeature does not define a cigar_string.\n" .
              "Assuming ungapped block with cigar_line=$cigar_string .");
    }

    my $hseqname = $feat->hseqname();
    if(!$hseqname) {
      throw("DnaDnaAlignFeature 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 $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); $sth->bind_param(5,$hstart,SQL_INTEGER); $sth->bind_param(6,$hend,SQL_INTEGER); $sth->bind_param(7,$hstrand,SQL_TINYINT); $sth->bind_param(8,$hseqname,SQL_VARCHAR); $sth->bind_param(9,$cigar_string,SQL_LONGVARCHAR); $sth->bind_param(10,$feat->analysis->dbID,SQL_INTEGER); $sth->bind_param(11,$feat->score,SQL_DOUBLE); $sth->bind_param(12,$feat->p_value,SQL_DOUBLE); $sth->bind_param(13,$feat->percent_id,SQL_FLOAT); $sth->bind_param(14,$feat->external_db_id,SQL_INTEGER); $sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE); $sth->bind_param(16,$feat->pair_dna_align_feature_id, SQL_INTEGER); $sth->execute(); $original->dbID($sth->{'mysql_insertid'}); $original->adaptor($self); } $sth->finish();
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.