Bio::EnsEMBL::DBSQL PredictionExonAdaptor
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Summary
Bio::EnsEMBL::DBSQL::PredictionExonAdaptor - Performs database interaction for
PredictionExons.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
Bio::EnsEMBL::PredictionExon
Bio::EnsEMBL::Utils::Exception qw ( warning throw deprecate )
Inherit
Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
Synopsis
  $pea   = $database_adaptor->get_PredictionExonAdaptor();
$pexon = $pea->fetch_by_dbID();
my $slice = $database_adaptor->get_SliceAdaptor->fetch_by_region( 'X', 1, 1e6 ); my @pexons = @{ $pea->fetch_all_by_Slice($slice) };
Description
No description!
Methods
_columns
No description
Code
_final_clause
No description
Code
_objs_from_sth
No description
Code
_tables
No description
Code
fetch_all_by_PredictionTranscriptDescriptionCode
list_dbIDsDescriptionCode
removeDescriptionCode
storeDescriptionCode
Methods description
fetch_all_by_PredictionTranscriptcode    nextTop
  Arg [1]    : Bio::EnsEMBL::PredcitionTranscript $transcript
Example : none
Description: Retrieves all Exons for the Transcript in 5-3 order
Returntype : listref Bio::EnsEMBL::Exon on Transcript slice
Exceptions : throws if transcript does not have a slice
Caller : Transcript->get_all_Exons()
Status : Stable
list_dbIDscodeprevnextTop
  Arg [1]    : none
Example : @exon_ids = @{$exon_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all exons 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
removecodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::PredictionExon $exon
the exon to remove from the database
Example : $exon_adaptor->remove($exon);
Description: Removes an exon from the database
Returntype : none
Exceptions : none
Caller : general
Status : Stable
storecodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::PredictionExon $exon
The exon to store in this database
Arg [2] : int $prediction_transcript_id
The internal identifier of the prediction exon that that this
exon is associated with.
Arg [3] : int $rank
The rank of the exon in the transcript (starting at 1)
Example : $pexon_adaptor->store($pexon, 1211, 2);
Description: Stores a PredictionExon in the database
Returntype : none
Exceptions : thrown if exon does not have a slice attached
or if $exon->start, $exon->end, $exon->strand, or $exon->phase
are not defined or if $exon is not a Bio::EnsEMBL::PredictionExon
Caller : general
Status : Stable
Methods code
_columnsdescriptionprevnextTop
sub _columns {
  my $self = shift;

  return qw( pe.prediction_exon_id
             pe.seq_region_id
             pe.seq_region_start
             pe.seq_region_end
             pe.seq_region_strand
             pe.start_phase
             pe.score
             pe.p_value );
}


# _final_clause
#
# Arg [1] : none
# Example : none
# Description: PROTECTED implementation of superclass abstract method
# returns a default end for the SQL-query (ORDER BY)
# Returntype : string
# Exceptions : none
# Caller : internal
}
_final_clausedescriptionprevnextTop
sub _final_clause {
  return "ORDER BY pe.prediction_transcript_id, pe.exon_rank";
}
_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.
#
my $sa = $self->db()->get_SliceAdaptor(); my @exons; my %slice_hash; my %sr_name_hash; my %sr_cs_hash; my($prediction_exon_id,$seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand, $start_phase, $score, $p_value); $sth->bind_columns(\$prediction_exon_id,\$seq_region_id,\$ seq_region_start,\$ seq_region_end,\$ seq_region_strand,\$ start_phase,\$ score,\$ p_value); 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 $asma; 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_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} = $slice->coord_system(); } #obtain a mapper if none was defined, but a dest_seq_region was
if(!$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($dest_mapper) { ($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 = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($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 PredictionExon.
push( @exons, $self->_create_feature( 'Bio::EnsEMBL::PredictionExon', { '-start' => $seq_region_start, '-end' => $seq_region_end, '-strand' => $seq_region_strand, '-adaptor' => $self, '-slice' => $slice, '-dbID' => $prediction_exon_id, '-phase' => $start_phase, '-score' => $score, '-p_value' => $p_value } ) ); } return\@ exons; } 1;
}
_tablesdescriptionprevnextTop
sub _tables {
  return ([ 'prediction_exon', 'pe' ] );
}



#_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
}
fetch_all_by_PredictionTranscriptdescriptionprevnextTop
sub fetch_all_by_PredictionTranscript {
  my ( $self, $transcript ) = @_;
  my $constraint = "pe.prediction_transcript_id = ".$transcript->dbID();

  # use 'keep_all' option to keep exons that are off end of slice
my $tslice = $transcript->slice(); my $slice; if(!$tslice) { throw("Transcript must have attached slice to retrieve exons."); } # use a small slice the same size as the prediction transcript
$slice = $self->db->get_SliceAdaptor->fetch_by_Feature($transcript); my $exons = $self->fetch_all_by_Slice_constraint($slice, $constraint); # remap exon coordinates if necessary
if($slice->name() ne $tslice->name()) { my @out; foreach my $ex (@$exons) { push @out, $ex->transfer($tslice); } $exons =\@ out; } return $exons;
}
list_dbIDsdescriptionprevnextTop
sub list_dbIDs {
   my ($self,$ordered) = @_;

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



#_objs_from_sth
# Arg [1] : Hashreference $hashref
# Example : none
# Description: PROTECTED implementation of abstract superclass method.
# responsible for the creation of Genes
# Returntype : listref of Bio::EnsEMBL::Genes in target coordinate system
# Exceptions : none
# Caller : internal
#
}
removedescriptionprevnextTop
sub remove {
  my $self = shift;
  my $pexon = shift;

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

  if(!$pexon->is_stored($db)) {
    warning('PredictionExon is not in this DB - not removing');
    return undef;
  }

  my $sth = $self->prepare(
            "DELETE FROM prediction_exon WHERE prediction_exon_id = ?");
  $sth->bind_param( 1, $pexon->dbID, SQL_INTEGER );
  $sth->execute();

  $pexon->dbID(undef);
  $pexon->adaptor(undef);
}
storedescriptionprevnextTop
sub store {
  my ( $self, $pexon, $pt_id, $rank ) = @_;

  if(!ref($pexon) || !$pexon->isa('Bio::EnsEMBL::PredictionExon') ) {
    throw("Expected PredictionExon argument");
  }

  throw("Expected PredictionTranscript id argument.") if(!$pt_id);
  throw("Expected rank argument.") if(!$rank);

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

  if($pexon->is_stored($db)) {
    warning('PredictionExon is already stored in this DB.');
    return $pexon->dbID();
  }

  if( ! $pexon->start || ! $pexon->end ||
      ! $pexon->strand || ! defined $pexon->phase ) {
    throw("PredictionExon does not have all attributes to store.\n" .
         "start, end, strand and phase attributes must be set.");
  }

  #maintain reference to original passed-in prediction exon
my $original = $pexon; my $seq_region_id; ($pexon, $seq_region_id) = $self->_pre_store($pexon); my $sth = $db->dbc->prepare ("INSERT into prediction_exon (prediction_transcript_id, exon_rank, " . "seq_region_id, seq_region_start, seq_region_end, " . "seq_region_strand, start_phase, score, p_value) " . "VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ? )"); $sth->bind_param(1,$pt_id,SQL_INTEGER); $sth->bind_param(2,$rank,SQL_SMALLINT); $sth->bind_param(3,$seq_region_id,SQL_INTEGER); $sth->bind_param(4,$pexon->start,SQL_INTEGER); $sth->bind_param(5,$pexon->end,SQL_INTEGER); $sth->bind_param(6,$pexon->strand,SQL_TINYINT); $sth->bind_param(7,$pexon->phase,SQL_TINYINT); $sth->bind_param(8,$pexon->score,SQL_DOUBLE); $sth->bind_param(9,$pexon->p_value,SQL_DOUBLE); $sth->execute(); my $dbID = $sth->{'mysql_insertid'}; #set the adaptor and dbID of the object they passed in
$original->dbID($dbID); $original->adaptor($self); return $dbID;
}
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>.