Inheritance diagram for Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor:

Public Member Functions
protected	_tables ()

protected	_columns ()

public Bio::EnsEMBL::PredictionTranscript	fetch_by_stable_id ()

public Reference	fetch_all_by_Slice ()

public Bio::EnsEMBL::PredictionTranscript	fetch_by_prediction_exon_id ()

protected Reference	_objs_from_sth ()

public void	store ()

public void	remove ()

public List	list_dbIDs ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
public Bio::EnsEMBL::BaseFeatureAdaptor	new ()

public Boolean	start_equals_end ()

public void	clear_cache ()

protected	_clear_slice_feature_cache ()

protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()

public Listref	fetch_all_by_Slice ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()

public Listref	fetch_all_by_Slice_and_score ()

public Listref	fetch_all_by_Slice_constraint ()

public Listref	fetch_all_by_logic_name ()

public Listref	fetch_all_by_stable_id_list ()

protected	_create_feature ()

protected	_create_feature_fast ()

public Int	count_by_Slice_constraint ()

protected ArrayRef	_get_and_filter_Slice_projections ()

protected ArrayRef	_generate_feature_bounds ()

protected Listref	_get_by_Slice ()

protected	_slice_fetch ()

public	get_seq_region_id_external ()

public	get_seq_region_id_internal ()

protected	_pre_store ()

protected	_pre_store_userdata ()

protected	_check_start_end_strand ()

protected	_remap ()

protected	_seq_region_boundary_from_db ()

public void	store ()

public void	remove ()

public void	remove_by_Slice ()

protected	_max_feature_length ()

protected	_list_seq_region_ids ()

public	remove_by_analysis_id ()

public	remove_by_feature_id ()

public Bio::EnsEMBL::Feature	fetch_nearest_by_Feature ()

public Listref	fetch_all_by_outward_search ()

public Listref	fetch_all_nearest_by_Feature ()

public Listref	select_nearest ()

protected Int	_compute_nearest_end ()

protected Int	_compute_prime_distance ()

protected Int	_compute_midpoint ()

protected	_discard_excess_features_from_matrix ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

# get a prediction transcript adaptor from the database
$pta = $database_adaptor->get_PredictionTranscriptAdaptor();
 
# get a slice on a region of chromosome 1
$sa = $database_adaptor->get_SliceAdaptor();
 
$slice = $sa->fetch_by_region( 'chromosome', 'x', 100000, 200000 );
 
# get all the prediction transcripts from the slice region
$prediction_transcripts = @{ $pta->fetch_all_by_Slice($slice) };

Definition at line 23 of file PredictionTranscriptAdaptor.pm.

Member Function Documentation

◆ _columns()

protected Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::_columns ( )

Undocumented method

Code:

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◆ _objs_from_sth()

protected Reference Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::_objs_from_sth ( )

  Arg [1]    : DBI:st $sth 
               An executed DBI statement handle
  Arg [2]    : (optional) Bio::EnsEMBL::Mapper $mapper 
               An mapper to be used to convert contig coordinates
               to assembly coordinates.
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice to map the prediction transcript to.   
  Example    :

$p_transcripts = $self->_objs_from_sth($sth);

  Description: Creates a list of Prediction transcripts from an executed DBI
               statement handle.  The columns retrieved via the statement 
               handle must be in the same order as the columns defined by the
               _columns method.  If the slice argument is provided then the
               the prediction transcripts will be in returned in the coordinate
               system of the $slice argument.  Otherwise the prediction 
               transcripts will be returned in the RawContig coordinate system.
  Returntype : reference to a list of Bio::EnsEMBL::PredictionTranscripts
  Exceptions : none
  Caller     : superclass generic_fetch
  Status     : Stable

Code:

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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 @ptranscripts;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;
 
  my (
    $prediction_transcript_id, $seq_region_id,     $seq_region_start,
    $seq_region_end,           $seq_region_strand, $analysis_id,
    $display_label);
 
  $sth->bind_columns(\(
                     $prediction_transcript_id, $seq_region_id,     $seq_region_start,
                     $seq_region_end,           $seq_region_strand, $analysis_id,
                     $display_label));
 
  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);
    $analysis_hash{$analysis_id} = $analysis;
 
    #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};
 
    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(!$mapper && $dest_slice && !$dest_slice_cs->equals($slice->coord_system)) {
      $mapper = $asma->fetch_by_CoordSystems($dest_slice_cs, $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
      $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)) {
      my $seq_region_len = $dest_slice->seq_region_length();
 
      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 ) {
        # Handle circular chromosomes.
 
          if ( $seq_region_start > $seq_region_end ) {
            # Looking at a feature overlapping the chromosome origin.
 
            if ( $seq_region_end > $dest_slice_start ) {
              # Looking at the region in the beginning of the chromosome
              $seq_region_start -= $seq_region_len;
            }
            if ( $seq_region_end < 0 ) {
              $seq_region_end += $seq_region_len;
            }
          } else {
            if ($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 += $seq_region_len;
              $seq_region_end   += $seq_region_len;
            }
          }
        }
      } else {
 
        my $start = $dest_slice_end - $seq_region_end + 1;
        my $end = $dest_slice_end - $seq_region_start + 1;
 
        if ($dest_slice->is_circular()) {
 
          if ($dest_slice_start > $dest_slice_end) {
            # slice spans origin or replication
 
            if ($seq_region_start >= $dest_slice_start) {
              $end += $seq_region_len;
              $start += $seq_region_len if $seq_region_end > $dest_slice_start;
 
            } elsif ($seq_region_start <= $dest_slice_end) {
              # do nothing
            } elsif ($seq_region_end >= $dest_slice_start) {
              $start += $seq_region_len;
              $end += $seq_region_len;
 
            } elsif ($seq_region_end <= $dest_slice_end) {
              $end += $seq_region_len if $end < 0;
 
            } elsif ($seq_region_start > $seq_region_end) {
              $end += $seq_region_len;
            }
 
          } else {
 
            if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
              # do nothing
            } elsif ($seq_region_start > $seq_region_end) {
              if ($seq_region_start <= $dest_slice_end) {
                $start -= $seq_region_len;
              } elsif ($seq_region_end >= $dest_slice_start) {
                $end += $seq_region_len;
              }
            }
          }
        }
 
        $seq_region_start = $start;
        $seq_region_end = $end;
        $seq_region_strand *= -1;
 
      } ## end else [ if ( $dest_slice_strand...)]
 
      # Throw away features off the end of the requested slice or on
      # different seq_region.
      if ($seq_region_end < 1
          || $seq_region_start > $dest_slice_length
          || ($dest_slice_sr_id != $seq_region_id)) {
        next FEATURE;
      }
      $slice = $dest_slice;
    }
 
    # Finally, create the new PredictionTranscript.
    push( @ptranscripts,
          $self->_create_feature('Bio::EnsEMBL::PredictionTranscript', {
                                   '-start'    => $seq_region_start,
                                   '-end'      => $seq_region_end,
                                   '-strand'   => $seq_region_strand,
                                   '-adaptor'  => $self,
                                   '-slice'    => $slice,
                                   '-analysis' => $analysis,
                                   '-dbID' => $prediction_transcript_id,
                                   '-display_label' => $display_label
                                 } ) );
 
  }
 
  return \@ptranscripts;
}

◆ _tables()

protected Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::_tables ( )

Undocumented method

Code:

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◆ fetch_all_by_Slice()

public Reference Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::fetch_all_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to fetch transcripts on.
  Arg [3]    : (optional) boolean $load_exons
               if true, exons will be loaded immediately rather than
               lazy loaded later.
  Example    :

$transcripts = $

  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 : reference to list of transcripts
  Exceptions : thrown if exon cannot be placed on transcript slice
  Caller     : Slice::get_all_Transcripts
  Status     : Stable

Code:

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sub fetch_all_by_Slice {
  my $self  = shift;
  my $slice = shift;
  my $logic_name = shift;
  my $load_exons = shift;
 
  my $transcripts = $self->SUPER::fetch_all_by_Slice($slice,$logic_name);
 
  # if there are 0 transcripts still do lazy-loading
  if(!$load_exons || @$transcripts < 1) {
    return $transcripts;
  }
 
  # preload all of the exons now, instead of lazy loading later
  # faster than 1 query per transcript
 
  # get extent of region spanned by transcripts
  my ($min_start, $max_end);
  my $ext_slice;
 
  unless ($slice->is_circular()) {
    foreach my $t (@$transcripts) {
      if (!defined($min_start) || $t->seq_region_start() < $min_start) {
    $min_start = $t->seq_region_start();
      }
      if (!defined($max_end) || $t->seq_region_end() > $max_end) {
    $max_end = $t->seq_region_end();
      }
    }
 
    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());
    }
 
  } else {
    # feature might be crossing the origin of replication (i.e. seq_region_start > seq_region_end)
    # the computation of min_start|end based on seq_region_start|end is not safe
    # use feature start/end relative to the slice instead
    my ($min_start_feature, $max_end_feature);
    foreach my $t (@$transcripts) {
      if (!defined($min_start) || ($t->start() >= 0 && $t->start() < $min_start)) {
    $min_start = $t->start();
    $min_start_feature = $t;
      }
      if (!defined($max_end) || ($t->end() >= 0 && $t->end() > $max_end)) {
    $max_end = $t->end();
    $max_end_feature = $t;
      }
    }
    
    # now we can reassign min_start|end to seq_region_start|end of
    # the feature which spans the largest region
    $min_start = $min_start_feature->seq_region_start();
    $max_end = $max_end_feature->seq_region_end();
 
    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 prediction_transcript_id, prediction_exon_id, exon_rank " .
     "FROM   prediction_exon " .
     "WHERE  prediction_transcript_id IN $tr_id_str");
 
  $sth->execute();
 
  my ($ex_id, $tr_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];
  }
 
  $sth->finish();
 
  my $ea = $self->db()->get_PredictionExonAdaptor();
  my $exons = $ea->fetch_all_by_Slice($ext_slice);
 
  # move exons onto transcript slice, and add them to transcripts
  foreach my $ex (@$exons) {
    $ex = $ex->transfer($slice) if($slice != $ext_slice);
 
    if(!$ex) {
      throw("Unexpected. PredictionExon could not be transfered onto " .
            "PredictionTranscript slice.");
    }
 
    foreach my $row (@{$ex_tr_hash{$ex->dbID()}}) {
      my ($tr, $rank) = @$row;
      $tr->add_Exon($ex, $rank);
    }
  }
 
  return $transcripts;
}

◆ fetch_by_prediction_exon_id()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::fetch_by_prediction_exon_id ( )

  Arg [1]    : Int $prediction_exon_id
               Unique database identifier for the prediction exon
               whose prediction transcript should be retrieved.
  Example    :

$prediction_transcript = $prediction_transcript_adaptor->fetch_by_exon_id(1241);

  Description: Retrieves a prediction transcript from the database via the database identifier
               of one of its exons.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_stable_id()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::fetch_by_stable_id ( )

  Arg [1]    : string $stable_id
               The stable id of the transcript to retrieve
  Example    :

$trans = $trans_adptr->fetch_by_stable_id('GENSCAN00000001234');

  Description: Retrieves a prediction transcript via its display_label.
               This method is called fetch_by_stable_id for polymorphism with
               the TranscriptAdaptor.  Prediction transcript display_labels are
               not necessarily stable in that the same identifier may be reused
               for a completely different prediction transcript in a subsequent
               database release.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Caller     : general
  Status     : Stable

Code:

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◆ list_dbIDs()

public List Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::list_dbIDs ( )

  Arg [1]    : none
  Example    :

@feature_ids = @{$prediction_transcript_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all prediction transcript
               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

Code:

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◆ remove()

public void Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::PredictionTranscript $pt 
  Example    :

$prediction_transcript_adaptor->remove($pt);

  Description: removes given prediction transcript $pt from database. 
  Returntype : none
  Exceptions : throws if argument not a  Bio::EnsEMBL::PredictionTranscript
  Caller     : general
  Status     : Stable

Code:

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◆ store()

public void Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor::store ( )

  Arg [1]    : list of Bio::EnsEMBL::PredictionTranscript @pre_transcripts 
  Example    :

$prediction_transcript_adaptor->store(@pre_transcripts);

  Description: Stores a list of given prediction transcripts in database. 
               Puts dbID and Adaptor into each object stored object.
  Returntype : none
  Exceptions : on wrong argument type 
  Caller     : general 
  Status     : Stable

Code:

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sub store {
  my ( $self, @pre_transcripts ) = @_;
 
  my $ptstore_sth = $self->prepare
    (qq{INSERT INTO prediction_transcript (seq_region_id, seq_region_start,
                                           seq_region_end, seq_region_strand, 
                                           analysis_id, display_label)
        VALUES( ?, ?, ?, ?, ?, ?)});
 
  my $ptupdate_sth = $self->prepare
    (qq{UPDATE prediction_transcript SET display_label = ?
        WHERE  prediction_transcript_id = ?});
 
  my $db = $self->db();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();
  my $pexon_adaptor = $db->get_PredictionExonAdaptor();
 
  FEATURE: foreach my $pt (@pre_transcripts) {
    if(!ref($pt) || !$pt->isa('Bio::EnsEMBL::PredictionTranscript')) {
      throw('Expected PredictionTranscript argument not [' . ref($pt).']');
    }
 
    #skip prediction transcripts that have already been stored
    if($pt->is_stored($db)) {
      warning('Not storing already stored prediction transcript '. $pt->dbID);
      next FEATURE;
    }
 
    #get analysis and store it if it is not in the db
    my $analysis = $pt->analysis();
    if(!$analysis) {
      throw('Prediction transcript must have analysis to be stored.');
    }
    if(!$analysis->is_stored($db)) {
      $analysis_adaptor->store($analysis);
    }
 
    #ensure that the transcript coordinates are correct, they may not be,
    #if somebody has done some exon coordinate juggling and not recalculated
    #the transcript coords.
    $pt->recalculate_coordinates();
 
    my $original = $pt;
    my $seq_region_id;
    ($pt, $seq_region_id) = $self->_pre_store($pt);
 
    #store the prediction transcript
    $ptstore_sth->bind_param(1,$seq_region_id,SQL_INTEGER);
    $ptstore_sth->bind_param(2,$pt->start,SQL_INTEGER);
    $ptstore_sth->bind_param(3,$pt->end,SQL_INTEGER);
    $ptstore_sth->bind_param(4,$pt->strand,SQL_TINYINT);
    $ptstore_sth->bind_param(5,$analysis->dbID,SQL_INTEGER);
    $ptstore_sth->bind_param(6,$pt->display_label,SQL_VARCHAR);
 
    $ptstore_sth->execute();
 
    my $pt_id = $self->last_insert_id('prediction_transcript_id', undef, 'prediction_transcript');
    $original->dbID($pt_id);
    $original->adaptor($self);
 
    #store the exons
    my $rank = 1;
    foreach my $pexon (@{$original->get_all_Exons}) {
      $pexon_adaptor->store($pexon, $pt_id, $rank++);
    }
 
    # if a display label was not defined autogenerate one
    if(!defined($pt->display_label())) {
      my $zeros = '0' x (11 - length($pt_id));
      my $display_label = uc($analysis->logic_name()) . $zeros . $pt_id;
      $ptupdate_sth->bind_param(1,$display_label,SQL_VARCHAR);
      $ptupdate_sth->bind_param(2,$pt_id,SQL_INTEGER);
      $ptupdate_sth->execute();
      $original->display_label($display_label);
    }
  }
}

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm

Public Member Functions

Detailed Description

Synopsis

Member Function Documentation

◆ _columns()

◆ _objs_from_sth()

◆ _tables()

◆ fetch_all_by_Slice()

◆ fetch_by_prediction_exon_id()

◆ fetch_by_stable_id()

◆ list_dbIDs()

◆ remove()

◆ store()