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lib/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm  view on Meta::CPAN

  foreach my $exon ( @{$transcript->get_all_Exons()} ) {
    # get the number of transcript references to this exon
    # only remove the exon if this is the last transcript to
    # reference it

    my $sth = $self->prepare( "SELECT count(*)
                               FROM   exon_transcript
                               WHERE  exon_id = ?" );
    $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
    $sth->execute();
    my ($count) = $sth->fetchrow_array();
    $sth->finish();

    if($count == 1){
      $exonAdaptor->remove( $exon );
    }
  }

  my $sth = $self->prepare( "DELETE FROM exon_transcript
                             WHERE transcript_id = ?" );
  $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
  $sth->execute();
  $sth->finish();

  my $gene = $transcript->get_Gene;

  $sth = $self->prepare( "DELETE FROM transcript
                          WHERE transcript_id = ?" );
  $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
  $sth->execute();
  $sth->finish();

  if ($update) {
    $gene->remove_Transcript($transcript);
  }

  $transcript->dbID(undef);
  $transcript->adaptor(undef);

  return;
}


=head2 update

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript to update
  Example    : $tr_adaptor->update($transcript);
  Description: Updates a transcript in the database.
  Returntype : None
  Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript.
               warn if the method is called on a transcript that does not exist 
               in the database.
               Should warn if trying to update the number of attached exons, but
               this is a far more complex process and is not yet implemented.
  Caller     : general
  Status     : Stable

=cut

sub update {
  my ( $self, $transcript ) = @_;

  if (    !defined($transcript)
       || !ref($transcript)
       || !$transcript->isa('Bio::EnsEMBL::Transcript') )
  {
    throw("Must update a transcript object, not a $transcript");
  }

  my $update_transcript_sql = 
    sprintf "UPDATE transcript SET stable_id = ?, analysis_id = ?, display_xref_id = ?, description = ?,%s biotype = ?, is_current = ?, canonical_translation_id = ?, version = ? WHERE transcript_id = ?", ($self->schema_version > 74)?" source = ?,":''...

  my $display_xref = $transcript->display_xref();
  my $display_xref_id;

  if ( defined($display_xref) && $display_xref->dbID() ) {
    $display_xref_id = $display_xref->dbID();
  } else {
    $display_xref_id = undef;
  }

  my $sth = $self->prepare($update_transcript_sql);
  my $i = 0;
  $sth->bind_param( ++$i, $transcript->stable_id(), SQL_VARCHAR );
  $sth->bind_param( ++$i, $transcript->analysis()->dbID(), SQL_INTEGER );
  $sth->bind_param( ++$i, $display_xref_id, SQL_INTEGER );
  $sth->bind_param( ++$i, $transcript->description(), SQL_LONGVARCHAR );

  $self->schema_version > 74 and 
    $sth->bind_param( ++$i,  $transcript->source(),      SQL_VARCHAR );

  $sth->bind_param( ++$i, $transcript->get_Biotype->name, SQL_VARCHAR );
  $sth->bind_param( ++$i, $transcript->is_current(),  SQL_TINYINT );
  $sth->bind_param( ++$i, (
                      defined( $transcript->translation() )
                      ? $transcript->translation()->dbID()
                      : undef ),
                    SQL_INTEGER );
  $sth->bind_param( ++$i, $transcript->version(), SQL_INTEGER );
  $sth->bind_param( ++$i, $transcript->dbID(), SQL_INTEGER );

  $sth->execute();

  # Check if transcript is canonical
  if ($transcript->is_canonical()) {
    my $gene = $transcript->get_Gene();
    my $gene_adaptor = $self->db()->get_GeneAdaptor();
    $gene->canonical_transcript($transcript);
    $gene_adaptor->update($gene);
  }

} ## end sub update


=head2 list_dbIDs

  Example    : @transcript_ids = @{ $t_adaptor->list_dbIDs };
  Description: Gets a list of internal ids for all transcripts in the db.
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.  Returntype : Listref of Ints
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub list_dbIDs {
   my ($self, $ordered) = @_;

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


=head2 list_stable_ids

  Example    : @stable_trans_ids = @{ $transcript_adaptor->list_stable_ids };
  Description: Gets a list of stable ids for all transcripts in the current
               database.
  Returntype : Listref of Strings
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub list_stable_ids {
   my ($self) = @_;

   return $self->_list_dbIDs("transcript", "stable_id");
}


#_objs_from_sth

#  Arg [1]    : StatementHandle $sth
#  Arg [2]    : Bio::EnsEMBL::AssemblyMapper $mapper
#  Arg [3]    : Bio::EnsEMBL::Slice $dest_slice
#  Description: PROTECTED implementation of abstract superclass method.
#               Responsible for the creation of Transcripts.
#  Returntype : Listref of Bio::EnsEMBL::Transcripts in target coord system
#  Exceptions : none
#  Caller     : internal
#  Status     : Stable

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.
  #

lib/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm  view on Meta::CPAN

  Description: Gets all the transcripts with evidence from a specified hit_name on a particular type of feature, stored in the  
               transcript_supporting_feature table. Optionally filter by analysis.  For hits stored in the supporting_feature 
               table (linked to exons) use fetch_all_by_exon_supporting_evidence instead.
  Returntype : Listref of Bio::EnsEMBL::Transcript objects
  Exceptions : If feature_type is not of correct type.
  Caller     : general
  Status     : Stable

=cut

sub fetch_all_by_transcript_supporting_evidence {
  
  my ($self, $hit_name, $feature_type, $analysis) = @_;

  if($feature_type !~ /(dna)|(protein)_align_feature/) {
    throw("feature type must be dna_align_feature or protein_align_feature");
  }

  my $anal_from = "";
  $anal_from = ", analysis a " if ($analysis);
  my $anal_where = "";
  $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? "
    if ($analysis);

  my $sql = qq(
      SELECT DISTINCT(t.transcript_id)
        FROM transcript t,
             transcript_supporting_feature sf,
             $feature_type f
             $anal_from
       WHERE t.transcript_id = sf.transcript_id
         AND t.is_current = 1
         AND sf.feature_id = f.${feature_type}_id
         AND sf.feature_type = ?
         AND f.hit_name=?
         $anal_where
  );

  my $sth = $self->prepare($sql);

  $sth->bind_param(1, $feature_type, SQL_VARCHAR);
  $sth->bind_param(2, $hit_name, SQL_VARCHAR);
  $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);

  $sth->execute();

  my @transcripts;

  while( my $id = $sth->fetchrow_array ) {
    my $transcript = $self->fetch_by_dbID( $id  );
    push(@transcripts, $transcript) if $transcript;
  }

  return \@transcripts;
}

sub _final_clause {
	return ' ORDER BY t.transcript_id'
}

sub update_canonical_attribute {
  my ($self, $transcript_id, $old_transcript_id) = @_;

  # Get canonical attribute id
  my $db = $self->db();
  my $attr_adaptor = $db->get_AttributeAdaptor();
  my $canonical_attrib_id = @{$attr_adaptor->fetch_by_code('is_canonical')}[0];
  throw("No attrib_type_id found for 'is_canonical' attribute in attrib_type table.") if (!defined($canonical_attrib_id));

  # Check if new canonical transcript attribute exists
  my $sth = $self->prepare("SELECT value FROM transcript_attrib WHERE transcript_id=? AND attrib_type_id=?");
  $sth->execute($transcript_id, $canonical_attrib_id);
  if (my ($exists) = $sth->fetchrow_array()) {
    $sth->finish();

    $sth = $self->prepare("UPDATE transcript_attrib SET value=? WHERE transcript_id=? AND attrib_type_id=?");
    $sth->execute('1', $transcript_id, $canonical_attrib_id);
  } else {
    $sth->finish();

    $sth = $self->prepare("INSERT INTO transcript_attrib (transcript_id, attrib_type_id, value) values(?,?,?)");
    $sth->execute($transcript_id, $canonical_attrib_id, '1');
  }
  $sth->finish();

  # Delete old canonical transcript attribute
  if (defined($old_transcript_id) && $old_transcript_id ne $transcript_id) {
    $sth = $self->prepare("DELETE FROM transcript_attrib WHERE transcript_id=? AND attrib_type_id=?");
    $sth->execute($old_transcript_id, $canonical_attrib_id);
    $sth->finish();
  }
}

1;