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Bio/DB/SeqFeature/Store/DBI/SQLite.pm  view on Meta::CPAN

  delete $self->{filehandles};
}

sub index_tables {
    my $self = shift;
    my @t    = $self->SUPER::index_tables;
    return (@t,$self->_feature_index_table);
}

sub _enable_keys  { }  # nullop
sub _disable_keys { }  # nullop

sub _fetch_indexed_features_sql {
    my $self = shift;
    my $location_table       = $self->_qualify('feature_location');
    my $feature_table        = $self->_qualify('feature');
    return <<END;
    SELECT typeid,seqid,start-1,end
  FROM $location_table as l,$feature_table as f
 WHERE l.id=f.id AND f.\"indexed\"=1
  ORDER BY typeid,seqid,start
END
}

###
# get primary sequence between start and end
#
sub _fetch_sequence {
  my $self = shift;
  my ($seqid,$start,$end) = @_;

  # backward compatibility to the old days when I liked reverse complementing
  # dna by specifying $start > $end
  my $reversed;
  if (defined $start && defined $end && $start > $end) {
    $reversed++;
    ($start,$end) = ($end,$start);
  }
  $start-- if defined $start;
  $end--   if defined $end;

  my $offset1 = $self->_offset_boundary($seqid,$start || 'left');
  my $offset2 = $self->_offset_boundary($seqid,$end   || 'right');
  my $sequence_table = $self->_sequence_table;
  my $locationlist_table = $self->_locationlist_table;

  # CROSS JOIN gives a hint to the SQLite query optimizer -- mucho speedup!
  my $sth     = $self->_prepare(<<END);
SELECT sequence,offset
   FROM $locationlist_table as ll CROSS JOIN $sequence_table as s
   WHERE ll.id=s.id
     AND ll.seqname= ?
     AND offset >= ?
     AND offset <= ?
   ORDER BY offset
END

  my $seq = '';
  $sth->execute($seqid,$offset1,$offset2) or $self->throw($sth->errstr);

  while (my($frag,$offset) = $sth->fetchrow_array) {
    substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset;
    $seq .= $frag;
  }
  substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq);
  if ($reversed) {
    $seq = reverse $seq;
    $seq =~ tr/gatcGATC/ctagCTAG/;
  }
  $sth->finish;
  $seq;
}

sub _offset_boundary {
  my $self = shift;
  my ($seqid,$position) = @_;

  my $sequence_table     = $self->_sequence_table;
  my $locationlist_table = $self->_locationlist_table;

  my $sql;
  # use "CROSS JOIN" to give a hint to the SQLite query optimizer.
  $sql =  $position eq 'left'  ? "SELECT min(offset) FROM $locationlist_table as ll CROSS JOIN $sequence_table as s ON ll.id=s.id WHERE ll.seqname=?"
         :$position eq 'right' ? "SELECT max(offset) FROM $locationlist_table as ll CROSS JOIN $sequence_table as s ON ll.id=s.id WHERE ll.seqname=?"
	 :"SELECT max(offset) FROM $locationlist_table as ll CROSS JOIN $sequence_table as s ON ll.id=s.id WHERE ll.seqname=? AND offset<=?";
  my $sth = $self->_prepare($sql);
  my @args = $position =~ /^-?\d+$/ ? ($seqid,$position) : ($seqid);
  $sth->execute(@args) or $self->throw($sth->errstr);
  my $boundary = $sth->fetchall_arrayref->[0][0];
  $sth->finish;
  return $boundary;
}

###
# Efficiently fetch a series of IDs from the database
# Can pass an array or an array ref
#
sub _fetch_many {
  my $self       = shift;
  @_ or $self->throw('usage: fetch_many($id1,$id2,$id3...)');
  my $ids = join ',',map {ref($_) ? @$_ : $_} @_ or return;
  my $features = $self->_feature_table;

  my $sth = $self->_prepare(<<END);
SELECT id,object FROM $features WHERE id IN ($ids)
END
  $sth->execute() or $self->throw($sth->errstr);
  return $self->_sth2objs($sth);
}

sub _features {
  my $self = shift;
  my ($seq_id,$start,$end,$strand,
      $name,$class,$allow_aliases,
      $types,
      $attributes,
      $range_type,
      $fromtable,
      $iterator,
      $sources
     ) = rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],'STRAND',
		    'NAME','CLASS','ALIASES',
		    ['TYPES','TYPE','PRIMARY_TAG'],