Bio::ASN1::Sequence::Indexer - Indexes NCBI Sequence files.

Bio-ASN1-EntrezGene documentation Contained in the Bio-ASN1-EntrezGene distribution.

Index

Code Index:

NAME

Top

Bio::ASN1::Sequence::Indexer - Indexes NCBI Sequence files.

SYNOPSIS

Top

  use Bio::ASN1::Sequence::Indexer;

  # creating & using the index is just a few lines
  my $inx = Bio::ASN1::Sequence::Indexer->new(
    -filename => 'seq.idx',
    -write_flag => 'WRITE'); # needed for make_index call, but if opening
                             # existing index file, don't set write flag!
  $inx->make_index('seq1.asn', 'seq2.asn');
  my $seq = $inx->fetch('AF093062'); # Bio::Seq obj for Sequence (doesn't work yet)
  # alternatively, if one prefers just a data structure instead of objects
  $seq = $inx->fetch_hash('AF093062'); # a hash produced by Bio::ASN1::Sequence
                            # that contains all data in the Sequence record

PREREQUISITE

Top

Bio::ASN1::Sequence, Bioperl and all dependencies therein.

INSTALLATION

Top

Same as Bio::ASN1::EntrezGene

DESCRIPTION

Top

Bio::ASN1::Sequence::Indexer is a Perl Indexer for NCBI Sequence genome databases. It processes an ASN.1-formatted Sequence record and stores the file position for each record in a way compliant with Bioperl standard (in fact its a subclass of Bioperl's index objects).

Note that this module does not parse record, because it needs to run fast and grab only the gene ids. For parsing record, use Bio::ASN1::Sequence.

As with Bio::ASN1::Sequence, this module is best thought of as beta version - it works, but is not fully tested.

SEE ALSO

Top

Please check out perldoc for Bio::ASN1::EntrezGene for more info.

AUTHOR

Top

Dr. Mingyi Liu <mingyi.liu@gpc-biotech.com>

COPYRIGHT

Top

The Bio::ASN1::EntrezGene module and its related modules and scripts are copyright (c) 2005 Mingyi Liu, GPC Biotech AG and Altana Research Institute. All rights reserved. I created these modules when working on a collaboration project between these two companies. Therefore a special thanks for the two companies to allow the release of the code into public domain.

You may use and distribute them under the terms of the Perl itself or GPL (http://www.gnu.org/copyleft/gpl.html).

CITATION

Top

Liu, M and Grigoriev, A (2005) "Fast Parsers for Entrez Gene" Bioinformatics. In press

OPERATION SYSTEMS SUPPORTED

Top

Any OS that Perl & Bioperl run on.

METHODS

Top

fetch

  Parameters: $geneid - id for the Sequence record to be retrieved
  Example:    my $hash = $indexer->fetch(10); # get Sequence #10
  Function:   fetch the data for the given Sequence id.
  Returns:    A Bio::Seq object produced by Bio::SeqIO::sequence
  Notes:      Bio::SeqIO::sequence does not exist and probably won't
                exist for a while!  So call fetch_hash instead

fetch_hash

  Parameters: $seqid - id for the Sequence record to be retrieved
  Example:    my $hash = $indexer->fetch_hash('AF093062');
  Function:   fetch a hash produced by Bio::ASN1::Sequence for given id
  Returns:    A data structure containing all data items from the Sequence
                record.
  Notes:      Alternative to fetch()

_file_handle

  Title   : _file_handle
  Usage   : $fh = $index->_file_handle( INT )
  Function: Returns an open filehandle for the file
            index INT.  On opening a new filehandle it
            caches it in the @{$index->_filehandle} array.
            If the requested filehandle is already open,
            it simply returns it from the array.
  Example : $fist_file_indexed = $index->_file_handle( 0 );
  Returns : ref to a filehandle
  Args    : INT
  Notes   : This function is copied from Bio::Index::Abstract. Once that module
              changes file handle code like I do below to fit perl 5.005_03, this
              sub would be removed from this module
Bio-ASN1-EntrezGene documentation Contained in the Bio-ASN1-EntrezGene distribution. 
package Bio::ASN1::Sequence::Indexer;

use strict;
use Carp qw(carp croak);
use vars qw ($VERSION @ISA);
use Bio::ASN1::Sequence;
use Bio::Index::AbstractSeq;

@ISA = qw(Bio::Index::AbstractSeq);
$VERSION = '1.09';

sub _version
{
  return $VERSION;
}

sub _type_stamp
{
  return '__Sequence_ASN1__';
}

sub _index_file
{
  my($self, $file, $idx) = @_;
  my $position;
  open(IN, $file) || $self->throw("Can't open $file - $!");
  local $/ = "Seq-entry ::= set {";
  while(<IN>)
  {
    chomp;
    while(/[,{}]\s+accession\s*"([^"]+)"\s+[,{}]/ig) # add both dna and protein
    {
      $self->add_record($1, $idx, $position);
    }
    $position = tell(IN) - 19; # $/'s length
  }
  close(IN);
  return 1;
}

sub _file_format
{
  return 'sequence';
}


sub fetch_hash
{
  my ($self, $seqid) = @_;
  if (my $seq = $self->db->{$seqid})
  {
    my ($fileno, $position) = $self->unpack_record($seq);
    my $parser = Bio::ASN1::Sequence->new('fh' => $self->_file_handle($fileno));
    seek($parser->fh, $position, 0);
    return $parser->next_seq;
  }
}


sub _file_handle {
	my( $self, $i ) = @_;

	unless ($self->{'_filehandle'}[$i]) {
		my @rec = $self->unpack_record($self->db->{"__FILE_$i"})
		  or $self->throw("Can't get filename for index : $i");
		my $file = $rec[0];
		local *FH;
		open *FH, $file or $self->throw("Can't read file '$file' : $!");
		$self->{'_filehandle'}[$i] = *FH; # Cache filehandle
	}
	return $self->{'_filehandle'}[$i];
}

1;