debian man page for bio::asn1::sequence::indexer

Bio::ASN1::Sequence::Indexer(3pm)			User Contributed Perl Documentation			 Bio::ASN1::Sequence::Indexer(3pm)

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

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

INSTALLATION
       Same as Bio::ASN1::EntrezGene

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

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

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

OPERATION SYSTEMS SUPPORTED
       Any OS that Perl & Bioperl run on.

METHODS
   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

perl v5.14.2							    2005-05-04					 Bio::ASN1::Sequence::Indexer(3pm)