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

NAME

       Bio::ASN1::EntrezGene::Indexer - Indexes NCBI Entrez Gene files.

SYNOPSIS

	 use Bio::ASN1::EntrezGene::Indexer;

	 # creating & using the index is just a few lines
	 my $inx = Bio::ASN1::EntrezGene::Indexer->new(
	   -filename => 'entrezgene.idx',
	   -write_flag => 'WRITE'); # needed for make_index call, but if opening
				    # existing index file, don't set write flag!
	 $inx->make_index('Homo_sapiens', 'Mus_musculus', 'Rattus_norvegicus');
	 my $seq = $inx->fetch(10); # Bio::Seq obj for Entrez Gene #10
	 # alternatively, if one prefers just a data structure instead of objects
	 $seq = $inx->fetch_hash(10); # a hash produced by Bio::ASN1::EntrezGene
				   # that contains all data in the Entrez Gene record

	 # note that in case you wonder, you can get the files 'Homo_sapiens'
	 # from NCBI Entrez Gene ftp download, DATA/ASN/Mammalia directory

PREREQUISITE

       Bio::ASN1::EntrezGene, Bioperl version that contains Stefan Kirov's entrezgene.pm and all dependencies therein.

INSTALLATION

       Same as Bio::ASN1::EntrezGene

DESCRIPTION

       Bio::ASN1::EntrezGene::Indexer is a Perl Indexer for NCBI Entrez Gene genome databases. It processes an ASN.1-formatted Entrez Gene 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::EntrezGene, or better yet, use Bio::SeqIO, format 'entrezgene'.

       It takes this module (version 1.07) 21 seconds to index the human genome Entrez Gene file (Apr. 5/2005 download) on one 2.4 GHz Intel Xeon
       processor.

SEE ALSO

       For details on various parsers I generated for Entrez Gene, example scripts that uses/benchmarks the modules, please see
       <http://sourceforge.net/projects/egparser/>.  Those other parsers etc. are included in V1.05 download.

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 Entrez Gene record to be retrieved
	 Example:    my $hash = $indexer->fetch(10); # get Entrez Gene #10
	 Function:   fetch the data for the given Entrez Gene id.
	 Returns:    A Bio::Seq object produced by Bio::SeqIO::entrezgene
	 Notes:      One needs to have Bio::SeqIO::entrezgene installed before
		       calling this function!

   fetch_hash
	 Parameters: $geneid - id for the Entrez Gene record to be retrieved
	 Example:    my $hash = $indexer->fetch_hash(10); # get Entrez Gene #10
	 Function:   fetch a hash produced by Bio::ASN1::EntrezGene for given Entrez
		       Gene id.
	 Returns:    A data structure containing all data items from the Entrez
		       Gene 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::EntrezGene::Indexer(3pm)