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Bio::ASN1::EntrezGene:UsereContributed Perl DBio::ASN1::EntrezGene::Indexer(3)

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

VERSION
       version 1.73

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

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.

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()

INTERNAL METHODS
   _version
   _type_stamp
   _index_file
   _file_format
   _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

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

INSTALLATION
       Same as Bio::ASN1::EntrezGene

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.

CITATION
       Liu, Mingyi, and	Andrei Grigoriev. "Fast	parsers	for Entrez Gene."
       Bioinformatics 21, no. 14 (2005): 3189-3190.

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

FEEDBACK
   Mailing lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org		    - General discussion
	 http://bioperl.org/Support.html    - About the	mailing	lists

   Support
       Please direct usage questions or	support	issues to the mailing list:
       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/bio-asn1-entrezgene/issues

AUTHOR
       Dr. Mingyi Liu <mingyiliu@gmail.com>

COPYRIGHT
       This software is	copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech
       AG, and 2005 by Altana Research Institute.

       This software is	available under	the same terms as the perl 5
       programming language system itself.

perl v5.32.0			  2018-09-25 Bio::ASN1::EntrezGene::Indexer(3)

NAME | VERSION | SYNOPSIS | DESCRIPTION | METHODS | INTERNAL METHODS | PREREQUISITE | INSTALLATION | SEE ALSO | CITATION | OPERATION SYSTEMS SUPPORTED | FEEDBACK | AUTHOR | COPYRIGHT

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