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Bio::ASN1::Sequence::IUsereContributed Perl DocBio::ASN1::Sequence::Indexer(3)

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

VERSION
       version 1.73

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

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.

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()

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::Sequence, Bioperl and	all dependencies therein.

INSTALLATION
       Same as Bio::ASN1::EntrezGene

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

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::Sequence::Indexer(3)

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

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