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Bio-ASN1-EntrezGene-1.72
River stage two • 2 direct dependents • 11 total dependents
/ Bio::ASN1::EntrezGene::Indexer

NAME

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

VERSION

version 1.72

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/wiki/Mailing_lists  - 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://redmine.open-bio.org/projects/bioperl/

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.