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¶

  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!

  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¶

  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¶

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

  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.