Bio::ASN1::Sequence::Indexer.3pm

Langue: en

Version: 2005-05-04 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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
 
 

PREREQUISITE

Bio::ASN1::Sequence, Bioperl and all dependencies therein.

INSTALLATION

Same as Bio::ASN1::EntrezGene

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.

SEE ALSO

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

AUTHOR

Dr. Mingyi Liu <mingyi.liu@gpc-biotech.com> 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 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()
 
 

_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