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.