NAME

Bio::Index::GenBank - Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format).

SYNOPSIS

# Complete code for making an index for several
# GenBank files
use Bio::Index::GenBank;

my $Index_File_Name = shift;
my $inx = Bio::Index::GenBank->new($Index_File_Name, 'WRITE');
$inx->make_index(@ARGV);

# Print out several sequences present in the index
# in gcg format
use Bio::Index::GenBank;

my $Index_File_Name = shift;
my $inx = Bio::Index::GenBank->new($Index_File_Name);

foreach my $id (@ARGV) {
    my $seq = $inx->fetch($id); # Returns Bio::Seq object
    print $seq->layout('GCG');
}

# alternatively

my $seq1 = $inx->get_Seq_by_id($id);
my $seq2 = $inx->get_Seq_by_acc($acc);   

DESCRIPTION

Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing GenBank files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system.

FEED_BACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org             - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney

Email - birney@sanger.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_index_file

Title   : _index_file
Usage   : $index->_index_file( $file_name, $i )
Function: Specialist function to index GenBank format files.
          Is provided with a filename and an integer
          by make_index in its SUPER class.
Example : 
Returns : 
Args    : 

_file_format

Title   : _file_format
Usage   : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns : 
Args    :