Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file
       GenBank format).


           # Complete code for making an index for one or more GenBank files
           use strict;
           use Bio::Index::GenBank;

           my $Index_File_Name = shift;
           my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name,
                                                                  -write_flag => 'WRITE');

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

           my $Index_File_Name = shift;
           my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name);
           my $seqio = Bio::SeqIO->new(-format => 'gcg');
           foreach my $id (@ARGV) {
               my $seq = $inx->fetch($id); # Returns Bio::Seq object

           # alternatively
           my ($locus, $acc);
           my $seq1 = $inx->get_Seq_by_id($locus);
           my $seq2 = $inx->get_Seq_by_acc($acc);


       By default the index that is created uses the LOCUS, ACCESSION, and VERSION identifiers as
       keys. Inherits functions for managing dbm files from, and provides
       the basic functionality for indexing GenBank files, and retrieving the sequence from them.
       For best results 'use strict'.

       You can also set or customize the unique key used to retrieve by writing your own function
       and calling the id_parser() method.  For example:

          # make the index

          # here is where the retrieval key is specified
          sub get_id {
             my $line = shift;
             $line =~ /clone="(\S+)"/;


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AUTHOR - Ewan Birney

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

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

         Title   : id_parser
         Usage   : $index->id_parser( CODE )
         Function: Stores or returns the code used by record_id to
                   parse the ID for record from a string.
                   Returns \&default_id_parser (see below) if not
                   set. An entry will be added to
                   the index for each string in the list returned.
         Example : $index->id_parser( \&my_id_parser )
         Returns : reference to CODE if called without arguments
         Args    : CODE

         Title   : default_id_parser
         Usage   : $id = default_id_parser($line)
         Function: The default parser for
         Returns : Array of specified ids
         Args    : a line string

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