Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.


         # Make an index for one or more Swissprot files:

           use Bio::Index::Swissprot;
           use strict;

           my $index_file_name = shift;
           my $inx = Bio::Index::Swissprot->new(
               -filename => $index_file_name,
               -write_flag => 1);

         # Print out several sequences present in the index in Genbank
         # format:

           use Bio::Index::Swissprot;
           use Bio::SeqIO;
           use strict;

           my $out = Bio::SeqIO->new( -format => 'genbank',
                                      -fh => \*STDOUT );
           my $index_file_name = shift;
           my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);

           foreach my $id (@ARGV) {
               my $seq = $inx->fetch($id); # Returns a Bio::Seq object

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


       By default the index that is created uses the AC and ID identifiers as keys. This module
       inherits functions for managing dbm files from, and provides the
       basic functionality for indexing Swissprot files and retrieving Sequence objects 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 =~ /^KW\s+([A-Z]+)/i;


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       participation is much appreciated.
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       rather than to the module maintainer directly. Many experienced and reponsive experts will
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       of the problem with code and data examples if at all possible.

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AUTHOR - Ewan Birney

       Also, bosborne at


       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: Specialist function to index Swissprot 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 : ref to CODE if called without arguments
         Args    : CODE

         Title   : default_id_parser
         Usage   : $id = default_id_parser( $line )
         Function: The default parser for
                   Returns $1 from applying the regexp /^ID\s*(\S+)/
                   or /^AC\s+([A-Z0-9]+)/ to the current line.
         Returns : ID string
         Args    : a line string

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