Bio::Index::Swissprot - Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).


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

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

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

    my $out = Bio::SeqIO->new( '-format' => 'gcg', '-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 Bio::Seq object

    # alternatively

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


Inherits functions for managing dbm files from, and provides the basic funtionallity for indexing Swissprot files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system.


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AUTHOR - Ewan Birney

Email - (Swissprot adaption:


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