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; use strict; my $Index_File_Name = shift; my $inx = Bio::Index::Swissprot->new('-filename' => $Index_File_Name, '-write_flag' => 'WRITE'); $inx->make_index(@ARGV); # Print out several sequences present in the index # in gcg format use Bio::Index::Swissprot; use Bio::SeqIO; use strict; 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 $out->write_seq($seq); } # alternatively my ($id, $acc); my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc); Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing Swissprot files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system. Note: for best results 'use strict'. Details on configuration and additional example code are available in the biodatabases.pod file.

Mailing Lists
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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://bugzilla.bioperl.org/ Email - birney@sanger.ac.uk (Swissprot adaption: lorenz@ist.org) 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 Swissprot 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 :