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'); $inx->make_index(@ARGV); # 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 $out->write_seq($seq); } # alternatively 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.

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://bio.perl.org/MailList.html - 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/ 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 :