Bio::Index::SwissPfam - Interface for indexing swisspfam files use Bio::Index::SwissPfam; my $Index_File_Name = shift; my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name, '-write_flag' => 'WRITE'); $inx->make_index(@ARGV); use Bio::Index::SwissPfam; my $Index_File_Name = shift; my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns stream while( <$seq> ) { if(/^>/) { print; last; } } } SwissPfam is one of the flat files released with Pfam. This modules provides a way of indexing this module. Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing SwissPfam files. Only retrieves FileStreams at the moment. Once we have something better (ie, an object!), will use that. 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://bioperl.org/MailList.shtml - 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 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 swisspfam format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args :

fetch
Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID