Raw content of Bio::Index::Swissprot # # $Id: Swissprot.pm,v 1.11 2002/10/22 07:38:33 lapp Exp $ # # BioPerl module for Bio::Index::Abstract # # Cared for by Ewan Birney <birney@sanger.ac.uk> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Index::Swissprot - Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). =head1 SYNOPSIS # 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 $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc); =head1 DESCRIPTION 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'. =head1 FEED_BACK =head2 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 =head2 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/ =head1 AUTHOR - Ewan Birney Email - birney@sanger.ac.uk (Swissprot adaption: lorenz@ist.org) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let's begin the code... package Bio::Index::Swissprot; use vars qw($VERSION @ISA); use strict; use Bio::Index::AbstractSeq; use Bio::Seq; @ISA = qw(Bio::Index::AbstractSeq); sub _type_stamp { return '__Swissprot_FLAT__'; # What kind of index are we? } # # Suggested fix by Michael G Schwern <schwern@pobox.com> to # get around a clash with CPAN shell... # BEGIN { $VERSION = 0.1; } sub _version { return $VERSION; } =head2 _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 : =cut sub _index_file { my( $self, $file, # File name $i # Index-number of file being indexed ) = @_; my( $begin, # Offset from start of file of the start # of the last found record. $id, # ID of last found record. @accs, # accession of last record. Also put into the index ); $begin = 0; open SWISSPROT, $file or $self->throw("Can't open file for read : $file"); # Main indexing loop $id = undef; @accs = (); while (<SWISSPROT>) { if( /^\/\// ) { if( ! defined $id ) { $self->throw("Got to a end of entry line for an Swissprot flat file with no parsed ID. Considering this a problem!"); next; } if( ! @accs ) { $self->warn("For id [$id] in Swissprot flat file, got no accession number. Storing id index anyway"); } $self->add_record($id, $i, $begin); foreach my $acc (@accs) { if( $acc ne $id ) { $self->add_record($acc, $i, $begin); } } @accs = (); # reset acc array $id = undef; # reset id } elsif (/^ID\s+(\S+)/) { $id = $1; # not sure if I like this. Assummes tell is in bytes. # we could tell before each line and save it. $begin = tell(SWISSPROT) - length( $_ ); } elsif (/^AC(.*)/) { # ignore ? if there. push(@accs, ($1 =~ /\s*(\S+);/g)); } else { # do nothing } } close SWISSPROT; return 1; } =head2 _file_format Title : _file_format Usage : Internal function for indexing system Function: Provides file format for this database Example : Returns : Args : =cut sub _file_format{ my ($self,@args) = @_; return 'swiss'; } 1;