Raw content of Bio::Tools::Prints # $Id: Prints.pm,v 1.7 2002/10/22 07:45:22 lapp Exp $ # # BioPerl module for Bio::Tools::Prints # # Cared for by Balamurugan Kumarasamy # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code # =head1 NAME Bio::Tools::Prints - Parser for FingerPRINTScanII program =head1 SYNOPSIS use Bio::Tools::Prints; my $prints_parser = new Bio::Tools::Prints(-fh =>$filehandle ); while( my $prints_feat = $prints_parser->next_result ) { push @prints_feat, $prints_feat; } =head1 DESCRIPTION PRINTScan II is a PRINTS fingerprint identification algorithm. Copyright (C) 1998,1999 Phil Scordis =head1 FEEDBACK =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 the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Balamurugan Kumarasamy Email: fugui@worf.fugu-sg.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Prints; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::SeqFeature::FeaturePair; use Bio::Root::IO; use Bio::SeqFeature::Generic; @ISA = qw(Bio::Root::Root Bio::Root::IO ); =head2 new Title : new Usage : my $obj = new Bio::Tools::Prints(-fh=>$filehandle); Function: Builds a new Bio::Tools::Prints object Returns : Bio::Tools::Prints Args : -filename -fh (filehandle) =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $feat = $prints_parser->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::Generic> Args : none =cut sub next_result { my ($self) = @_; my %printsac; my @features; my $line; my $sequenceId; while ($_=$self->_readline()) { $line = $_; chomp $line; if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following: ($sequenceId) = $line =~ /^\s*(\w+)/; $self->seqname($sequenceId); next; } if ($line =~ s/^1TBH//) { my ($id) = $line =~ /^\s*(\w+)/; my ($ac) = $line =~ /(PR\w+)\s*$/; $printsac{$id} = $ac; $self->print_sac(\%printsac); next; } if ($line =~ s/^3TB//) { if ($line =~ s/^[HN]//) { my($num)=""; $line =~ s/^\s+//; my @elements = split /\s+/, $line; my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements; my $start = $matchPosition; my $end = $matchPosition + $motifLength - 1; my $print_sac = $self->print_sac; my %printsac = %{$print_sac}; my $print = $printsac{$fingerprintName}; my $seqname=$self->seqname; my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue"; my $new_feat = $self->create_feature($feat,$seqname); return $new_feat; } if ($line =~ s/^F//) { return; } next; } next; } } =head2 create_feature Title : create_feature Usage : my $feat=$prints_parser->create_feature($feature,$seqname) Function: creates a SeqFeature Generic object Returns : L<Bio::SeqFeature::Generic> Args : =cut sub create_feature { my ($self, $feat,$sequenceId) = @_; my @f = split (/,/,$feat); # create feature object my $feature= Bio::SeqFeature::Generic->new(-seq_id =>$sequenceId, -start=>$f[1], -end => $f[2], -score => $f[4], -source => "PRINTS", -primary =>$f[0], -logic_name => "PRINTS", ); $feature->add_tag_value('evalue',$f[5]); $feature->add_tag_value('percent_id',$f[3]); return $feature; } =head2 print_sac Title : print_sac Usage : $prints_parser->print_sac($print_sac) Function: get/set for print_sac Returns : Args : =cut sub print_sac{ my($self,$printsac)=@_; if(defined($printsac)) { $self->{'print_sac'}=$printsac; } return $self->{'print_sac'}; } =head2 seqname Title : seqname Usage : $prints_parser->seqname($seqname) Function: get/set for seqname Returns : Args : =cut sub seqname{ my($self,$seqname)=@_; if(defined($seqname)) { $self->{'seqname'}=$seqname; } return $self->{'seqname'}; } 1;