Raw content of Bio::Tools::Eponine # $Id: Eponine.pm,v 1.7 2002/10/22 07:38:45 lapp Exp $ # # BioPerl module for Bio::Tools::Eponine # # Cared for by Tania Oh <gisoht@nus.edu.sg> # # Copyright Tania Oh # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Eponine - Results of one Eponine run =head1 SYNOPSIS use Bio::Tools::Run::Eponine; use strict; my $seq = "/data/seq.fa"; my $threshold = "0.999"; my @params = ( '-seq' => $seq, '-threshold' => $threshold); my $factory = Bio::Tools::Run::Eponine->new(@params); # run eponine against fasta my $r = $factory->run_eponine($seq); my $parser = Bio::Tools::Eponine->new($r); while (my $feat = $parser->next_prediction){ #$feat contains array of SeqFeature foreach my $orf($feat) { print $orf->seq_id. "\n"; } } =head1 DESCRIPTION Parser for Eponine, a probabilistic transcription start site detector optimized for mammalian genomic sequence. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI (see L<Bio::Tools::AnalysisResult> and L<Bio::SeqAnalysisParserI>). =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Tania Oh Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Eponine; use vars qw(@ISA); use strict; use Bio::Tools::AnalysisResult; use Bio::Tools::Prediction::Gene; use Bio::Tools::Prediction::Exon; @ISA = qw(Bio::Tools::AnalysisResult); sub _initialize_state { my($self,@args) = @_; # first call the inherited method! my $make = $self->SUPER::_initialize_state(@args); # handle our own parameters # our private state variables $self->{'_preds_parsed'} = 0; #array of Bio::SeqFeatures $self->{'_flist'} =[]; } =head2 analysis_method Usage : $mzef->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /mzef/i. Returns : String Argument : n/a =cut #------------- sub analysis_method { #------------- my ($self, $method) = @_; if($method && ($method !~ /epo/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method); } =head2 next_feature Title : next_feature Usage : while($gene = $mzef->next_feature()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_feature { my ($self,@args) = @_; # even though next_prediction doesn't expect any args (and this method # does neither), we pass on args in order to be prepared if this changes # ever return $self->next_prediction(@args); } =head2 next_prediction Title : next_prediction Usage : while($gene = $mzef->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : =cut sub next_prediction { my ($self) = @_; my $gene; # if the prediction section hasn't been parsed yet, we do this now $self->_parse_predictions() unless $self->_predictions_parsed(); # return the next gene structure (transcript) return $self->_prediction(); } =head2 _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : =cut sub _parse_predictions { my ($self) = @_; while(defined($_ = $self->_readline())) { if (! /^\#/){ #ignore introductory lines my @element = split; my (%feature); $feature {name} = $element[0]; $feature {score} = $element[5]; $feature {start} = $element[3]; $feature {end} = $element[4]; $feature {strand} = $element[6]; $feature {source}= 'Eponine'; $feature {primary}= 'TSS'; $feature {program} = 'eponine-scan'; $feature {program_version} = '2'; $self->create_feature(\%feature); next; } } $self->_predictions_parsed(1); } =head2 create_feature Title : create_feature Usage : obj->create_feature($feature) Function: Returns an array of features Returns : Returns an array of features Args : none =cut sub create_feature { my ($self, $feat) = @_; #create and fill Bio::EnsEMBL::Seqfeature object my $tss = Bio::SeqFeature::Generic->new ( -seq_id => $feat->{'name'}, -start => $feat->{'start'}, -end => $feat->{'end'}, -strand => $feat->{'strand'}, -score => $feat->{'score'}, -source_tag => $feat->{'source'}, -primary_tag => $feat->{'primary'}); if ($tss) { # add to _flist push(@{$self->{'_flist'}}, $tss); } #print $tss->gff_string; } =head2 _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : =cut sub _prediction { my ($self) = @_; return undef unless(exists($self->{'_flist'}) && @{$self->{'_flist'}}); return shift(@{$self->{'_flist'}}); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; # array of pre-parsed predictions if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } 1;