diff variant_effect_predictor/Bio/Tools/Eponine.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Eponine.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,299 @@
+# $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 <[e-mail]>
+#
+# 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 $orf->seq_id. "\n";
+               }
+       }
+
+=head1 DESCRIPTION
+
+Parser for Eponine, a probabilistic transcription start site detector
+optimized for mammalian genomic sequence. This module inherits off
+Bio::Tools::AnalysisResult and therefore implements 
+Bio::SeqAnalysisParserI (see L<Bio::Tools::AnalysisResult> and
+L<Bio::SeqAnalysisParserI>).
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]          - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Tania Oh 
+
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::Eponine;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Tools::AnalysisResult;
+use Bio::Tools::Prediction::Gene;
+use Bio::Tools::Prediction::Exon;
+
+@ISA = qw(Bio::Tools::AnalysisResult);
+
+sub _initialize_state {
+    my($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;