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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Genewise.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,294 @@
+# $Id: Genewise.pm,v 1.10 2002/12/18 01:54:51 jason Exp $
+#
+# BioPerl module for Bio::Tools::Genewise
+#
+# Copyright Fugu Team 
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Genewise - Results of one Genewise run
+
+=head1 SYNOPSIS
+
+  use Bio::Tools::Genewise;
+  my $gw = Bio::Tools::Genewise(-file=>"genewise.out");
+
+  while (my $gene = $gw->next_prediction){
+    my @transcripts = $gene->transcripts;
+      foreach my $t(@transcripts){
+        my @exons =  $t->exons;
+        foreach my $e(@exons){
+            print $e->start." ".$e->end."\n";
+        }
+      }
+  }
+
+=head1 DESCRIPTION
+
+This is the parser for the output of Genewise. It takes either a file handle or
+a file name and returns a Bio::SeqFeature::Gene::GeneStructure object.
+
+=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 - Fugu Team 
+
+ Email: [e-mail]
+
+=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::Genewise;
+use vars qw(@ISA $Srctag);
+use strict;
+use Symbol;
+
+use Bio::Root::Root;
+use Bio::Root::IO;
+use Bio::Tools::AnalysisResult;
+use Bio::SeqFeature::Generic;
+use Bio::SeqFeature::Gene::Exon;
+use Bio::SeqFeature::FeaturePair;
+use Bio::SeqFeature::Gene::Transcript;
+use Bio::SeqFeature::Gene::GeneStructure;
+
+@ISA = qw(Bio::Root::Root Bio::Root::IO);
+$Srctag = 'genewise';
+
+=head2 new
+
+ Title   : new
+ Usage   : $obj->new(-file=>"genewise.out");
+           $obj->new(-fh=>\*GW);
+ Function: Constructor for genewise wrapper. Takes either a file or filehandle
+ Example :
+ Returns : L<Bio::Tools::Genewise>
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);
+  $self->_initialize_io(@args);
+  return $self;
+}
+
+=head2 _get_strand
+
+ Title   : _get_strand
+ Usage   : $obj->_get_strand
+ Function: takes start and end values, swap them if start>end and returns end
+ Example :
+ Returns :$start,$end,$strand
+
+=cut
+
+sub _get_strand {
+  my ($self,$start,$end) = @_;
+  $start || $self->throw("Need a start");
+  $end   || $self->throw("Need an end");
+  my $strand;
+  if ($start > $end) {
+    my $tmp = $start;
+    $start = $end;
+    $end = $tmp;
+    $strand = -1;
+  }
+  else {
+    $strand = 1;
+  }
+  return ($start,$end,$strand);
+}
+
+=head2 score
+
+ Title   : score
+ Usage   : $obj->score
+ Function: get/set for score info
+ Example :
+ Returns : a score value
+
+=cut
+
+sub _score {
+  my ($self,$val) = @_;
+  if($val){
+    $self->{'_score'} = $val;
+  }
+  return $self->{'_score'};
+}
+
+=head2 _prot_id
+
+ Title   : _prot_id
+ Usage   : $obj->_prot_id
+ Function: get/set for protein id 
+ Example :
+ Returns :a protein id
+
+=cut
+
+sub _prot_id {
+  my ($self,$val) = @_;
+  if($val){
+    $self->{'_prot_id'} = $val;
+  }
+  return $self->{'_prot_id'};
+}
+
+=head2 _target_id
+
+ Title   : _target_id
+ Usage   : $obj->_target_id
+ Function: get/set for genomic sequence id
+ Example :
+ Returns :a target id
+
+=cut
+
+sub _target_id {
+  my ($self,$val) = @_;
+  if($val){
+    $self->{'_target_id'} = $val;
+  }
+  return $self->{'_target_id'};
+}
+
+
+=head2 next_prediction
+
+ Title   : next_prediction
+ Usage   : while($gene = $genewise->next_prediction()) {
+                  # do something
+           }
+ Function: Returns the gene structure prediction of the Genewise result
+           file. Call this method repeatedly until FALSE is returned.
+
+ Example :
+ Returns : a Bio::SeqFeature::Gene::GeneStructure object
+ Args    :
+
+=cut
+
+
+sub next_prediction {
+    my ($self) = @_;
+
+    my $genes = new Bio::SeqFeature::Gene::GeneStructure(-source => $Srctag);
+    my $transcript = new Bio::SeqFeature::Gene::Transcript(-source => $Srctag);
+
+    local ($/) = "//";
+    my $score;
+    my $prot_id;
+    my $target_id;
+    while ( defined($_ = $self->_readline) ) {
+	$self->debug( $_ ) if( $self->verbose > 0);
+        ($score) = $_=~m/Score\s+(\d+[\.][\d]+)/;
+        $self->_score($score) unless defined $self->_score;
+        ($prot_id) = $_=~m/Query protein:\s+(\S+)/;
+        $self->_prot_id($prot_id) unless defined $self->_prot_id;
+        ($target_id) = $_=~m/Target Sequence\s+(\S+)/;	
+        $self->_target_id($target_id) unless defined $self->_target_id;
+        next unless /Gene\s+\d+\n/;
+
+        #grab exon + supporting feature info
+        my @exons;
+	
+	unless ( @exons = $_ =~ m/(Exon .+\s+Supporting .+)/g ) {
+	    @exons = $_ =~ m/(Exon .+\s+)/g;
+
+	}
+        my $nbr = 1;
+
+        #loop through each exon-supporting feature pair
+        foreach my $e (@exons){
+	    my ($e_start,$e_end,$phase) = $e =~ m/Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/;
+	    my $e_strand;
+	    ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start,$e_end);
+	    $transcript->strand($e_strand) unless $transcript->strand != 0;
+	    
+	    my $exon = new Bio::SeqFeature::Gene::Exon
+		(-seq_id=>$self->_target_id,
+		 -source => $Srctag,
+		 -start=>$e_start, 
+		 -end=>$e_end, 
+		 #-frame => $phase,
+		 -strand=>$e_strand);
+	    $exon->add_tag_value('phase',$phase);
+	    if( $self->_prot_id ) {
+		$exon->add_tag_value('Sequence',"Protein:".$self->_prot_id);
+	    }
+	    $exon->add_tag_value("Exon",$nbr++);
+
+	    if( $e =~ m/Supporting\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/) {
+		my ($geno_start,$geno_end,
+		    $prot_start,
+		    $prot_end) = ($1,$2,$3,$4);
+          
+		my $prot_strand;
+		($prot_start,$prot_end,
+		 $prot_strand) = $self->_get_strand($prot_start,$prot_end);
+		
+		my $pf = new Bio::SeqFeature::Generic
+		    ( -start   => $prot_start,
+		      -end     => $prot_end,
+		      -seq_id  => $self->_prot_id,
+		      -score   => $self->_score,
+		      -strand  => $prot_strand,
+		      -source  => $Srctag,
+		      -primary=> 'supporting_protein_feature',
+		      );
+		my $geno_strand;
+		($geno_start,$geno_end,
+		 $geno_strand) = $self->_get_strand($geno_start,$geno_end);
+		my $gf = new Bio::SeqFeature::Generic
+		    ( -start   => $geno_start,
+		      -end     => $geno_end,
+		      -seq_id  => $self->_target_id,
+		      -score   => $self->_score,
+		      -strand  => $geno_strand,
+		      -source  => $Srctag,
+		      -primary => 'supporting_genomic_feature',
+		      );
+		my $fp = new Bio::SeqFeature::FeaturePair(-feature1=>$gf,
+							  -feature2=>$pf);
+	  
+		$exon->add_tag_value( 'supporting_feature' => $fp );
+	    }
+          $transcript->add_exon($exon);
+        }
+	$transcript->seq_id($self->_target_id);
+	$genes->add_transcript($transcript);
+	$genes->seq_id($self->_target_id);
+	return $genes;
+    }
+}
+1;