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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Genomewise.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,219 @@
+# $Id: Genomewise.pm,v 1.1.2.1 2003/03/25 12:32:16 heikki Exp $
+#
+# BioPerl module for Bio::Tools::Genomewise
+#
+# Copyright Jason Stajich <[e-mail]>
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Genomewise - Results of one Genomewise run
+
+=head1 SYNOPSIS
+
+  use Bio::Tools::Genomewise;
+  my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out");
+
+  while (my $gene = $gw->next_prediction){
+      my @transcripts = $gw->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.  You will need to specify
+the proper target sequence id on the object with the
+$feature-E<gt>seq_id($seqid).
+
+=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::Genomewise;
+use vars qw(@ISA $Srctag);
+use strict;
+
+use Bio::Tools::Genewise;
+use Bio::Tools::AnalysisResult;
+use Bio::SeqFeature::Generic;
+use Bio::SeqFeature::Gene::Exon;
+use Bio::SeqFeature::FeaturePair;
+use Bio::SeqFeature::Gene::Transcript;
+use Bio::SeqFeature::Gene::GeneStructure;
+
+@ISA = qw(Bio::Tools::Genewise);
+
+$Srctag = 'genomewise';
+
+=head2 new
+
+ Title   : new
+ Usage   : $obj->new(-file=>"genewise.out");
+           $obj->new(-fh=>\*GW);
+ Function: Constructor for genomewise wrapper. Takes either a file or filehandle
+ Example :
+ Returns : L<Bio::Tools::Genomewise>
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@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
+
+=head2 score
+
+ Title   : score
+ Usage   : $obj->score
+ Function: get/set for score info
+ Example :
+ Returns : a score value
+
+=cut
+
+=head2 _prot_id
+
+ Title   : _prot_id
+ Usage   : $obj->_prot_id
+ Function: get/set for protein id 
+ Example :
+ Returns :a protein id
+
+=cut
+
+=head2 _target_id
+
+ Title   : _target_id
+ Usage   : $obj->_target_id
+ Function: get/set for genomic sequence id
+ Example :
+ Returns :a target id
+
+=cut
+
+
+=head2 next_prediction
+
+ Title   : next_prediction
+ Usage   : while($gene = $genewise->next_prediction()) {
+                  # do something
+           }
+ Function: Returns the gene structure prediction of the Genomewise result
+           file. Call this method repeatedly until FALSE is returned.
+
+ Example :
+ Returns : a Bio::SeqFeature::Gene::GeneStructure object
+ Args    :
+
+=cut
+
+
+sub next_prediction {
+    my ($self) = @_;
+
+    my $genes;
+    while ($_ = $self->_readline) {
+	$self->debug( $_ ) if( $self->verbose > 0);
+	last if( /^\/\//);
+
+	if( /^Gene\s+\d+\s*$/ ) {
+	    $genes = new Bio::SeqFeature::Gene::GeneStructure
+		(-source => $Srctag,
+		 -seq_id => $self->_target_id, # if this had been specified
+		 );
+	    $_ = $self->_readline;
+	    $self->debug( $_ ) if( $self->verbose > 0);
+
+	    unless ( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) {
+		$self->warn("Unparseable genomewise output");
+		last;
+	    }
+	    my $transcript = new Bio::SeqFeature::Gene::Transcript
+		(-source => $Srctag,
+		 -seq_id => $self->_target_id, # if this had been specified
+		 -start  => $1,
+		 -end    => $2,
+		 );
+	    my $nbr = 1;
+	    while( $_ = $self->_readline ) {    
+		$self->debug( $_ ) if( $self->verbose > 0);
+
+		unless( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){
+		    $self->_pushback($_);
+		    last;
+		}
+		my ($e_start,$e_end,$phase,$e_strand) = ($1,$2,$3);
+		
+		($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);
+		$exon->add_tag_value("Exon",$nbr++);
+		$exon->add_tag_value('phase',$phase);
+		$transcript->add_exon($exon);
+	    }
+	    $genes->add_transcript($transcript);
+	    last; # only process a single gene at a time
+	}
+    }
+    return $genes;
+}
+1;