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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Coil.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,290 @@
+# Parser module for Coil Bio::Tools::Coil
+#
+# Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
+# originally written by Marc Sohrmann ([e-mail])
+# Written in BioPipe by Balamurugan Kumarasamy <[e-mail]>
+# Cared for by the Fugu Informatics team ([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::Coil
+
+=head1 SYNOPSIS
+
+ use Bio::Tools::Coil
+ my $parser = new Bio::Tools::Coil();
+ while( my $sp_feat = $parser->next_result($file) ) {
+       #do something
+       #eg
+       push @sp_feat, $sp_feat;
+ }
+
+=head1 DESCRIPTION
+
+ Parser for Coil output
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+ User feedback is an integral part of the evolution of this and other
+ Bioperl modules. Send your comments and suggestions preferably to
+ the Bioperl mailing list.  Your participation is much appreciated.
+
+ [e-mail]              - General discussion
+ http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+ Report bugs to the Bioperl bug tracking system to help us keep track
+ of the bugs and their resolution. Bug reports can be submitted via
+ email or the web:
+
+ [e-mail]
+ http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+ Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
+ originally written by Marc Sohrmann ([e-mail])
+ Written in BioPipe by Balamurugan Kumarasamy <[e-mail]>
+ Cared for by the Fugu Informatics team ([e-mail])
+
+=head1 APPENDIX
+
+ The rest of the documentation details each of the object methods.
+ Internal methods are usually preceded with a _
+
+
+=cut
+
+package Bio::Tools::Coil;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::SeqFeature::FeaturePair;
+use Bio::Root::IO;
+use Bio::SeqFeature::Generic;
+@ISA = qw(Bio::Root::Root Bio::Root::IO);
+
+
+
+sub new {
+      my($class,@args) = @_;
+
+      my $self = $class->SUPER::new(@args);
+      $self->_initialize_io(@args);
+
+      return $self;
+}
+
+=head2 parse_results
+
+ Title   : parse_results
+ Usage   : obj->parse_results
+ Function: Parses the coil output. Automatically called by
+           next_result() if not yet done.
+ Example :
+ Returns :
+
+=cut
+
+sub parse_results {
+  my ($self,$resfile) = @_;
+        my $filehandle = $resfile;
+        my %result_hash =_read_fasta($filehandle);#bala no file handle
+        my @ids = keys %result_hash;
+        my @feats; 
+        foreach my $id (keys %result_hash){      
+                my $pep = reverse ($result_hash{$id});
+                my $count = my $switch = 0;
+                my ($start, $end);
+                while (my $aa = chop $pep) {
+                       $count++;
+                       if (!$switch && $aa eq "x") {
+                            $start = $count;
+                            $switch = 1;
+                        }
+                       elsif ($switch && $aa ne "x") {
+                            $end = $count-1;
+                            my (%feature);
+                            $feature{name}       = $id;
+                            $feature{start}      = $start;
+                            $feature{end}        = $end;
+                            $feature{source}     = "Coils";
+                            $feature{primary}    = 'ncoils';
+                           ($feature{program})   = 'ncoils';
+                            $feature{logic_name} = 'Coils';
+                            my $new_feat = $self->create_feature (\%feature);
+                            $self->_add_prediction($new_feat);
+                            $switch = 0;
+                       }
+                 }
+         }
+        
+        $self->_predictions_parsed(1);
+        
+}
+=head2 next_result
+
+ Title   : next_result
+ Usage   : while($feat = $coil->next_result($file)) {
+                  # do something
+           }
+ Function: Returns the next protein feature of the coil output file
+ Returns : 
+ Args    :
+
+=cut
+
+sub next_result{
+    
+    my ($self,$resfile) = @_;
+    my $gene;
+
+    $self->parse_results($resfile) unless $self->_predictions_parsed();
+
+    $gene = $self->_result();
+
+    return $gene;
+
+}
+
+=head2 _result
+
+ Title   : _result
+ Usage   : $feat = $obj->_result()
+ Function: internal
+ Example :
+ Returns :
+
+=cut
+
+sub _result{
+    my ($self) = @_;
+
+    return undef unless(exists($self->{'_feats'}) && @{$self->{'_feats'}});
+    return shift(@{$self->{'_feats'}});
+
+}
+
+=head2 _add_prediction
+
+ Title   : _add_prediction()
+ Usage   : $obj->_add_prediction($feat)
+ Function: internal
+ Example :
+ Returns :
+
+=cut
+
+sub _add_prediction {
+    my ($self, $gene) = @_;
+
+    if(! exists($self->{'_feats'})) {
+        $self->{'_feats'} = [];
+    }
+    push(@{$self->{'_feats'}}, $gene);
+}
+
+=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 $val;
+    if(! exists($self->{'_preds_parsed'})) {
+        $self->{'_preds_parsed'} = 0;
+    }
+    return $self->{'_preds_parsed'};
+}
+
+
+=head2 create_feature
+
+ Title   : create_feature
+ Usage   : obj->create_feature(\%feature)
+ Function: Internal(not to be used directly)
+ Returns :
+ Args    :
+
+
+=cut
+
+sub create_feature {
+       my ($self, $feat) = @_;
+
+
+       # create feature object
+       my $feature = Bio::SeqFeature::Generic->new(-seq_id     => $feat->{name},
+                                                 -start       => $feat->{start},
+                                                 -end         => $feat->{end},
+                                                 -score       => $feat->{score},
+                                                 -source      => $feat->{source},
+                                                 -primary     => $feat->{primary},
+                                                 -logic_name  => $feat->{logic_name}, 
+                                               );
+        $feature->add_tag_value('evalue',0);
+        $feature->add_tag_value('percent_id','NULL');
+        $feature->add_tag_value("hid",$feat->{primary});
+        
+        
+        return $feature;
+        
+}
+
+=head2 _read_fasta
+
+ Title   : _read_fasta
+ Usage   : obj->_read_fasta($file)
+ Function: Internal(not to be used directly)
+ Returns :
+ Args    :
+
+
+=cut
+
+sub _read_fasta {
+        local (*FILE) = @_;
+        my( $id , $seq , %name2seq);#bala
+        while (<FILE>) {
+       chomp;#bala
+             if (/^>(\S+)/) {
+              
+              my $new_id = $1;
+                    if ($id) {
+                           $name2seq{$id} = $seq;
+                    }
+                    $id = $new_id ; $seq = "" ;
+             }
+             elsif (eof) {
+                    if ($id) {
+                           $seq .= $_ ;#bala line instead of $_
+                           $name2seq{$id} = $seq;
+                    }
+             }
+             else {
+                     $seq .= $_
+             }
+        }
+                                                                                                                                                   return %name2seq;
+}
+
+
+
+1;
+
+