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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Profile.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,169 @@
+# BioPerl module for Bio::Tools::Profile
+#
+# Cared for by Balamurugan Kumarasamy
+#
+# You may distribute this module under the same terms as perl itself
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Profile - parse Profile output
+
+=head1 SYNOPSIS
+
+ use Bio::Tools::Profile;
+ my $profile_parser = new Bio::Tools::Profile(-fh =>$filehandle );
+ while( my $profile_feat = $profile_parser->next_result ) {
+       push @profile_feat, $profile_feat;
+}
+
+=head1 DESCRIPTION
+
+ Parser for Profile 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 - Balamurugan Kumarasamy
+
+ Email: [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::Profile;
+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 );
+
+
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Profile();
+ Function: Builds a new Bio::Tools::Profile object
+ Returns : Bio::Tools::Profile
+ Args    : -filename
+           -fh ($filehandle)
+
+=cut
+
+sub new {
+    my($class,@args) = @_;
+
+    my $self = $class->SUPER::new(@args);
+    $self->_initialize_io(@args);
+
+    return $self;
+}
+
+=head2 next_result
+
+ Title   : next_result
+ Usage   : my $feat = $profile_parser->next_result
+ Function: Get the next result set from parser data
+ Returns : L<Bio::SeqFeature::FeaturePair>
+ Args    : none
+
+
+=cut
+
+sub next_result {
+        my ($self) = @_;
+
+        my %printsac;
+        my $line;
+        my @features;
+        while ($_=$self->_readline()) { 
+                $line = $_;
+                chomp $line;
+                my ($nscore,$rawscore,$from,$to,$hfrom,$hto,$ac) = $line =~ /(\S+)\s+(\d+)\s*pos.\s+(\d*)\s*-\s+(\d*)\s*\[\s+(\d*),\s+(\S*)\]\s*(\w+)/;
+                #for example in this output line 
+                #38.435   2559 pos.  19958 - 20212 [    1,    -1] PS50011|PROTEIN_KINASE_DOM Protein kinase domain profile.
+                #$nscore = 38.435
+                #$rawscore = 2559
+                #$from = 19958
+                #$end = 20212
+                #$hfrom = 1
+                #$hto =-1
+                #$ac = PS50011
+                my $feat = "$ac,$from,$to,$hfrom,$hto,$nscore";
+                my $new_feat= $self->create_feature($feat);
+                return $new_feat
+
+        } 
+}
+
+
+=head2 create_feature
+
+ Title   : create_feature
+ Usage   : my $feat= $profile_parser->create_feature($feature)
+ Function: creates a Bio::SeqFeature::FeaturePair object
+ Returns : L<Bio::SeqFeature::FeaturePair>
+ Args    :
+
+
+=cut
+
+sub create_feature {
+        my ($self, $feat) = @_;
+
+        my @f = split (/,/,$feat);
+
+
+        my $hto = $f[4];
+
+        if ($f[4] =~ /-1/) {
+ 
+           $hto = $f[2] - $f[1] + 1;
+        
+        }
+
+
+        my $feat1 = new Bio::SeqFeature::Generic ( -start => $f[1],
+                                                   -end => $f[2],
+                                                   -score => $f[5],
+                                                   -source=>'pfscan',
+                                                   -primary=>$f[0]);  
+        
+        my $feat2 = new Bio::SeqFeature::Generic (-start => $f[3],
+                                                  -end => $hto,
+                                                  );  
+
+        my $feature = new Bio::SeqFeature::FeaturePair(-feature1 => $feat1,
+                                                    -feature2 => $feat2);
+
+        return $feature;
+        
+}
+1;