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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Hmmpfam.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,215 @@
+#BioPerl module for Bio::Tools::Hmmpfam
+#
+# 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::Hmmpfam  
+
+=head1 SYNOPSIS
+
+  use Bio::Tools::Hmmpfam;
+  my $hmmpfam_parser = new Bio::Tools::Hmmpfam(-fh =>$filehandle );
+  while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) {
+        push @hmmpfam_feat, $hmmpfam_feat;
+  }
+
+=head1 DESCRIPTION
+
+ Parser for Hmmpfam  program
+
+=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::Hmmpfam;
+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 $obj = new Bio::Tools::Hmmpfam(-fh=>$filehandle);
+ Function: Builds a new Bio::Tools::Hmmpfam object
+ Returns : Bio::Tools::Hmmpfam
+ 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 = $hmmpfam_parser->next_result
+ Function: Get the next result set from parser data
+ Returns : L<Bio::SeqFeature::Generic>
+ Args    : none
+
+=cut
+
+sub next_result {
+    my ($self) = @_;
+    my $filehandle;
+    
+ my $line;
+
+    my $id;
+    while ($_=$self->_readline()) {
+         $line = $_;
+         chomp $line;
+    
+        
+        last if $line=~m/^Alignments of top-scoring domains/;
+        next if ($line=~m/^Model/ || /^\-/ || /^$/);
+        
+        if ($line=~m/^Query sequence:\s+(\S+)/) {
+           $id = $1;
+           $self->seqname($id);
+        }
+       
+       if (my ($hid, $start, $end, $hstart, $hend, $score, $evalue) = $line=~m/^(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)/) {
+            my %feature;
+            
+            ($feature{name}) = $self->seqname;
+            $feature{score} = $score;
+            $feature{p_value} = sprintf ("%.3e", $evalue);
+            $feature{start} = $start;
+            $feature{end} = $end;
+            $feature{hname} = $hid;
+            $feature{hstart} = $hstart;
+            $feature{hend} = $hend;
+            ($feature{source}) = 'pfam';
+            $feature{primary} = $hid;
+            ($feature{program}) = 'pfam';
+            ($feature{db}) = 'db1';
+            ($feature{logic_name}) = 'hmmpfam';
+            my $new_feat = $self->create_feature (\%feature);
+            return $new_feat
+        
+        }
+        next;
+
+    }
+    return;
+}
+
+=head2 create_feature
+
+ Title   : create_feature
+ Usage   : my $feat=$hmmpfam_parser->create_feature($feature,$seqname)
+ Function: creates a SeqFeature Generic object
+ Returns : L<Bio::SeqFeature::Generic>
+ Args    :
+
+
+=cut
+
+sub create_feature {
+    my ($self, $feat) = @_;
+
+
+
+    my $feature1= Bio::SeqFeature::Generic->new( -seqname    =>$feat->{name},
+                                                -start      =>$feat->{start},
+                                                -end        =>$feat->{end},
+                                                -score      =>$feat->{score},
+                                                -source     =>$feat->{source},
+                                                -primary    =>$feat->{primary},
+                                                   );
+    
+
+
+    my $feature2= Bio::SeqFeature::Generic->new(
+                                                 -start      =>$feat->{hstart},
+                                                 -end        =>$feat->{hend},
+                                                  );
+
+
+
+
+    my $featurepair = Bio::SeqFeature::FeaturePair->new;
+    $featurepair->feature1 ($feature1);
+    $featurepair->feature2 ($feature2);
+   
+   $featurepair->add_tag_value('evalue',$feat->{p_value});
+   $featurepair->add_tag_value('percent_id','NULL');
+   $featurepair->add_tag_value("hid",$feat->{primary});
+    return  $featurepair; 
+        
+}
+
+=head2 seqname
+
+ Title   :   seqname
+ Usage   :   obj->seqname($seqname)
+ Function:   Internal(not to be used directly)
+ Returns :
+ Args    :   seqname
+
+=cut
+
+sub seqname{
+    my($self,$seqname)=@_;
+
+    if(defined($seqname))
+    {
+        $self->{'seqname'}=$seqname;
+    }
+
+    return $self->{'seqname'};
+
+}
+
+1;
+
+