diff variant_effect_predictor/Bio/Tools/Phylo/Phylip/ProtDist.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Phylo/Phylip/ProtDist.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,143 @@
+# BioPerl module for Bio::Tools::Phylo::Phylip::ProtDist
+#
+# Cared for by Shawn Hoon <[e-mail]>
+#
+# Copyright Shawn Hoon
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Phylo::Phylip::ProtDist - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+    use Bio::Tools::Phylo::Phylip::ProtDist;
+    my $parser = new Bio::Tools::Phylo::Phylip::ProtDist(-file => 'outfile');
+    while( my $result = $parser->next_matrix) {
+
+    }
+
+=head1 DESCRIPTION
+
+A parser for ProtDist  output into a Bio::Matrix::PhylipDist 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
+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 - Shawn Hoon 
+
+Email [e-mail] 
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=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::Phylo::Phylip::ProtDist;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Matrix::PhylipDist;
+
+use Bio::Root::IO;
+
+@ISA = qw(Bio::Root::Root Bio::Root::IO );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Phylo::Phylip::ProtDist();
+ Function: Builds a new Bio::Tools::Phylo::Phylip::ProtDist object 
+ Returns : Bio::Tools::ProtDist
+ Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO
+
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  $self->_initialize_io(@args);
+
+  return $self;
+}
+
+=head2 next_result
+
+ Title   : next_result
+ Usage   : my $matrix = $parser->next_result
+ Function: Get the next result set from parser data
+ Returns : L<Bio::Matrix::PhylipDist>
+ Args    : none
+
+
+=cut
+
+sub next_matrix{
+   my ($self) = @_;
+   my @names;
+   my @values;
+   my $entry;
+   while ($entry=$self->_readline) {
+       if($#names >=0 && $entry =~/^\s+\d+$/){
+           last;
+       }
+       elsif($entry=~/^\s+\d+\n$/){
+           next;
+       }
+       my ($n,@line) = split( /\s+/,$entry);
+       push @names, $n;
+       push @values, [@line];
+    }
+    $#names>=0 || return;
+    my %dist;
+    my $i=0;
+    foreach my $name(@names){
+      my $j=0;
+      foreach my $n(@names) {
+        $dist{$name}{$n} = [$i,$j];
+        $j++;
+      }
+     $i++;
+    }
+    my $matrix = Bio::Matrix::PhylipDist->new(-matrix=>\%dist,
+                                              -names =>\@names,
+                                              -values=>\@values);
+    return $matrix;
+}
+
+1;