diff variant_effect_predictor/Bio/Symbol/ProteinAlphabet.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Symbol/ProteinAlphabet.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,123 @@
+# $Id: ProteinAlphabet.pm,v 1.3 2002/10/22 07:45:21 lapp Exp $
+#
+# BioPerl module for Bio::Symbol::ProteinAlphabet
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
+
+=head1 SYNOPSIS
+
+    use Bio::Symbol::ProteinAlphabet;
+    my $alpha = new Bio::Symbol::ProteinAlphabet();
+    foreach my $symbol ( $alpha->symbols ) {
+	print "symbol is $symbol\n";
+    }
+
+=head1 DESCRIPTION
+
+This object builds an Alphabet with Protein symbols.
+
+=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 - Jason Stajich
+
+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::Symbol::ProteinAlphabet;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Symbol::Alphabet;
+use Bio::Symbol::Symbol;
+use Bio::Tools::IUPAC;
+use Bio::SeqUtils;
+
+@ISA = qw(Bio::Symbol::Alphabet);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Symbol::ProteinAlphabet();
+ Function: Builds a new Bio::Symbol::ProteinAlphabet object 
+ Returns : Bio::Symbol::ProteinAlphabet
+ Args    :
+
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);  
+  my %aa = Bio::SeqUtils->valid_aa(2);
+  my %codes = Bio::Tools::IUPAC->iupac_iup();
+  my %symbols;
+  my @left;
+  
+  foreach my $let ( keys %codes  ) {  
+      next if( $let eq 'U');
+      if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
+      $symbols{$let} = new Bio::Symbol::Symbol(-name => $aa{$let},
+					       -token => $let);      
+  }
+  foreach my $l ( @left ) {
+      my @subsym;
+      foreach my $sym ( @{$codes{$l}} ) {
+	  push @subsym, $symbols{$sym};
+      }
+      my $alpha = new Bio::Symbol::Alphabet(-symbols => \@subsym);
+      $symbols{$l} = new Bio::Symbol::Symbol(-name => $aa{$l},
+					       -token => $l,
+					       -matches => $alpha,
+					       -symbols => \@subsym);
+  }
+  
+  $self->symbols(values %symbols); 
+  return $self;
+}
+
+
+1;