diff dir_plugins/Blosum62.pm @ 0:e545d0a25ffe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dir_plugins/Blosum62.pm	Mon Jul 15 05:17:17 2019 -0400
@@ -0,0 +1,125 @@
+=head1 LICENSE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2018] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=head1 CONTACT
+
+ Ensembl <http://www.ensembl.org/info/about/contact/index.html>
+    
+=cut
+
+=head1 NAME
+
+ Blosum62
+
+=head1 SYNOPSIS
+
+ mv Blosum62.pm ~/.vep/Plugins
+ ./vep -i variations.vcf --plugin Blosum62
+
+=head1 DESCRIPTION
+
+ This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
+ looks up the BLOSUM 62 substitution matrix score for the reference
+ and alternative amino acids predicted for a missense mutation. It adds
+ one new entry to the VEP's Extra column, BLOSUM62 which is the 
+ associated score. 
+
+=cut
+
+package Blosum62;
+
+use strict;
+use warnings;
+
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+my @BLOSUM_62 = qw(
+ 4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 
+-1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3
+-2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3
+-2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3
+ 0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
+-1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2
+-1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2
+ 0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 
+-2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3
+-1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3
+-1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1
+-1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2 
+-1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1
+-2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1
+-1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2
+ 1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2
+ 0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0
+-3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3
+-2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1
+ 0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4
+);
+
+my @AAs = qw(A R N D C Q E G H I L K M F P S T W Y V);
+
+sub new {
+    my $class = shift;
+
+    my $self = $class->SUPER::new(@_);
+
+    # construct a hash representing the matrix for quick lookups
+
+    my $num = @AAs;
+
+    for (my $i = 0; $i < $num; $i++) {
+        for (my $j = 0; $j < $num; $j++) {
+            $self->{matrix}->{$AAs[$i]}->{$AAs[$j]} = $BLOSUM_62[($i * $num) + $j];
+        }
+    }
+
+    return $self;
+}
+
+sub version {
+    return '2.3';
+}
+
+sub feature_types {
+    return ['Transcript'];
+}
+
+sub get_header_info {
+    return {
+        BLOSUM62 => "BLOSUM62 substitution score for the reference and alternative amino acids",
+    };
+}
+
+sub run {
+    my ($self, $tva) = @_;
+
+    if ($tva->pep_allele_string && $tva->pep_allele_string =~ /^([A-Z])\/([A-Z])$/) {
+        
+        my $score = $self->{matrix}->{$1}->{$2};
+        
+        if (defined $score) {
+            return {
+                BLOSUM62 => $score
+            };
+        }
+    }
+
+    return {};
+}
+
+1;
+