From 2576eaecdeb589fe4bcc06cf99fb2171a8352cc2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Carn=C3=AB=20Draug?= <carandraug+dev@gmail.com>
Date: Thu, 10 Dec 2015 09:41:42 +0000
Subject: [PATCH] pairwise_dnds: fix too low values of dn/ds due to zero values
 (issue #24)

When the sequences were the same, both dN and dS would be zero and dn/ds
ratio would be 99.  The 99 value would shift the mean dn/ds value which
would become too high.
---
 scripts/pairwise_dnds.pl | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/scripts/pairwise_dnds.pl b/scripts/pairwise_dnds.pl
index 92ba7e4..15c0951 100755
--- a/scripts/pairwise_dnds.pl
+++ b/scripts/pairwise_dnds.pl
@@ -115,8 +115,16 @@ sub get_dNdS_stats
     {
       for my $j (($i +1) .. ($n_seqs -1))
         {
-          push @{$stats->{'dN'}}, $MLmatrix->[$i]->[$j]->{'dN'};
-          push @{$stats->{'dS'}}, $MLmatrix->[$i]->[$j]->{'dS'};
+          my $dn = $MLmatrix->[$i]->[$j]->{'dN'};
+          my $ds = $MLmatrix->[$i]->[$j]->{'dS'};
+
+          ## Some sequences are exactly the same and will have a dN and
+          ## dS of zero, which then takes a dn/ds of 99.  This is all
+          ## non-sense so we just skip those cases.  See issue #23
+          next if $dn == 0 && $ds == 0;
+
+          push @{$stats->{'dN'}}, $dn;
+          push @{$stats->{'dS'}}, $ds;
           push @{$stats->{'omega'}}, $MLmatrix->[$i]->[$j]->{'omega'};
 #          say join("\t", $otus[$i]->display_id,
 #                         $otus[$j]->display_id,