From 91a236513db32d6d2ba0c1e4dc4afe0362430d31 Mon Sep 17 00:00:00 2001
From: igortru <itolstoy@gmail.com>
Date: Sun, 21 Apr 2024 22:45:11 -0400
Subject: [PATCH] Bio::Tools::CodonTable: add codon table 15 (#389)

The codon table 15 was removed in 7f52ed56 to address #256 (updating
CodonTable for current version which added codon tables 26-31 and
removed codon table 15).  However, it seems that codon table was added
back to NCBI.  This commit adds codon table #15 again.
---
 Changes                     | 5 +++--
 lib/Bio/Tools/CodonTable.pm | 6 +++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/Changes b/Changes
index 3a4680622f..1627f07ed9 100644
--- a/Changes
+++ b/Changes
@@ -6,13 +6,14 @@ Summary of important user-visible changes for BioPerl
       using SUPER::new() [#307].
     * Fix test for BSML SAX by using lax parser XML::SAX::PurePerl since
       the external DTD URL now 404s [#376].
+    * Added codon table 15 Bio::Tools::CodonTable [#389].
 
 1.7.8     2021-02-02 23:02:18-06:00 America/Chicago
     * Bio::SeqIO::interpro has been moved to a separate repository to
       deal with issues with XML::DOM::XPath bitrot [#347]
     * Pull requests:
       * Adjust Swiss-Prot FT A..B lines [#348] from @smoe
-      * Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from 
+      * Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
         @hdevillers
 
 1.7.7     2019-12-07 13:41:36-06:00 America/Chicago
@@ -27,7 +28,7 @@ Summary of important user-visible changes for BioPerl
       and a 'private' _sleep() function that mirror those from
       Bio::DB::WebDBSeqI, primarily for compliance with potential website
       restrictions for the number and frequency of queries (e.g. NCBI eUtils).
-      
+
     * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
       in last release.
 
diff --git a/lib/Bio/Tools/CodonTable.pm b/lib/Bio/Tools/CodonTable.pm
index 315c541d48..6eccb2fdd0 100644
--- a/lib/Bio/Tools/CodonTable.pm
+++ b/lib/Bio/Tools/CodonTable.pm
@@ -215,7 +215,7 @@ BEGIN {
      'Alternative Yeast Nuclear',# 12
      'Ascidian Mitochondrial',# 13
      'Alternative Flatworm Mitochondrial',# 14
-     '',
+     'Blepharisma Nuclear',#15
      'Chlorophycean Mitochondrial',# 16
      '', '',  '', '',
      'Trematode Mitochondrial',# 21
@@ -247,7 +247,7 @@ BEGIN {
        FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
        FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
        FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
-       ''
+       FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
        FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
        '' '' '' ''
        FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
@@ -284,7 +284,7 @@ BEGIN {
            ----------**--*----M---------------M----------------------------
            ---M------**----------------------MM---------------M------------
            -----------*-----------------------M----------------------------
-           ''
+           ---M------**--*----M------------MMMM---------------M------------
            ----------*---*--------------------M----------------------------
            '' ''  '' ''
            ----------**-----------------------M---------------M------------