From 7fb67928e4eb16440945d0fcb06bdac9e5985ed6 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@illinois.edu>
Date: Sun, 22 Sep 2019 17:01:58 -0500
Subject: [PATCH] fix text wrapping with #321

---
 lib/Bio/SeqIO/genbank.pm | 15 ++++++++-------
 t/SeqIO/genbank.t        | 34 +++++++++++++++++++++++++++++++++-
 2 files changed, 41 insertions(+), 8 deletions(-)

diff --git a/lib/Bio/SeqIO/genbank.pm b/lib/Bio/SeqIO/genbank.pm
index 94663102e..dc56239eb 100644
--- a/lib/Bio/SeqIO/genbank.pm
+++ b/lib/Bio/SeqIO/genbank.pm
@@ -1303,18 +1303,19 @@ sub _print_GenBank_FTHelper {
 
                # If this breaks *NCBI* examples please file an issue with
                # example files
-                elsif (   not $FTQUAL_NO_QUOTE{$tag}
-
-                    ) {
-                    my ($pat) = ( $value =~ /\s/ ? '\s|$' : '.|$' );
+                elsif (   not $FTQUAL_NO_QUOTE{$tag} ) {
+                    my ($pat) = ( $value =~ /\s/ ? '\s|$' :
+                                  '.|$' );
                     $self->_write_line_GenBank_regex
                         ( " " x 21, " " x 21,
                           "/$tag=\"$value\"", $pat, 80 );
                 }
                 else {
+                    my ($pat) = ( $value =~ /[,]/ ? '[,]|$' :
+                                  '.|$' );
                     $self->_write_line_GenBank_regex
                         ( " " x 21, " " x 21,
-                          "/$tag=$value", "\.\|\$", 80 );
+                          "/$tag=$value", $pat, 80 );
                 }
             }
         }
@@ -1841,14 +1842,14 @@ sub _write_line_GenBank {
 sub _write_line_GenBank_regex {
     my ($self, $pre1, $pre2, $line, $regex, $length) = @_;
 
-    #print STDOUT "Going to print with $line!\n";
+    # print STDOUT "Going to print with $line!\n";
 
     $length or $self->throw("Miscalled write_line_GenBank without length. Programming error!");
 
     my $subl  = $length - (length $pre1) - 2;
     my @lines = ();
 
-  CHUNK:
+    CHUNK:
     while ($line) {
         foreach my $pat ($regex, '[,;\.\/-]\s|'.$regex, '[,;\.\/-]|'.$regex) {
             if ($line =~ m/^(.{0,$subl})($pat)(.*)/ ) {
diff --git a/t/SeqIO/genbank.t b/t/SeqIO/genbank.t
index 29a99cd6e..8f0af8cb7 100644
--- a/t/SeqIO/genbank.t
+++ b/t/SeqIO/genbank.t
@@ -4,7 +4,7 @@ use strict;
 
 BEGIN {
     use Bio::Root::Test;
-    test_begin(-tests => 304);
+    test_begin(-tests => 306);
     use_ok('Bio::SeqIO::genbank');
 }
 
@@ -718,3 +718,35 @@ like( $comment->as_text, qr/^Subtype :: H1N1/m,
     "Got correct Structured Comment");
 like( $comment->as_text, qr/^##GISAID_EpiFlu\(TM\)Data-END##/m,
     "Got correct Structured Comment" );
+
+# Issue #321 (github)
+
+{
+    # Create blank sequence
+    my $seq=Bio::Seq->new(-seq => 'N' x 1200000,
+                          -id  => 'abacab');
+    my $feature= Bio::SeqFeature::Generic->new(-primary=>'tRNA',
+        -start=>1123552, -end=>1123554);
+    my $text='(pos:complement(1123552..1123554),aa:Leu,seq:caa)';
+    $feature->add_tag_value(anticodon => $text);
+    $seq->add_SeqFeature($feature);
+
+    # Write genbank
+    my $string;
+    open my $str_fh, '>', \$string or skip("Could not write string, skipping", 2);
+    my $out = Bio::SeqIO->new(-format => 'genbank',
+                              -fh     => $str_fh,
+                              -verbose => -1);
+    $out->write_seq($seq);
+
+    like($string, qr/,$/m, 'unquoted labels wrap at comma');
+
+    # Read genbank
+    my $in = Bio::SeqIO->new(-format => 'genbank',
+                              -string => $string,
+                              -verbose => -1);
+    my $genbank = $in->next_seq;
+    my ($read_feature) = $genbank->get_SeqFeatures;
+    my ($read_text) = $read_feature->get_tag_values('anticodon');
+    is($read_text, $text, 'Label is the same');
+}
-- 
2.11.4.GIT