ENSCORESW-140. Bringing edits back from HEAD to sort out the bug.

modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm

@@ -164,22 +164,17 @@ sub print_Seq {
         
     my $start = 1;
     my $end = $slice->length();
-    
-#    my $FORMAT = sprintf ("^%s
-#", ('<'x($width-1))  );
 
   #chunk the sequence to conserve memory, and print
   
   my $here = $start;
   
-  while($here < $end) {
+  while($here <= $end) {
     my $there = $here + $chunk_size - 1;
     $there = $end if($there > $end); 
     my $seq = $slice->subseq($here, $there);
     $seq =~ s/(.{1,$width})/$1\n/g;
     print $fh $seq;
-#    $self->formatted_write($FORMAT, $seq);
-    
     $here = $there + 1;
   }
   

modules/t/fastaSerializer.t

@@ -8,6 +8,7 @@ use IO::String;
 use Bio::EnsEMBL::Utils::IO::FASTASerializer;
 use Bio::EnsEMBL::Slice;
 use Bio::EnsEMBL::CoordSystem;
+use Bio::Seq;
 
 #
 # TEST - Slice creation from adaptor
@@ -77,7 +78,7 @@ $fh_Serializer->close;
   my $s = Bio::EnsEMBL::Slice->new(-SEQ_REGION_NAME => 'a', -COORD_SYSTEM => $coord_system, -SEQ => $seq, -SEQ_REGION_LENGTH => 120, -START => 1, -END => 120);
   my $header = sub { return 'a'; };
   my $io = IO::String->new();
-  my $ser = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($io, $header, 60, 20);
+  my $ser = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($io, $header, 6, 20);
   my $expected = <<'FASTA';
 >a
 AAAAAAAAAAAAAAAAAAAA
@@ -91,4 +92,31 @@ FASTA
   is(${$io->string_ref()}, $expected, 'Testing round number serialisation');
 }
 
+{
+  my $seq = 'A'x21;
+  my $s = Bio::EnsEMBL::Slice->new(-SEQ_REGION_NAME => 'a', -COORD_SYSTEM => $coord_system, -SEQ => $seq, -SEQ_REGION_LENGTH => 21, -START => 1, -END => 21);
+  my $header = sub { return 'a'; };
+  my $io = IO::String->new();
+  my $ser = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($io, $header, 1, 20);
+  my $expected = <<'FASTA';
+>a
+AAAAAAAAAAAAAAAAAAAA
+A
+FASTA
+  $ser->print_Seq($s);
+  is(${$io->string_ref()}, $expected, 'Testing odd (as in strange) number line length serialisation');
+}
+
+{
+  my $seq = Bio::Seq->new(-SEQ => 'M', -DISPLAY_ID => 'A');
+  my $io = IO::String->new();
+  my $ser = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($io);
+  my $expected = <<'FASTA';
+>A
+M
+FASTA
+  $ser->print_Seq($seq);
+  is(${$io->string_ref()}, $expected, 'Testing single base serialisation');
+}
+
 done_testing();
\ No newline at end of file