dont align if sequences same length and nearly the same

dist.ini

@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.3.1
+version = 3.3.2
 author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute

lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm

@@ -27,6 +27,7 @@ has 'nucleotide_fasta_files' => ( is => 'rw', isa => 'ArrayRef' );
 has '_error_message'         => ( is => 'rw', isa => 'Str' );
 has 'verbose'                => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'mafft'                  => ( is => 'rw', isa => 'Bool', default => 0 );
+has '_min_similarity'        => ( is => 'rw', isa => 'Num',  default  => 0.98 );
 
 sub BUILD {
     my ($self) = @_;
@@ -76,7 +77,7 @@ sub run {
         );
         $sort_fasta_before->sort_fasta->replace_input_with_output_file;
 
-        if ( $sort_fasta_before->variation_detected == 1 ) {
+        if ( $sort_fasta_before->sequences_unaligned == 1  || $sort_fasta_before->sequences_unaligned == 0 && $sort_fasta_before->similarity <= $self->_min_similarity) {
 
             if ( $self->mafft == 1 ) {
                 my $mafft_obj = Bio::Roary::External::Mafft->new(

lib/Bio/Roary/SortFasta.pm

@@ -22,8 +22,8 @@ has 'input_filename'         => ( is => 'ro', isa => 'Str',  required => 1 );
 has 'output_filename'        => ( is => 'ro', isa => 'Str',  lazy     => 1, builder => '_build_output_filename' );
 has 'make_multiple_of_three' => ( is => 'ro', isa => 'Bool', default  => 0 );
 has 'remove_nnn_from_end'    => ( is => 'ro', isa => 'Bool', default  => 0 );
-has 'variation_detected'     => ( is => 'rw', isa => 'Bool', default  => 0 );
-
+has 'similarity'             => ( is => 'rw', isa => 'Num',  default  => 1 );
+has 'sequences_unaligned'    => ( is => 'rw', isa => 'Bool', default  => 0 );
 
 has '_input_seqio'  => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__input_seqio' );
 has '_output_seqio' => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__output_seqio' );
@@ -79,19 +79,23 @@ sub sort_fasta {
     while ( my $input_seq = $self->_input_seqio->next_seq() ) {
 		$sequence = $input_seq->seq if(!defined($sequence));
         $self->_add_padding_to_make_sequence_length_multiple_of_three($input_seq) if ( $self->make_multiple_of_three );
-
         $nnn_at_end_of_all_sequences = 0 if ( $nnn_at_end_of_all_sequences == 1 && !( $input_seq->seq() =~ /NNN$/i ) );
-
         $input_sequences{ $input_seq->display_id } = $input_seq;
-		if($sequence ne $input_seq->seq)
-		{
-			$self->variation_detected(1);
-		}
+
+		my $factor = $self->_percentage_similarity($sequence, $input_seq->seq);
+        if($factor < $self->similarity)
+        {
+            $self->similarity($factor);
+        }
     }
 
     $self->_remove_nnn_from_all_sequences( \%input_sequences ) if ( $self->remove_nnn_from_end && $nnn_at_end_of_all_sequences );
 
+    my $sequence_length = 0;
+    my $sequences_unaligned = 0;
     for my $sequence_name ( sort keys %input_sequences ) {
+        $sequence_length = $input_sequences{$sequence_name}->length if($sequence_length == 0);
+        $self->sequences_unaligned(1) if($input_sequences{$sequence_name}->length != $sequence_length);
         $self->_output_seqio->write_seq( $input_sequences{$sequence_name} );
     }
     return $self;
@@ -103,6 +107,20 @@ sub replace_input_with_output_file {
     return $self;
 }
 
+sub _percentage_similarity
+{
+    my ($self, $string1, $string2) = @_;
+    my $num_differences = 0;
+    my $string1_length = length($string1);
+    for(my $i = 0; $i < $string1_length && $i< length($string2); $i++)
+    {
+        $num_differences++ if( substr($string1, $i, 1) ne substr($string2, $i, 1));
+    }
+    return 1 if($num_differences == 0);
+    return 0 if($string1_length == 0);
+    return (1.0 - ($num_differences/$string1_length));
+}
+
 no Moose;
 __PACKAGE__->meta->make_immutable;
 

t/Bio/Roary/CommandLine/Roary.t

@@ -91,7 +91,7 @@ SKIP:
     );
 
     my @keys = keys %{ $seq_len->sequence_lengths };
-    is( $seq_len->sequence_lengths->{ $keys[0] }, 64932, 'length of first sequence' );
+    is( $seq_len->sequence_lengths->{ $keys[0] }, 64983, 'length of first sequence' );
 
     ok( -e 'accessory.tab' );
     ok( -e 'core_accessory.tab' );

t/Bio/Roary/SortFasta.t

@@ -2,7 +2,6 @@
 use strict;
 use warnings;
 use Data::Dumper;
-use File::Slurp::Tiny qw(read_file write_file);
 use Test::Files;
 
 BEGIN { unshift( @INC, './lib' ) }
@@ -24,7 +23,7 @@ ok( $obj = Bio::Roary::SortFasta->new(
 ok($obj->sort_fasta, 'sort the fasta file');
 ok(-e 't/data/out_of_order_fasta.fa.sorted.fa', 'the new file exists');
 
-is(read_file('t/data/out_of_order_fasta.fa.sorted.fa'), read_file('t/data/expected_out_of_order_fasta.fa.sorted.fa'), 'check order of sorted fasta');
+compare_ok('t/data/out_of_order_fasta.fa.sorted.fa', 't/data/expected_out_of_order_fasta.fa.sorted.fa', 'check order of sorted fasta');
 
 
 ok( $obj = Bio::Roary::SortFasta->new(
@@ -50,4 +49,10 @@ ok( $obj = Bio::Roary::SortFasta->new(
 ok($obj->sort_fasta, 'sort the fasta file');
 compare_ok($obj->output_filename, 't/data/expected_uneven_sequences.fa', "output sequences are now divisible by three and no nnn removed");
 
+
+is(0,$obj->_percentage_similarity("AAA","BBB"), 'totally different');
+is(1,$obj->_percentage_similarity("AAA","AAA"), 'all the same');
+is(0.5,$obj->_percentage_similarity("AAAA","AABB"), 'half different');
+is(1,$obj->_percentage_similarity("AAAA","AAAABB"), 'first half the same');
+
 done_testing();

t/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln

@@ -12,7 +12,7 @@ GCTAAAAGATATTTGAATAATTTTATTGAAGCTTTAGAAGAGAGAATAGACCTAGAAAAA
 GCTAAATTATTTAAAGAAAAAGACGTGTTAAACTATTTAAAAGAAAATAAAGAATTAAGA
 GTTAAGTTAAAAAACATATTAGATAAAGAACTTGTTCATATTAAACAACATCGTCCAGAT
 ATAGTAGCTTCTTGGAAATACTATCAAGAATTTGAACAAATGTGCAAGGAGTTGAATGGT
-AATATT
+AATATTTAG
 >query_2
 ATGAATCTACCTTTACCTGATAATTATGAATTTGTGTTTTTATCTGGTGGATTATCTGGG
 CATGCTGCAATGATGTCATTTTTTAATGTTTGTGGCATTGGATATTTGTATCATCATATG
@@ -27,7 +27,7 @@ GCTAAAAGATATTTGAATAATTTTATTGAAGCTTTAGAAGAGAGAATAGACCTAGAAAAA
 GCTAAATTATTTAAAGAAAAAGACGTGTTAAACTATTTAAAAGAAAATAAAGAATTAAGA
 GTTAAGTTAAAAAACATATTAGATAAAGAACTTGTTCATATTAAACAACATCGTCCAGAT
 ATAGTAGCTTCTTGGAAATACTATCAAGAATTTGAACAAATGTGCAAGGAGTTGAATGGT
-AATATT
+AATATTTAG
 >query_3
 ATGAATCTACCTTTACCTGATAATTATGAATTTGTGTTTTTATCTGGTGGATTATCTGGG
 CATGCTGCAATGATGTCATTTTTTAATGTTTGTGGCATTGGATATTTGTATCATCATATG
@@ -42,4 +42,4 @@ GCTAAAAGATATTTGAATAATTTTATTGAAGCTTTAGAAGAGAGAATAGACCTAGAAAAA
 GCTAAATTATTTAAAGAAAAAGACGTGTTAAACTATTTAAAAGAAAATAAAGAATTAAGA
 GTTAAGTTAAAAAACATATTAGATAAAGAACTTGTTCATATTAAACAACATCGTCCAGAT
 ATAGTAGCTTCTTGGAAATACTATCAAGAATTTGAACAAATGTGCAAGGAGTTGAATGGT
-AATATT
+AATATTTAG

t/data/mdoH.fa.aln

@@ -41,7 +41,7 @@ ACCGCGATGGCCACCGCGCGTCACCGCGCCAGTAAGGTGCTGGAAATAGCCCGCGATCGT
 CATGTGGAGCAGGCGCTAAACGAAACGCCGGAGAAACTGAACCGCGATCGGCGTCTGGTT
 TTGCTCAGCGATCCGGTGACGATGGCGCGTTTACACTATCGGGTCTGGAATGCGCCAGAG
 AGATACTCTTCCTGGGTAAACCATTATCAGTCTCTCGTCCTGAATCCGCAGGCGTTGCAG
-GGACGAACATCGTCAGCGGGA
+GGACGAACATCGTCAGCGGGATAA
 >22222_2#22_04119
 ATGAATAAAACAACTGAGTATATTGACGCACTGCTGCTTTCTGAACGTGAGAAAGCGGCA
 TTGCCGAAAACTGACATCCGCGCCGTGCATCAGGCGCTGGATGCCGAGCATCGGACTTAC
@@ -85,4 +85,4 @@ ACCGCGATGGCCACCGCGCGTCACCGCGCCAGTAAGGTGCTGGAAATAGCCCGCGATCGT
 CATGTGGAGCAGGCGCTAAACGAAACGCCGGATAAACTGAACCGCGATCGGCGTCTGGTT
 TTGCTCAGCGATCCGGTGACGATGGCGCGTTTTCACTATCGGGTCTGGAATGCGCCAGAG
 AGATACTCTTCCTGGGTAAACCATTATCAGTCTCTCGTCCTGAATCCGCAGGCGTTGCAG
-GGACGAACATCGTCAGCGGGA
+GGACGAACATCGTCAGCGGGATAA

t/data/mdoH_mafft.fa.aln

@@ -1,88 +1,88 @@
 >11111_1#11_04119
-atgaataaaacaactgagtatattgacgcactgctgctttctgaacgtgagaaagcggca
-ttgccgaaaactgacatccgcgccgtgcatcaggcgctggatgccgagcatcggacttac
-tcgcgagaagacgattcaccgcagggttccgtaaaagcccgccttgaacacgcctggccg
-gattcattggcgaaggggcagttaattaaagatgatgaagggcgcgatcagttgcaggct
-atgccaaaagcgacgcgctcttcgatgtttcctgatccctggcgaaccaacccggttggc
-cgtttctgggatcgcctgcgtgggcgggatgtaacgccgcgctatgtttctcgtctgaca
-aaagaagagcaggcgagtgagcaaaaatggcgtaccgtcggcactatacgccgctatatt
-ttgttaattttgactctggcgcaaaccgtcgtcgcgacctggtatatgaagaccattctg
-ccctatcagggatgggcgctcatcaatcctatggatatggtggggcaggatatttgggtc
-tcctttatgcagctcctgccctacatgctgcaaaccggtatcctgattttgtttgccgtg
-ctgttctgctgggtgtctgccggattctggacggcgctgatgggcttcctgcaactgctt
-atcgggcgcgataagtacagtatctccgcgtctacggttggcgatgagcccctcaatccg
-gaacaccagacggcgctgatcatgcctatctgtaatgaagacgttagccgcgttttcgcc
-ggtctgcgcgcgacctgggagtccgttaaagccacaggcaacgccgcgcattttgacgtc
-tatatccttagcgatagttataacccggatatctgcgtggcggagcaaaaggcgtggatg
-gagctcatcgcggaagtgcagggcgaaggccaaattttttaccgtcgccgccgccgccgt
-atgaaacgcaaaagcggcaatattgacgatttttgccgccgctggggcaatcagtacagc
-tatatggtggtgctggacgcggactcagtgatgagcggcgagtgtctgagcgggctggtg
-cgcctgatggaagcgaaccctaacgccgggattatccagtcttcgccgaaagcgtcgggg
-atggatactctgtatgcccgctgccaacagttcgcgacccgtgtttatggaccgctgttt
-accgccgggctgcacttctggcagttgggggagtcgcactactgggggcacaatgccatt
-atccgcgtgaagccgtttatcgagcactgcgctctggcgccgctgccgggagaaggttcg
-ttcgccggatcgattctttcccacgactttgtggaggcggcgctaatgcgtcgggcaggg
-tggggcgtctggattgcctacgatctccccggctcctatgaagagctgccgccaaacctg
-ctggatgagcttaaacgcgaccgccgctggtgtcacggcaacctgatgaactttcgtctg
-ttcctggtgaaaggaatgcacccggtgcatcgcgccgtgttcctgaccggggtaatgtca
-tacctgtccgcgccgttatggtttatgttcctcgcgctttctaccgcgctgcaggtcgtt
-catgcgttaacagagccgcaatatttccttcagccgcgccagctttttccggtctggccg
-cagtggcgtccggaactggcaatcgcgctgtttgcgtcaacgatggtgctgctgttcctg
-ccgaagctgctcagtattatgctgatctggtgtaaaggcaccaaagagtatggcggtttc
-tggcgcgttacgctgtcgctattgctggaagtgctgttctccgtgttgctggcgccggtg
-cgtatgctgtttcataccgtgtttgtggtcagcgcgttcctcggctgggaagtggtctgg
-aactcaccgcaacgcgacgatgattctacgccgtggggagaagcctttatgcgtcacggc
-tctcaactgctgctggggctggtctgggcggtgggtatggcgtggctggatttacgcttt
-ctgttctggctggcgccgattgtcttttcgctgattctgtcgccatttgtttcggtgatc
-tccagtcgttcaacggtaggattacgcaccaaacgctggaagctgttcctgatcccggaa
-gagtattcgccgcctcaggtgttggtcgataccgataaatatctggagatgaatcgccgc
-cgtattctggacgatggctttatgcatgcggtatttaacccgtcgcttaatgcgctggcg
-accgcgatggccaccgcgcgtcaccgcgccagtaaggtgctggaaatagcccgcgatcgt
-catgtggagcaggcgctaaacgaaacgccggagaaactgaaccgcgatcggcgtctggtt
-ttgctcagcgatccggtgacgatggcgcgtttacactatcgggtctggaatgcgccagag
-agatactcttcctgggtaaaccattatcagtctctcgtcctgaatccgcaggcgttgcag
-ggacgaacatcgtcagcgggataa
+ATGAATAAAACAACTGAGTATATTGACGCACTGCTGCTTTCTGAACGTGAGAAAGCGGCA
+TTGCCGAAAACTGACATCCGCGCCGTGCATCAGGCGCTGGATGCCGAGCATCGGACTTAC
+TCGCGAGAAGACGATTCACCGCAGGGTTCCGTAAAAGCCCGCCTTGAACACGCCTGGCCG
+GATTCATTGGCGAAGGGGCAGTTAATTAAAGATGATGAAGGGCGCGATCAGTTGCAGGCT
+ATGCCAAAAGCGACGCGCTCTTCGATGTTTCCTGATCCCTGGCGAACCAACCCGGTTGGC
+CGTTTCTGGGATCGCCTGCGTGGGCGGGATGTAACGCCGCGCTATGTTTCTCGTCTGACA
+AAAGAAGAGCAGGCGAGTGAGCAAAAATGGCGTACCGTCGGCACTATACGCCGCTATATT
+TTGTTAATTTTGACTCTGGCGCAAACCGTCGTCGCGACCTGGTATATGAAGACCATTCTG
+CCCTATCAGGGATGGGCGCTCATCAATCCTATGGATATGGTGGGGCAGGATATTTGGGTC
+TCCTTTATGCAGCTCCTGCCCTACATGCTGCAAACCGGTATCCTGATTTTGTTTGCCGTG
+CTGTTCTGCTGGGTGTCTGCCGGATTCTGGACGGCGCTGATGGGCTTCCTGCAACTGCTT
+ATCGGGCGCGATAAGTACAGTATCTCCGCGTCTACGGTTGGCGATGAGCCCCTCAATCCG
+GAACACCAGACGGCGCTGATCATGCCTATCTGTAATGAAGACGTTAGCCGCGTTTTCGCC
+GGTCTGCGCGCGACCTGGGAGTCCGTTAAAGCCACAGGCAACGCCGCGCATTTTGACGTC
+TATATCCTTAGCGATAGTTATAACCCGGATATCTGCGTGGCGGAGCAAAAGGCGTGGATG
+GAGCTCATCGCGGAAGTGCAGGGCGAAGGCCAAATTTTTTACCGTCGCCGCCGCCGCCGT
+ATGAAACGCAAAAGCGGCAATATTGACGATTTTTGCCGCCGCTGGGGCAATCAGTACAGC
+TATATGGTGGTGCTGGACGCGGACTCAGTGATGAGCGGCGAGTGTCTGAGCGGGCTGGTG
+CGCCTGATGGAAGCGAACCCTAACGCCGGGATTATCCAGTCTTCGCCGAAAGCGTCGGGG
+ATGGATACTCTGTATGCCCGCTGCCAACAGTTCGCGACCCGTGTTTATGGACCGCTGTTT
+ACCGCCGGGCTGCACTTCTGGCAGTTGGGGGAGTCGCACTACTGGGGGCACAATGCCATT
+ATCCGCGTGAAGCCGTTTATCGAGCACTGCGCTCTGGCGCCGCTGCCGGGAGAAGGTTCG
+TTCGCCGGATCGATTCTTTCCCACGACTTTGTGGAGGCGGCGCTAATGCGTCGGGCAGGG
+TGGGGCGTCTGGATTGCCTACGATCTCCCCGGCTCCTATGAAGAGCTGCCGCCAAACCTG
+CTGGATGAGCTTAAACGCGACCGCCGCTGGTGTCACGGCAACCTGATGAACTTTCGTCTG
+TTCCTGGTGAAAGGAATGCACCCGGTGCATCGCGCCGTGTTCCTGACCGGGGTAATGTCA
+TACCTGTCCGCGCCGTTATGGTTTATGTTCCTCGCGCTTTCTACCGCGCTGCAGGTCGTT
+CATGCGTTAACAGAGCCGCAATATTTCCTTCAGCCGCGCCAGCTTTTTCCGGTCTGGCCG
+CAGTGGCGTCCGGAACTGGCAATCGCGCTGTTTGCGTCAACGATGGTGCTGCTGTTCCTG
+CCGAAGCTGCTCAGTATTATGCTGATCTGGTGTAAAGGCACCAAAGAGTATGGCGGTTTC
+TGGCGCGTTACGCTGTCGCTATTGCTGGAAGTGCTGTTCTCCGTGTTGCTGGCGCCGGTG
+CGTATGCTGTTTCATACCGTGTTTGTGGTCAGCGCGTTCCTCGGCTGGGAAGTGGTCTGG
+AACTCACCGCAACGCGACGATGATTCTACGCCGTGGGGAGAAGCCTTTATGCGTCACGGC
+TCTCAACTGCTGCTGGGGCTGGTCTGGGCGGTGGGTATGGCGTGGCTGGATTTACGCTTT
+CTGTTCTGGCTGGCGCCGATTGTCTTTTCGCTGATTCTGTCGCCATTTGTTTCGGTGATC
+TCCAGTCGTTCAACGGTAGGATTACGCACCAAACGCTGGAAGCTGTTCCTGATCCCGGAA
+GAGTATTCGCCGCCTCAGGTGTTGGTCGATACCGATAAATATCTGGAGATGAATCGCCGC
+CGTATTCTGGACGATGGCTTTATGCATGCGGTATTTAACCCGTCGCTTAATGCGCTGGCG
+ACCGCGATGGCCACCGCGCGTCACCGCGCCAGTAAGGTGCTGGAAATAGCCCGCGATCGT
+CATGTGGAGCAGGCGCTAAACGAAACGCCGGAGAAACTGAACCGCGATCGGCGTCTGGTT
+TTGCTCAGCGATCCGGTGACGATGGCGCGTTTACACTATCGGGTCTGGAATGCGCCAGAG
+AGATACTCTTCCTGGGTAAACCATTATCAGTCTCTCGTCCTGAATCCGCAGGCGTTGCAG
+GGACGAACATCGTCAGCGGGATAA
 >22222_2#22_04119
-atgaataaaacaactgagtatattgacgcactgctgctttctgaacgtgagaaagcggca
-ttgccgaaaactgacatccgcgccgtgcatcaggcgctggatgccgagcatcggacttac
-tcgcgagaagacgattcaccgcagggttccgtaaaagcccgccttgaacacgcctggccg
-gattcattggcgaaggggcagttaattaaagatgatgaagggcgcgatcagttgcaggct
-atgccaaaagcgacgcgctcttcgatgtttcctgatccctggcgaaccaacccggttggc
-cgtttctgggatcgcctgcgtgggcgggatgttacgccgcgctatgtttctcgtctgaca
-aaagaagagcaggcgagtgagcaaaaatggcgtaccgtcggcactatacgccgctatatt
-ttgttaattttgactctggcgcaaaccgtcgttgcgacctggtatatgaagaccattctg
-ccctatcagggatgggcgctcatcaatcctattgatatggtggggcaggatatttgggtc
-tcctttatgcagctcctgccctacatgctgcataccggtatcctgattttgtttgccgtg
-ctgttctgctgggtgtctgccggattctggactgcgctgatgggcttcctgcaactgctt
-atcgggcgcgataagtacagtatctccgcgtctacggttggcgatgagcccctcaatccg
-gaacaccagacggcgctgatcatgcctatctgtaatgaagacgttagccgcgttttcgcc
-ggtctgcgcgcgacctgggagtccgttaaagctacaggcaacgccgcgcattttgacgtc
-tatatccttagcgatagttataacccggatatttgcgtggcggagcaaaaggcgtggatg
-gagctcatcgcggaagtgcagggcgaaggccatattttttaccgtcgccgccgccgccgt
-atgaaacgcaaaagcggcaatattgacgatttttgccgccgctggggcaatcagtacagc
-tatatggtggtgctggacgcggactcagtgattagcggcgagtgtctgagcgggctggtg
-cgcctgatggaagcgaaccctaacgccgggattatccagtcttcgccgaaagcgtcgggg
-atggatactctgtatgcccgctgccaacagtttgcgacccgtgtttatggaccgctgttt
-accgccgggctgcacttctggcagttgggggattcgcactactgggggcacaatgccatt
-atccgcgtgaagccgtttatcgagcactgcgctctggcgccgctgccgggagaaggttcg
-ttcgccggatcgattctttcccacgactttgttgaggcggcgctaatgcgtcgggcaggg
-tggggcgtctggattgcctacgatctccccggttcctatgaagagctgccgccaaacctg
-ctggatgagcttaaacgcgaccgccgctggtgtcacggcaacctgatgaactttcgtctg
-ttcctggtgaaaggaatgcacccggtgcatcgtgccgtgttcctgaccggggtaatgtca
-tacctgtccgcgccgttatggtttatgttccttgcgctttctaccgcgctgcaggtcgtt
-catgcgttaacagagccgcaatatttccttcatccgcgccagctttttccggtctggccg
-cagtggcgtccggaactggcaatcgcgctgtttgcgtcaacgatggtgctgctgttcctg
-ccgaagctgctcagtattatgctgatctggtgtaaaggcaccaaagagtatggcggtttc
-tggcgcgttacgctgtcgctattgctggaagttctgttctccgtgttgctggcgccggtg
-cgtatgctgtttcataccgtgtttgtggtcagtgcgttcctcggctgggaagtggtctgg
-aactcaccgcaacgcgacgatgattctacgccttggggagaagcctttatgcgtcacggc
-tctcaactgctgctggggctggtctgggcggttggtatggcgtggctggatttacgcttt
-ctgttctggctggcgccgattgtcttttcgcttattctgtcgccatttgtttcggtgatc
-tccagtcgttcaacggtaggattacgcaccaatcgctggaagctgttcctgatcccggaa
-gagtattcgccgcctcaggtgttggtcgatactgataaatatctggagatgaatcgccgc
-cgtattctggacgatggctttatgcatgcggtttttaacccgtcgcttaatgcgctggcg
-accgcgatggccaccgcgcgtcaccgcgccagtaaggtgctggaaatagcccgcgatcgt
-catgtggagcaggcgctaaacgaaacgccggataaactgaaccgcgatcggcgtctggtt
-ttgctcagcgatccggtgacgatggcgcgttttcactatcgggtctggaatgcgccagag
-agatactcttcctgggtaaaccattatcagtctctcgtcctgaatccgcaggcgttgcag
-ggacgaacatcgtcagcgggataa
+ATGAATAAAACAACTGAGTATATTGACGCACTGCTGCTTTCTGAACGTGAGAAAGCGGCA
+TTGCCGAAAACTGACATCCGCGCCGTGCATCAGGCGCTGGATGCCGAGCATCGGACTTAC
+TCGCGAGAAGACGATTCACCGCAGGGTTCCGTAAAAGCCCGCCTTGAACACGCCTGGCCG
+GATTCATTGGCGAAGGGGCAGTTAATTAAAGATGATGAAGGGCGCGATCAGTTGCAGGCT
+ATGCCAAAAGCGACGCGCTCTTCGATGTTTCCTGATCCCTGGCGAACCAACCCGGTTGGC
+CGTTTCTGGGATCGCCTGCGTGGGCGGGATGTTACGCCGCGCTATGTTTCTCGTCTGACA
+AAAGAAGAGCAGGCGAGTGAGCAAAAATGGCGTACCGTCGGCACTATACGCCGCTATATT
+TTGTTAATTTTGACTCTGGCGCAAACCGTCGTTGCGACCTGGTATATGAAGACCATTCTG
+CCCTATCAGGGATGGGCGCTCATCAATCCTATTGATATGGTGGGGCAGGATATTTGGGTC
+TCCTTTATGCAGCTCCTGCCCTACATGCTGCATACCGGTATCCTGATTTTGTTTGCCGTG
+CTGTTCTGCTGGGTGTCTGCCGGATTCTGGACTGCGCTGATGGGCTTCCTGCAACTGCTT
+ATCGGGCGCGATAAGTACAGTATCTCCGCGTCTACGGTTGGCGATGAGCCCCTCAATCCG
+GAACACCAGACGGCGCTGATCATGCCTATCTGTAATGAAGACGTTAGCCGCGTTTTCGCC
+GGTCTGCGCGCGACCTGGGAGTCCGTTAAAGCTACAGGCAACGCCGCGCATTTTGACGTC
+TATATCCTTAGCGATAGTTATAACCCGGATATTTGCGTGGCGGAGCAAAAGGCGTGGATG
+GAGCTCATCGCGGAAGTGCAGGGCGAAGGCCATATTTTTTACCGTCGCCGCCGCCGCCGT
+ATGAAACGCAAAAGCGGCAATATTGACGATTTTTGCCGCCGCTGGGGCAATCAGTACAGC
+TATATGGTGGTGCTGGACGCGGACTCAGTGATTAGCGGCGAGTGTCTGAGCGGGCTGGTG
+CGCCTGATGGAAGCGAACCCTAACGCCGGGATTATCCAGTCTTCGCCGAAAGCGTCGGGG
+ATGGATACTCTGTATGCCCGCTGCCAACAGTTTGCGACCCGTGTTTATGGACCGCTGTTT
+ACCGCCGGGCTGCACTTCTGGCAGTTGGGGGATTCGCACTACTGGGGGCACAATGCCATT
+ATCCGCGTGAAGCCGTTTATCGAGCACTGCGCTCTGGCGCCGCTGCCGGGAGAAGGTTCG
+TTCGCCGGATCGATTCTTTCCCACGACTTTGTTGAGGCGGCGCTAATGCGTCGGGCAGGG
+TGGGGCGTCTGGATTGCCTACGATCTCCCCGGTTCCTATGAAGAGCTGCCGCCAAACCTG
+CTGGATGAGCTTAAACGCGACCGCCGCTGGTGTCACGGCAACCTGATGAACTTTCGTCTG
+TTCCTGGTGAAAGGAATGCACCCGGTGCATCGTGCCGTGTTCCTGACCGGGGTAATGTCA
+TACCTGTCCGCGCCGTTATGGTTTATGTTCCTTGCGCTTTCTACCGCGCTGCAGGTCGTT
+CATGCGTTAACAGAGCCGCAATATTTCCTTCATCCGCGCCAGCTTTTTCCGGTCTGGCCG
+CAGTGGCGTCCGGAACTGGCAATCGCGCTGTTTGCGTCAACGATGGTGCTGCTGTTCCTG
+CCGAAGCTGCTCAGTATTATGCTGATCTGGTGTAAAGGCACCAAAGAGTATGGCGGTTTC
+TGGCGCGTTACGCTGTCGCTATTGCTGGAAGTTCTGTTCTCCGTGTTGCTGGCGCCGGTG
+CGTATGCTGTTTCATACCGTGTTTGTGGTCAGTGCGTTCCTCGGCTGGGAAGTGGTCTGG
+AACTCACCGCAACGCGACGATGATTCTACGCCTTGGGGAGAAGCCTTTATGCGTCACGGC
+TCTCAACTGCTGCTGGGGCTGGTCTGGGCGGTTGGTATGGCGTGGCTGGATTTACGCTTT
+CTGTTCTGGCTGGCGCCGATTGTCTTTTCGCTTATTCTGTCGCCATTTGTTTCGGTGATC
+TCCAGTCGTTCAACGGTAGGATTACGCACCAATCGCTGGAAGCTGTTCCTGATCCCGGAA
+GAGTATTCGCCGCCTCAGGTGTTGGTCGATACTGATAAATATCTGGAGATGAATCGCCGC
+CGTATTCTGGACGATGGCTTTATGCATGCGGTTTTTAACCCGTCGCTTAATGCGCTGGCG
+ACCGCGATGGCCACCGCGCGTCACCGCGCCAGTAAGGTGCTGGAAATAGCCCGCGATCGT
+CATGTGGAGCAGGCGCTAAACGAAACGCCGGATAAACTGAACCGCGATCGGCGTCTGGTT
+TTGCTCAGCGATCCGGTGACGATGGCGCGTTTTCACTATCGGGTCTGGAATGCGCCAGAG
+AGATACTCTTCCTGGGTAAACCATTATCAGTCTCTCGTCCTGAATCCGCAGGCGTTGCAG
+GGACGAACATCGTCAGCGGGATAA

t/lib/TestHelper.pm

@@ -136,7 +136,6 @@ sub mock_execute_script_and_check_output {
 
             my $actual_output_file_name   = $scripts_and_expected_files->{$script_parameters}->[0];
             my $expected_output_file_name = $scripts_and_expected_files->{$script_parameters}->[1];
-
             ok( -e $actual_output_file_name, "Actual output file exists $actual_output_file_name  $script_parameters" );
             if ( defined($columns_to_exclude) ) {
                 is(