From 5bfb8eb7395b26684715aa26276828046cfae8ee Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Mon, 28 Sep 2015 11:27:38 +0100 Subject: [PATCH] dont align if sequences same length and nearly the same --- dist.ini | 2 +- .../GeneAlignmentFromNucleotides.pm | 3 +- lib/Bio/Roary/SortFasta.pm | 34 +++- t/Bio/Roary/CommandLine/Roary.t | 2 +- t/Bio/Roary/SortFasta.t | 9 +- .../expected_core_gene_alignment.aln | 6 +- t/data/mdoH.fa.aln | 4 +- t/data/mdoH_mafft.fa.aln | 172 +++++++++--------- t/lib/TestHelper.pm | 1 - 9 files changed, 128 insertions(+), 105 deletions(-) diff --git a/dist.ini b/dist.ini index b351bc3..7d3b99e 100644 --- a/dist.ini +++ b/dist.ini @@ -1,5 +1,5 @@ name = Bio-Roary -version = 3.3.1 +version = 3.3.2 author = Andrew J. Page license = GPL_3 copyright_holder = Wellcome Trust Sanger Institute diff --git a/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm b/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm index 0daf4e6..f929629 100644 --- a/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm +++ b/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( diff --git a/lib/Bio/Roary/SortFasta.pm b/lib/Bio/Roary/SortFasta.pm index 955725f..85ed0e4 100644 --- a/lib/Bio/Roary/SortFasta.pm +++ b/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; diff --git a/t/Bio/Roary/CommandLine/Roary.t b/t/Bio/Roary/CommandLine/Roary.t index fcd5289..d59c935 100755 --- a/t/Bio/Roary/CommandLine/Roary.t +++ b/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' ); diff --git a/t/Bio/Roary/SortFasta.t b/t/Bio/Roary/SortFasta.t index ec31390..3450084 100755 --- a/t/Bio/Roary/SortFasta.t +++ b/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(); diff --git a/t/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln b/t/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln index 0074953..227cd1c 100644 --- a/t/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln +++ b/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 diff --git a/t/data/mdoH.fa.aln b/t/data/mdoH.fa.aln index 527410e..9cbdc63 100644 --- a/t/data/mdoH.fa.aln +++ b/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 diff --git a/t/data/mdoH_mafft.fa.aln b/t/data/mdoH_mafft.fa.aln index 0a0fb1a..9cbdc63 100644 --- a/t/data/mdoH_mafft.fa.aln +++ b/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 diff --git a/t/lib/TestHelper.pm b/t/lib/TestHelper.pm index 697e297..09950fe 100644 --- a/t/lib/TestHelper.pm +++ b/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(