diff Roary/t/Bio/Roary/CommandLine/Roary.t @ 0:c47a5f61bc9f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/CommandLine/Roary.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,188 @@
+#!/usr/bin/env perl
+use Moose;
+use Data::Dumper;
+use File::Path qw( remove_tree);
+use File::Which;
+use File::Path qw(make_path);
+use Cwd qw(abs_path getcwd); 
+use File::Find::Rule;
+
+#Test changes current working directory so relative paths can get out of sync
+local $ENV{PERL5LIB} = join(':', ("$ENV{PERL5LIB}", abs_path('./lib'), abs_path('./t/lib')));
+local $ENV{PATH} = join(':', ("$ENV{PATH}", abs_path('./bin')));
+
+BEGIN { unshift( @INC, abs_path('./lib') ) }
+BEGIN { unshift( @INC, abs_path('./t/lib') ) }
+with 'TestHelper';
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::CommandLine::Roary');
+    use_ok('Bio::Roary::CommandLine::CreatePanGenome');
+    use Bio::Roary::SequenceLengths;
+}
+my $script_name = 'Bio::Roary::CommandLine::Roary';
+my $cwd         = getcwd();
+
+local $ENV{PATH} = "$ENV{PATH}:./bin";
+my %scripts_and_expected_files;
+system('touch empty_file');
+cleanup_files();
+
+%scripts_and_expected_files = (
+   ' -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff    ' =>
+     [ 'gene_presence_absence.csv', 't/data/overall_gene_presence_absence.csv' ],
+   ' -j Local -t 1 --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff' =>
+     [ 'gene_presence_absence.csv', 't/data/genbank_gbff/genbank_gene_presence_absence.csv' ],
+    '-h' => [ 'empty_file', 't/data/empty_file' ],
+);
+
+mock_execute_script_and_check_output_sorted( $script_name, \%scripts_and_expected_files, [ 0, 6, 7, 8, 9 ] );
+
+cleanup_files();
+
+stderr_should_have($script_name,'-a', 'Looking for');
+
+my $current_cwd = getcwd();
+stderr_should_have($script_name,'-v --output_directory t/data/directory_which_doesnt_exist  t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff', 'Output directory created');
+ok( ( -e 't/data/directory_which_doesnt_exist/clustered_proteins' ), 'pan genome files should be in directory' );
+is(getcwd(),$current_cwd , 'current working directory should not have changed after script is finished'); 
+
+SKIP:
+{
+    skip "prank not installed", 11 unless ( which('prank') );
+
+    %scripts_and_expected_files =
+      ( '-j Local --dont_delete_files --dont_split_groups  --output_multifasta_files t/data/real_data_1.gff t/data/real_data_2.gff' =>
+          [ 'pan_genome_sequences/mdoH.fa.aln', 't/data/mdoH.fa.aln' ], );
+    mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
+
+    ok( -e 'core_gene_alignment.aln', 'Core gene alignment exists' );
+
+    ok(
+        my $seq_len = Bio::Roary::SequenceLengths->new(
+            fasta_file => 'core_gene_alignment.aln',
+        ),
+        'Check size of the core_gene_alignment.aln init'
+    );
+
+    my @keys = keys %{ $seq_len->sequence_lengths };
+    is( $seq_len->sequence_lengths->{ $keys[0] }, 64983, 'length of first sequence' );
+		
+		ok( -e 'core_alignment_header.embl', 'Core gene alignment header exists' );
+
+    ok( -e 'accessory.tab' );
+    ok( -e 'core_accessory.tab' );
+    ok( -e 'number_of_conserved_genes.Rtab' );
+    ok( -e 'number_of_genes_in_pan_genome.Rtab' );
+    ok( -e 'number_of_new_genes.Rtab' );
+    ok( -e 'number_of_unique_genes.Rtab' );
+    ok( -e 'blast_identity_frequency.Rtab' );
+
+    cleanup_files();
+    %scripts_and_expected_files =
+      (
+'-j Local --output_multifasta_files t/data/core_alignment_gene_lookup/query_1.gff t/data/core_alignment_gene_lookup/query_2.gff t/data/core_alignment_gene_lookup/query_3.gff'
+          => [ 'core_gene_alignment.aln', 't/data/core_alignment_gene_lookup/expected_core_gene_alignment.aln' ], );
+    mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
+
+    cleanup_files();
+}
+
+SKIP:
+{
+	skip "extended tests not run",  40 unless ( defined($ENV{ROARY_FULL_TESTS}));
+
+    %scripts_and_expected_files = (
+        '-o some_different_output -i 90 -p 2 --translation_table 1 t/data/real_data_1.gff t/data/real_data_2.gff' => [ 'some_different_output', 't/data/expected_some_different_output' ],
+    	);
+    mock_execute_script_and_check_output_sorted( $script_name, \%scripts_and_expected_files, [ 0 ] );
+    
+    stderr_should_have($script_name,'--translation_table 1  -o some_different_output --core_definition 60 -p 2 -e --mafft  --group_limit 10 t/data/real_data_1.gff t/data/real_data_2.gff', 'Exiting early because number of clusters is too high');
+    stderr_should_have($script_name,'--verbose_stats --group_limit 10 -e t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff', 'Exiting early because number of clusters is too high');
+    stderr_should_not_have($script_name,'-e --group_limit 10 t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ', 'Cant access the multifasta base directory');
+    stderr_should_have($script_name,'-i 90 --core_definition 60 -p 2 -v t/data/real_data_1.gff t/data/real_data_2.gff ','Cleaning up files'); 
+    stderr_should_have($script_name,'-i 30 t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff','The percentage identity is too low');
+    stderr_should_not_have($script_name,'--dont_delete_files -v t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ','Cleaning up files');
+    stderr_should_have($script_name,'-v --group_limit 100000 -e t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ' ,'Running command: pan_genome_core_alignment');
+    stderr_should_have($script_name,'--translation_table 1 -v t/data/real_data_1.gff t/data/real_data_2.gff ' ,'Cleaning up files');
+    stderr_should_have($script_name,'-e -v t/data/real_data_1.gff t/data/real_data_2.gff ','Creating files with the nucleotide sequences for every cluster');
+    
+    SKIP:
+    {
+        skip "kraken not installed",        2 unless ( which('kraken') );
+        skip "kraken-report not installed", 2 unless ( which('kraken-report') );
+        stderr_should_have($script_name,'-v --qc t/data/real_data_1.gff t/data/real_data_2.gff' ,'Running Kraken on each input assembly');
+    }
+    
+    %scripts_and_expected_files = (
+        # output
+        '-o some_different_output -e --dont_delete_files t/data/real_data_1.gff t/data/real_data_2.gff' =>
+          [ 'pan_genome_sequences/mdoH.fa.aln', 't/data/mdoH.fa.aln' ],
+        '-o some_different_output --core_definition 60 t/data/real_data_1.gff t/data/real_data_2.gff' =>
+          [ 'summary_statistics.txt', 't/data/expected_core_60_summary_statistics.txt' ],
+        '-e -i 95.3 --translation_table 1 -v --group_limit 100000 --qc t/data/real_data_1.gff t/data/real_data_2.gff'   => [ 'core_gene_alignment.aln', 't/data/expected_real_data_core_gene_alignment.aln' ],
+	
+        '-e --verbose_stats t/data/real_data_1.gff t/data/real_data_2.gff'            => [ 'core_gene_alignment.aln', 't/data/expected_real_data_core_gene_alignment.aln' ],
+        '--core_definition 60 t/data/real_data_1.gff t/data/real_data_2.gff'          => [ 'summary_statistics.txt', 't/data/expected_core_60_summary_statistics.txt' ],
+        '-p 2 -e --dont_delete_files t/data/real_data_1.gff t/data/real_data_2.gff'   => [ 'pan_genome_sequences/mdoH.fa.aln', 't/data/mdoH.fa.aln' ],
+        '-p 2 --core_definition 60 t/data/real_data_1.gff t/data/real_data_2.gff'     => [ 'summary_statistics.txt', 't/data/expected_core_60_summary_statistics.txt' ],
+        '-p 2 -e --mafft t/data/real_data_1.gff t/data/real_data_2.gff'               => [ 'core_gene_alignment.aln', 't/data/expected_mafft_real_data_core_gene_alignment.aln' ],
+
+    );
+    mock_execute_script_and_check_output_sorted( $script_name, \%scripts_and_expected_files );
+
+}
+
+cleanup_files();
+
+done_testing();
+
+sub cleanup_files {
+    remove_tree('pan_genome_sequences');
+    remove_tree('fixed_input_files');
+    remove_tree('t/data/directory_which_doesnt_exist');
+    remove_tree('locus_tags_gffs_output');
+    unlink('_blast_results');
+    unlink('_clustered');
+    unlink('_clustered.bak.clstr');
+    unlink('_clustered.clstr');
+    unlink('_combined_files');
+    unlink('_combined_files.groups');
+    unlink('_fasta_files');
+    unlink('_gff_files');
+    unlink('_inflated_mcl_groups');
+    unlink('_inflated_unsplit_mcl_groups');
+    unlink('_labeled_mcl_groups');
+    unlink('_uninflated_mcl_groups');
+    unlink('accessory.header.embl');
+    unlink('accessory.header.tab');
+    unlink('accessory.tab');
+    unlink('blast_identity_frequency.Rtab');
+    unlink('clustered_proteins');
+    unlink('core_accessory.header.embl');
+    unlink('core_accessory.header.tab');
+    unlink('core_accessory.tab');
+    unlink('core_gene_alignment.aln');
+    unlink('database_masking.asnb');
+    unlink('example_1.faa.tmp.filtered.fa');
+    unlink('example_2.faa.tmp.filtered.fa');
+    unlink('example_3.faa.tmp.filtered.fa');
+    unlink('gene_presence_absence.csv');
+    unlink('number_of_conserved_genes.Rtab');
+    unlink('number_of_genes_in_pan_genome.Rtab');
+    unlink('number_of_new_genes.Rtab');
+    unlink('number_of_unique_genes.Rtab');
+    unlink('pan_genome.fa');
+    unlink('query_1.gff.proteome.faa');
+    unlink('query_2.gff.proteome.faa');
+    unlink('query_3.gff.proteome.faa');
+    unlink('query_5.gff.proteome.faa');
+    unlink('real_data_1.gff.proteome.faa');
+    unlink('real_data_2.gff.proteome.faa');
+    unlink('pan_genome_reference.fa');
+    unlink('accessory_graph.dot');
+    unlink('core_accessory_graph.dot');
+	  unlink('some_different_output');
+	  unlink('core_alignment_header.embl');
+}