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#!/usr/bin/env perl
use Moose;
use Data::Dumper;
use File::Path qw( remove_tree);
use Cwd;
BEGIN { unshift( @INC, './lib' ) }
BEGIN { unshift( @INC, './t/lib' ) }
with 'TestHelper';
BEGIN {
use Test::Most;
use_ok('Bio::Roary::CommandLine::RoaryPostAnalysis');
}
my $script_name = 'Bio::Roary::CommandLine::RoaryPostAnalysis';
my $cwd = getcwd();
local $ENV{PATH} = "$ENV{PATH}:./bin";
system('cp t/data/post_analysis/* .');
system('touch empty_file');
my %scripts_and_expected_files = (
'-o clustered_proteins -p pan_genome.fa -s gene_presence_absence.csv -c _clustered.clstr -i _gff_files -f _fasta_files -j Local --dont_create_rplots --dont_split_groups' =>
[ 'clustered_proteins', 't/data/clustered_proteins_post_analysis' ],
'-h' =>
[ 'empty_file', 't/data/empty_file' ],
);
SKIP:
{
skip "Tests dont take variablity into account", 2 if(1);
mock_execute_script_and_check_output_sorted_groups( $script_name, \%scripts_and_expected_files );
ok( -e 'number_of_unique_genes.Rtab', 'number_of_unique_genes.Rtab exists');
ok( -e 'number_of_new_genes.Rtab', 'number_of_new_genes exists');
ok( -e 'number_of_genes_in_pan_genome.Rtab', 'number_of_genes_in_pan_genome exists');
ok( -e 'number_of_conserved_genes.Rtab','number_of_conserved_genes');
ok( -e 'gene_presence_absence.csv', 'gene_presence_absence exists');
ok( -e 'core_accessory.tab', 'core_accessory.tab exists');
ok( -e 'core_accessory.header.embl','core_accessory.header.embl exists');
ok( -e 'accessory.tab','accessory.tab exists');
ok( -e 'accessory.header.embl','accessory.header.embl exists');
ok( -e 'summary_statistics.txt' ,'summary_statistics.txt exists');
compare_tab_files_with_variable_coordinates('accessory.header.embl', 't/data/post_analysis_expected/accessory.header.embl');
compare_tab_files_with_variable_coordinates('accessory.tab', 't/data/post_analysis_expected/accessory.tab');
compare_tab_files_with_variable_coordinates('core_accessory.header.embl', 't/data/post_analysis_expected/core_accessory.header.embl');
compare_tab_files_with_variable_coordinates('core_accessory.tab', 't/data/post_analysis_expected/core_accessory.tab');
cleanup_files();
system('cp t/data/post_analysis/* .');
system('touch empty_file');
%scripts_and_expected_files = (
'-t 1 -o clustered_proteins -p pan_genome.fa -s gene_presence_absence.csv -c _clustered.clstr -i _gff_files -f _fasta_files -j Local --dont_create_rplots --dont_split_groups' =>
[ 'clustered_proteins', 't/data/clustered_proteins_post_analysis' ],
'-h' =>
[ 'empty_file', 't/data/empty_file' ],
);
mock_execute_script_and_check_output_sorted_groups( $script_name, \%scripts_and_expected_files );
ok( -e 'number_of_unique_genes.Rtab', 'number_of_unique_genes.Rtab exists');
ok( -e 'number_of_new_genes.Rtab', 'number_of_new_genes exists');
ok( -e 'number_of_genes_in_pan_genome.Rtab', 'number_of_genes_in_pan_genome exists');
ok( -e 'number_of_conserved_genes.Rtab','number_of_conserved_genes');
ok( -e 'gene_presence_absence.csv', 'gene_presence_absence exists');
ok( -e 'core_accessory.tab', 'core_accessory.tab exists');
ok( -e 'core_accessory.header.embl','core_accessory.header.embl exists');
ok( -e 'accessory.tab','accessory.tab exists');
ok( -e 'accessory.header.embl','accessory.header.embl exists');
compare_tab_files_with_variable_coordinates('accessory.header.embl', 't/data/post_analysis_expected/accessory.header.embl');
compare_tab_files_with_variable_coordinates('accessory.tab', 't/data/post_analysis_expected/accessory.tab');
compare_tab_files_with_variable_coordinates('core_accessory.header.embl', 't/data/post_analysis_expected/core_accessory.header.embl');
compare_tab_files_with_variable_coordinates('core_accessory.tab', 't/data/post_analysis_expected/core_accessory.tab');
}
cleanup_files();
done_testing();
sub cleanup_files
{
unlink('_clustered');
unlink('_clustered.bak.clstr');
unlink('_clustered.clstr');
unlink('_combined_files');
unlink('_combined_files.groups');
unlink('_fasta_files');
unlink('_gff_files');
unlink('_uninflated_mcl_groups');
unlink('query_1.gff.proteome.faa');
unlink('query_2.gff.proteome.faa');
unlink('query_6.gff.proteome.faa');
unlink('accessory.header.embl');
unlink('accessory.tab');
unlink('core_accessory.header.embl');
unlink('core_accessory.tab');
unlink('gene_presence_absence.csv');
unlink('number_of_unique_genes.Rtab');
unlink('number_of_new_genes.Rtab');
unlink('number_of_genes_in_pan_genome.Rtab');
unlink('number_of_conserved_genes.Rtab');
}
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