comparison Roary/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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-1:000000000000 0:c47a5f61bc9f
1 #!/usr/bin/env perl
2 use Moose;
3 use Data::Dumper;
4 use Cwd;
5 use File::Which;
6
7 BEGIN { unshift( @INC, './lib' ) }
8 BEGIN { unshift( @INC, './t/lib' ) }
9 with 'TestHelper';
10
11 BEGIN {
12 use Test::Most;
13 use_ok('Bio::Roary::CommandLine::GeneAlignmentFromNucleotides');
14 }
15
16 my $script_name = 'Bio::Roary::CommandLine::GeneAlignmentFromNucleotides';
17 my $cwd = getcwd();
18 system('touch empty_file');
19 system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa');
20 my %scripts_and_expected_files = (
21 't/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta.fa.aln' ],
22 '-h' => [ 'empty_file', 't/data/empty_file' ],
23 );
24
25 SKIP:
26 {
27 skip "prank not installed", 2 unless ( which('prank') );
28 mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
29 }
30
31 SKIP:
32 {
33 skip "mafft not installed", 2 unless ( which('mafft') );
34 system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa');
35 %scripts_and_expected_files = (
36 '--mafft t/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta_mafft.fa.aln' ],
37 );
38 mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
39 }
40
41 done_testing();