Mercurial > repos > dereeper > roary_plots
diff Roary/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t @ 0:c47a5f61bc9f draft
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author | dereeper |
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date | Fri, 14 May 2021 20:27:06 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Roary/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t Fri May 14 20:27:06 2021 +0000 @@ -0,0 +1,41 @@ +#!/usr/bin/env perl +use Moose; +use Data::Dumper; +use Cwd; +use File::Which; + +BEGIN { unshift( @INC, './lib' ) } +BEGIN { unshift( @INC, './t/lib' ) } +with 'TestHelper'; + +BEGIN { + use Test::Most; + use_ok('Bio::Roary::CommandLine::GeneAlignmentFromNucleotides'); +} + +my $script_name = 'Bio::Roary::CommandLine::GeneAlignmentFromNucleotides'; +my $cwd = getcwd(); +system('touch empty_file'); +system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa'); +my %scripts_and_expected_files = ( + 't/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta.fa.aln' ], + '-h' => [ 'empty_file', 't/data/empty_file' ], +); + +SKIP: +{ + skip "prank not installed", 2 unless ( which('prank') ); + mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files ); +} + +SKIP: +{ + skip "mafft not installed", 2 unless ( which('mafft') ); + system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa'); + %scripts_and_expected_files = ( + '--mafft t/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta_mafft.fa.aln' ], + ); + mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files ); +} + +done_testing();