Mercurial > repos > dereeper > roary_plots
diff Roary/t/Bio/Roary/External/Prank.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/External/Prank.t Fri May 14 20:27:06 2021 +0000 @@ -0,0 +1,44 @@ +#!/usr/bin/env perl +use strict; +use warnings; +use Data::Dumper; +use Cwd; +use Test::Files; +use Bio::Roary::SortFasta; + +BEGIN { unshift( @INC, './lib' ) } + +BEGIN { + use Test::Most; + use_ok('Bio::Roary::External::Prank'); +} + +ok( + my $obj = Bio::Roary::External::Prank->new( + input_filename => 't/data/prank_input.fa', + output_filename => 't/data/prank_input.fa.aln', + job_runner => 'Local' + ), + 'initialise prank obj' +); + +is( + $obj->_command_to_run, +'prank -d=t/data/prank_input.fa -o=t/data/prank_input.fa.aln -codon -F -quiet -once > /dev/null 2>&1 && mv t/data/prank_input.fa.aln*.fas t/data/prank_input.fa.aln', + 'Command constructed as expected' +); + +ok( $obj->run(), 'run prank' ); + +ok(-e 't/data/prank_input.fa.aln', 'output file exists'); +my $sort_fasta_after_revtrans = Bio::Roary::SortFasta->new( + input_filename => 't/data/prank_input.fa.aln', + remove_nnn_from_end => 1, +); +$sort_fasta_after_revtrans->sort_fasta->replace_input_with_output_file; + +compare_ok( 't/data/prank_input.fa.aln', 't/data/expected_prank_input.fa.aln', "output for prank matches" ); + +unlink('t/data/prank_input.fa.aln'); + +done_testing();