Mercurial > repos > dereeper > roary_plots
view Roary/t/Bio/Roary/External/Prank.t @ 3:e95344f6dfc5 draft default tip
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author | dereeper |
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date | Fri, 12 Nov 2021 16:32:26 +0000 |
parents | c47a5f61bc9f |
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#!/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();