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comparison Roary/t/Bio/Roary/External/Prank.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 strict;
3 use warnings;
4 use Data::Dumper;
5 use Cwd;
6 use Test::Files;
7 use Bio::Roary::SortFasta;
8
9 BEGIN { unshift( @INC, './lib' ) }
10
11 BEGIN {
12 use Test::Most;
13 use_ok('Bio::Roary::External::Prank');
14 }
15
16 ok(
17 my $obj = Bio::Roary::External::Prank->new(
18 input_filename => 't/data/prank_input.fa',
19 output_filename => 't/data/prank_input.fa.aln',
20 job_runner => 'Local'
21 ),
22 'initialise prank obj'
23 );
24
25 is(
26 $obj->_command_to_run,
27 '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',
28 'Command constructed as expected'
29 );
30
31 ok( $obj->run(), 'run prank' );
32
33 ok(-e 't/data/prank_input.fa.aln', 'output file exists');
34 my $sort_fasta_after_revtrans = Bio::Roary::SortFasta->new(
35 input_filename => 't/data/prank_input.fa.aln',
36 remove_nnn_from_end => 1,
37 );
38 $sort_fasta_after_revtrans->sort_fasta->replace_input_with_output_file;
39
40 compare_ok( 't/data/prank_input.fa.aln', 't/data/expected_prank_input.fa.aln', "output for prank matches" );
41
42 unlink('t/data/prank_input.fa.aln');
43
44 done_testing();