Mercurial > repos > dereeper > roary_plots
comparison 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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-1:000000000000 | 0:c47a5f61bc9f |
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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(); |