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comparison Roary/t/Bio/Roary/PrepareInputFiles.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 File::Basename;
6
7 BEGIN { unshift( @INC, './lib' ) }
8 $ENV{PATH} .= ":./bin";
9
10 BEGIN {
11 use Test::Most;
12 use_ok('Bio::Roary::PrepareInputFiles');
13 }
14
15 my $obj;
16
17 ok(
18 $obj = Bio::Roary::PrepareInputFiles->new(
19 input_files => [
20 't/data/example_annotation.gff', 't/data/example_1.faa',
21 't/data/example_annotation_2.gff', 't/data/example_2.faa','t/data/sequences_with_unknowns.faa'
22 ],
23 ),
24 'initalise'
25 );
26
27 my @sorted_fasta_files = sort map { basename($_) } sort @{$obj->fasta_files};
28 my @expected_fasta_files = sort((
29 'example_1.faa.tmp.filtered.fa',
30 'example_2.faa.tmp.filtered.fa',
31 'example_annotation.gff.proteome.faa',
32 'example_annotation_2.gff.proteome.faa',
33 'sequences_with_unknowns.faa.tmp.filtered.fa'
34 ));
35
36 is_deeply(
37 \@sorted_fasta_files,
38 \@expected_fasta_files,
39 'proteome extracted from gff files, input fasta files filtered'
40 );
41
42 my @input_files_lookup = sort map { basename($_) } @{$obj->lookup_fasta_files_from_unknown_input_files( [ 't/data/example_annotation_2.gff', 't/data/example_1.faa' ] )};
43 is_deeply(
44 \@input_files_lookup,
45 ['example_1.faa.tmp.filtered.fa','example_annotation_2.gff.proteome.faa'],
46 'previously created faa file looked up from gff filename'
47 );
48
49 unlink('example_annotation.gff.proteome.faa');
50 unlink('example_annotation_2.gff.proteome.faa');
51 unlink('sequences_with_unknowns.faa.tmp.filtered.fa');
52 unlink('example_1.faa.tmp.filtered.fa');
53 unlink('example_2.faa.tmp.filtered.fa');
54
55 done_testing();
56