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|
#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use File::Basename;
BEGIN { unshift( @INC, './lib' ) }
$ENV{PATH} .= ":./bin";
BEGIN {
use Test::Most;
use_ok('Bio::Roary::PrepareInputFiles');
}
my $obj;
ok(
$obj = Bio::Roary::PrepareInputFiles->new(
input_files => [
't/data/example_annotation.gff', 't/data/example_1.faa',
't/data/example_annotation_2.gff', 't/data/example_2.faa','t/data/sequences_with_unknowns.faa'
],
),
'initalise'
);
my @sorted_fasta_files = sort map { basename($_) } sort @{$obj->fasta_files};
my @expected_fasta_files = sort((
'example_1.faa.tmp.filtered.fa',
'example_2.faa.tmp.filtered.fa',
'example_annotation.gff.proteome.faa',
'example_annotation_2.gff.proteome.faa',
'sequences_with_unknowns.faa.tmp.filtered.fa'
));
is_deeply(
\@sorted_fasta_files,
\@expected_fasta_files,
'proteome extracted from gff files, input fasta files filtered'
);
my @input_files_lookup = sort map { basename($_) } @{$obj->lookup_fasta_files_from_unknown_input_files( [ 't/data/example_annotation_2.gff', 't/data/example_1.faa' ] )};
is_deeply(
\@input_files_lookup,
['example_1.faa.tmp.filtered.fa','example_annotation_2.gff.proteome.faa'],
'previously created faa file looked up from gff filename'
);
unlink('example_annotation.gff.proteome.faa');
unlink('example_annotation_2.gff.proteome.faa');
unlink('sequences_with_unknowns.faa.tmp.filtered.fa');
unlink('example_1.faa.tmp.filtered.fa');
unlink('example_2.faa.tmp.filtered.fa');
done_testing();
|
