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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();
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