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