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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
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8 BEGIN { unshift( @INC, './lib' ) }
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9
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10 BEGIN {
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11 use Test::Most;
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12 use_ok('Bio::Roary::External::Mcl');
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13 }
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14
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15 my $cwd = getcwd();
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16 my $obj;
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17
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18
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19 ok(
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20 $obj = Bio::Roary::External::Mcl->new(
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21 blast_results => 'some_blast_results',
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22 mcxdeblast_exec => $cwd . '/t/bin/dummy_mcxdeblast',
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23 mcl_exec => $cwd . '/t/bin/dummy_mcl',
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24 output_file => 'output.groups'
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25 ),
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26 'initialise object with dummy values'
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27 );
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28
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29 is(
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30 $obj->_command_to_run,
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31 $cwd
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32 . '/t/bin/dummy_mcxdeblast -m9 --score=r --line-mode=abc some_blast_results 2> /dev/null | '
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33 . $cwd
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34 . '/t/bin/dummy_mcl - --abc -I 1.5 -o output.groups > /dev/null 2>&1',
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35 'Command constructed as expected'
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36 );
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37 ok( $obj->run(), 'run dummy command' );
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38
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39 unlink('output.groups');
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40
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41 ok(
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42 $obj = Bio::Roary::External::Mcl->new(
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43 blast_results => 't/data/blast_results',
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44 ),
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45 'initialise object with real values'
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46 );
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47 ok( $obj->run(), 'run the real command' );
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48 compare_ok('output_groups', 't/data/expected_output_groups', 'outgroups as expected');
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49
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50 unlink('output_groups');
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51
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52 1;
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53
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54 done_testing();
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