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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 Moose;
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6 BEGIN { unshift( @INC, './t/lib' ) }
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7 with 'TestHelper';
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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::Output::QueryGroups');
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14 }
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15
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16 my $plot_groups_obj = Bio::Roary::AnalyseGroups->new(
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17 fasta_files => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
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18 groups_filename => 't/data/query_groups'
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19 );
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20
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21 my $obj;
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22 ok($obj = Bio::Roary::Output::QueryGroups->new(
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23 analyse_groups => $plot_groups_obj,
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24 input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ]
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25 ),'initialise groups query object');
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26
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27 ok($obj->groups_union(), 'create the union file');
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28 ok($obj->groups_intersection(), 'create the intersection file');
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29 ok($obj->groups_complement(), 'create the complement file');
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30
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31 compare_files('union_of_groups.gg','t/data/expected_union_of_groups.gg', 'contents of the union groups as expected');
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32 compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups.gg', 'contents of the intersection groups as expected');
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33 compare_files('complement_of_groups.gg', 't/data/expected_complement_of_groups.gg', 'contents of the complement groups as expected');
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34
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35 ######################################
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36 # test varying core definition
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37 ok($obj = Bio::Roary::Output::QueryGroups->new(
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38 analyse_groups => $plot_groups_obj,
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39 input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
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40 core_definition => 0.66
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41 ),'initialise groups query object');
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42
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43 ok($obj->groups_intersection(), 'create the intersection file');
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44 ok($obj->groups_complement(), 'create the complement file');
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45
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46 compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups_core0.66.gg', 'contents of the intersection groups as expected');
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47 compare_files('complement_of_groups.gg', 't/data/expected_complement_of_groups_core0.66.gg', 'contents of the complement groups as expected');
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48
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49
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50 unlink('union_of_groups.gg');
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51 unlink('intersection_of_groups.gg');
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52 unlink('complement_of_groups.gg');
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53
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54 ######################################
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55
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56 $plot_groups_obj = Bio::Roary::AnalyseGroups->new(
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57 fasta_files => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
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58 groups_filename => 't/data/query_groups_paralogs'
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59 );
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60
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61 ok($obj = Bio::Roary::Output::QueryGroups->new(
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62 analyse_groups => $plot_groups_obj,
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63 input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ]
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64 ),'initialise groups query object with paralogs');
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65
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66 ok($obj->groups_intersection(), 'create the intersection file');
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67
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68 compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups_paralogs.gg', 'contents of the intersection groups with paralogs as expected');
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69 unlink('intersection_of_groups.gg');
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70
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71
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72 done_testing();
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73
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