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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 Test::Files;
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6
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7 BEGIN { unshift( @INC, './lib' ) }
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8 $ENV{PATH} .= ":./bin";
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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::GroupStatistics');
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13 }
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14
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15 my $annotate_groups = Bio::Roary::AnnotateGroups->new(
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16 gff_files => ['t/data/query_1.gff','t/data/query_2.gff','t/data/query_3.gff'],
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17 groups_filename => 't/data/query_groups',
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18 );
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19
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20 my $analyse_groups = Bio::Roary::AnalyseGroups->new(
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21 fasta_files => ['t/data/query_1.fa','t/data/query_2.fa','t/data/query_3.fa'],
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22 groups_filename => 't/data/query_groups'
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23 );
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24
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25 my $obj;
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26
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27 ok($obj = Bio::Roary::GroupStatistics->new(
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28 annotate_groups_obj => $annotate_groups,
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29 analyse_groups_obj => $analyse_groups
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30 ),'Initialise group statistics object');
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31 ok($obj->create_spreadsheet,'Create the CSV file');
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32 ok(-e 'gene_presence_absence.csv', 'CSV file exists');
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33 compare_ok('gene_presence_absence.csv','t/data/expected_group_statitics.csv', 'Spreadsheet content as expected');
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34 ok($obj->create_rtab,'Create the Rtab file');
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35 ok(-e 'gene_presence_absence.Rtab', 'Rtab file exists');
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36 compare_ok('gene_presence_absence.Rtab','t/data/expected_gene_presence_and_absence.Rtab', 'Rtab matrix content as expected');
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37
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38 unlink('gene_presence_absence.csv');
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39 unlink('gene_presence_absence.Rtab');
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40
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41 ############################
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42
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43 my $annotate_groups_2 = Bio::Roary::AnnotateGroups->new(
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44 gff_files => ['t/data/query_1.gff','t/data/query_2.gff','t/data/query_3.gff','t/data/query_4_missing_genes.gff'],
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45 groups_filename => 't/data/query_groups_missing_genes',
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46 );
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47
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48 my $analyse_groups_2 = Bio::Roary::AnalyseGroups->new(
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49 fasta_files => ['t/data/query_1.fa','t/data/query_2.fa','t/data/query_3.fa','t/data/query_4_missing_genes.fa'],
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50 groups_filename => 't/data/query_groups_missing_genes'
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51 );
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52
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53 ok($obj = Bio::Roary::GroupStatistics->new(
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54 annotate_groups_obj => $annotate_groups_2,
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55 analyse_groups_obj => $analyse_groups_2,
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56 output_filename => 'missing_genes_stats.csv'
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57 ),'Initialise group statistics object where one isolate has only 1 gene');
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58 ok($obj->create_spreadsheet,'Create the CSV file');
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59 ok(-e 'missing_genes_stats.csv', 'CSV file exists');
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60 compare_ok('missing_genes_stats.csv','t/data/expected_group_statitics_missing_genes.csv', 'Spreadsheet content as expected with missing genes');
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61
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62 unlink('missing_genes_stats.csv');
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63
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64
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65 ## TEST VERBOSE STATS ##
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66
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67 ok($obj = Bio::Roary::GroupStatistics->new(
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68 annotate_groups_obj => $annotate_groups,
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69 analyse_groups_obj => $analyse_groups,
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70 _verbose => 1,
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71 output_filename => 'verbose_stats.csv'
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72 ),'Initialise group statistics object');
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73 ok($obj->create_spreadsheet,'Create the CSV file');
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74 ok(-e 'verbose_stats.csv', 'CSV file exists');
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75 compare_ok('verbose_stats.csv','t/data/expected_group_statitics_verbose.csv', 'Verbose spreadsheet content as expected');
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76
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77 unlink('verbose_stats.csv');
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78
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79 done_testing();
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