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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
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9 BEGIN {
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10 use Test::Most;
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11 use_ok('Bio::Roary::AssemblyStatistics');
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12 }
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13
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14 my $obj;
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15 ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/input_block_spreadsheet.csv' ), 'initialise spreadsheet' );
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16
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17 my @genes = sort keys %{ $obj->_genes_to_rows };
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18 is_deeply(
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19 \@genes,
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20 [
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21 'SBOV29371', 'SBOV38871', 'SBOV43201', 'STY3593', 'STY4162', 'bcsC_1', 'betC_2', 'comM_2',
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22 'dmsA4_1', 'dosC', 'dsbA_3', 'fadH_1', 'fimD_3', 'fliB_2', 'fliF', 'ftsN',
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23 'gatY_1', 'glfT2', 'group_1000', 'group_1001', 'group_1004', 'group_1006', 'group_1009', 'group_220',
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24 'group_277', 'group_281', 'group_283', 'group_284', 'group_288', 'hemD', 'hsrA_2', 'icsA',
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25 'kdpD', 'ligB_1', 'marT_1', 'nepI', 'rffH', 'rpoS', 'selA_1', 'speC_3',
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26 'sptP', 'srgB', 'stp', 'tmcA', 'tub', 'yadA', 'ybbW_1', 'yhaO_2',
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27 'yicJ_1', 'yigZ'
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28 ],
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29 'all gene rows available'
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30 );
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31
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32 is_deeply(
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33 $obj->ordered_genes,
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34 [
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35 'dmsA4_1', 'group_1000', 'group_1001', 'SBOV43201', 'dosC', 'stp', 'fliB_2', 'fliF',
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36 'dsbA_3', 'srgB', 'fimD_3', 'betC_2', 'tmcA', 'tub', 'rffH', 'hemD',
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37 'group_1006', 'STY3593', 'group_1004', 'yigZ', 'group_220', 'glfT2', 'kdpD', 'speC_3',
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38 'ybbW_1', 'sptP', 'SBOV29371', 'rpoS', 'fadH_1', 'yhaO_2', 'bcsC_1', 'STY4162',
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39 'yadA', 'ligB_1', 'icsA', 'marT_1', 'selA_1', 'nepI', 'gatY_1', 'SBOV38871',
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40 'group_288', 'hsrA_2', 'group_281', 'group_283', 'group_284', 'yicJ_1', 'ftsN', 'group_277',
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41 'group_1009', 'comM_2'
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42 ],
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43 'ordered genes'
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44 );
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45
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46 is_deeply(
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47 $obj->sample_names_to_column_index,
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48 {
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49 'threeblocks' => 18,
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50 'nocontigs' => 17,
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51 'contigwithgaps' => 16,
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52 'oneblock' => 14,
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53 'threeblocksinversion' => 19,
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54 'oneblockrev' => 15
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55 },
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56 'sample names to column index'
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57 );
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58
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59 is_deeply( $obj->_sample_statistics('oneblock'), { num_blocks => 1, largest_block_size => 50 }, 'one block' );
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60 is_deeply( $obj->_sample_statistics('oneblockrev'), { num_blocks => 1, largest_block_size => 50 }, 'one block reversed' );
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61 is_deeply(
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62 $obj->_sample_statistics('contigwithgaps'),
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63 { num_blocks => 1, largest_block_size => 50 },
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64 'one block where there are gaps everywhere'
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65 );
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66 is_deeply( $obj->_sample_statistics('nocontigs'), { num_blocks => 50, largest_block_size => 1 }, 'no contiguous blocks' );
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67 is_deeply( $obj->_sample_statistics('threeblocks'), { num_blocks => 3, largest_block_size => 21 }, 'three blocks' );
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68 is_deeply(
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69 $obj->_sample_statistics('threeblocksinversion'),
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70 { num_blocks => 3, largest_block_size => 20 },
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71 'three blocks with an inversion in the middle'
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72 );
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73 is_deeply( $obj->gene_category_count, { core => 50 }, 'Gene category counts' );
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74
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75 # t/data/gene_category_count.csv
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76 ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv' ),
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77 'initialise spreadsheet with variable numbers of genes in samples' );
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78 is_deeply(
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79 $obj->gene_category_count,
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80 {
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81 'core' => 1,
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82 'cloud' => 4,
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83 'soft_core' => 1,
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84 'shell' => 24
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85 },
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86 'Categories as expected'
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87 );
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88 ok($obj->create_summary_output, 'create output file');
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89 compare_ok('summary_statistics.txt', 't/data/expected_summary_statistics.txt', 'summary statistics as expected');
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90
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91
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92 # t/data/gene_category_count.csv
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93 ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv', core_definition => 0.9667 ),
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94 'initialise spreadsheet with core of 96.67%' );
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95 is_deeply(
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96 $obj->gene_category_count,
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97 {
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98 'core' => 1,
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99 'soft_core' => 1,
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100 'cloud' => 4,
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101 'shell' => 24
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102 },
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103 'Categories as expected with cd of 96.67%'
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104 );
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105
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106 # t/data/gene_category_count.csv
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107 ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv', core_definition => 0.9666 ),
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108 'initialise spreadsheet with core of 96.66%' );
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109 is_deeply(
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110 $obj->gene_category_count,
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111 {
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112 'core' => 2,
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113 'cloud' => 4,
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114 'shell' => 24
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115 },
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116 'Categories as expected with cd of 96.66%'
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117 );
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118
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119
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120 unlink('summary_statistics.txt');
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121 done_testing();
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