Mercurial > repos > dereeper > roary_plots
view Roary/t/Bio/Roary/AssemblyStatistics.t @ 3:e95344f6dfc5 draft default tip
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author | dereeper |
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date | Fri, 12 Nov 2021 16:32:26 +0000 |
parents | c47a5f61bc9f |
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#!/usr/bin/env perl use strict; use warnings; use Data::Dumper; use Test::Files; BEGIN { unshift( @INC, './lib' ) } BEGIN { use Test::Most; use_ok('Bio::Roary::AssemblyStatistics'); } my $obj; ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/input_block_spreadsheet.csv' ), 'initialise spreadsheet' ); my @genes = sort keys %{ $obj->_genes_to_rows }; is_deeply( \@genes, [ 'SBOV29371', 'SBOV38871', 'SBOV43201', 'STY3593', 'STY4162', 'bcsC_1', 'betC_2', 'comM_2', 'dmsA4_1', 'dosC', 'dsbA_3', 'fadH_1', 'fimD_3', 'fliB_2', 'fliF', 'ftsN', 'gatY_1', 'glfT2', 'group_1000', 'group_1001', 'group_1004', 'group_1006', 'group_1009', 'group_220', 'group_277', 'group_281', 'group_283', 'group_284', 'group_288', 'hemD', 'hsrA_2', 'icsA', 'kdpD', 'ligB_1', 'marT_1', 'nepI', 'rffH', 'rpoS', 'selA_1', 'speC_3', 'sptP', 'srgB', 'stp', 'tmcA', 'tub', 'yadA', 'ybbW_1', 'yhaO_2', 'yicJ_1', 'yigZ' ], 'all gene rows available' ); is_deeply( $obj->ordered_genes, [ 'dmsA4_1', 'group_1000', 'group_1001', 'SBOV43201', 'dosC', 'stp', 'fliB_2', 'fliF', 'dsbA_3', 'srgB', 'fimD_3', 'betC_2', 'tmcA', 'tub', 'rffH', 'hemD', 'group_1006', 'STY3593', 'group_1004', 'yigZ', 'group_220', 'glfT2', 'kdpD', 'speC_3', 'ybbW_1', 'sptP', 'SBOV29371', 'rpoS', 'fadH_1', 'yhaO_2', 'bcsC_1', 'STY4162', 'yadA', 'ligB_1', 'icsA', 'marT_1', 'selA_1', 'nepI', 'gatY_1', 'SBOV38871', 'group_288', 'hsrA_2', 'group_281', 'group_283', 'group_284', 'yicJ_1', 'ftsN', 'group_277', 'group_1009', 'comM_2' ], 'ordered genes' ); is_deeply( $obj->sample_names_to_column_index, { 'threeblocks' => 18, 'nocontigs' => 17, 'contigwithgaps' => 16, 'oneblock' => 14, 'threeblocksinversion' => 19, 'oneblockrev' => 15 }, 'sample names to column index' ); is_deeply( $obj->_sample_statistics('oneblock'), { num_blocks => 1, largest_block_size => 50 }, 'one block' ); is_deeply( $obj->_sample_statistics('oneblockrev'), { num_blocks => 1, largest_block_size => 50 }, 'one block reversed' ); is_deeply( $obj->_sample_statistics('contigwithgaps'), { num_blocks => 1, largest_block_size => 50 }, 'one block where there are gaps everywhere' ); is_deeply( $obj->_sample_statistics('nocontigs'), { num_blocks => 50, largest_block_size => 1 }, 'no contiguous blocks' ); is_deeply( $obj->_sample_statistics('threeblocks'), { num_blocks => 3, largest_block_size => 21 }, 'three blocks' ); is_deeply( $obj->_sample_statistics('threeblocksinversion'), { num_blocks => 3, largest_block_size => 20 }, 'three blocks with an inversion in the middle' ); is_deeply( $obj->gene_category_count, { core => 50 }, 'Gene category counts' ); # t/data/gene_category_count.csv ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv' ), 'initialise spreadsheet with variable numbers of genes in samples' ); is_deeply( $obj->gene_category_count, { 'core' => 1, 'cloud' => 4, 'soft_core' => 1, 'shell' => 24 }, 'Categories as expected' ); ok($obj->create_summary_output, 'create output file'); compare_ok('summary_statistics.txt', 't/data/expected_summary_statistics.txt', 'summary statistics as expected'); # t/data/gene_category_count.csv ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv', core_definition => 0.9667 ), 'initialise spreadsheet with core of 96.67%' ); is_deeply( $obj->gene_category_count, { 'core' => 1, 'soft_core' => 1, 'cloud' => 4, 'shell' => 24 }, 'Categories as expected with cd of 96.67%' ); # t/data/gene_category_count.csv ok( $obj = Bio::Roary::AssemblyStatistics->new( spreadsheet => 't/data/gene_category_count.csv', core_definition => 0.9666 ), 'initialise spreadsheet with core of 96.66%' ); is_deeply( $obj->gene_category_count, { 'core' => 2, 'cloud' => 4, 'shell' => 24 }, 'Categories as expected with cd of 96.66%' ); unlink('summary_statistics.txt'); done_testing();