Mercurial > repos > dereeper > roary_plots
view Roary/t/Bio/Roary/ContigsToGeneIDsFromGFF.t @ 0:c47a5f61bc9f draft
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author | dereeper |
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date | Fri, 14 May 2021 20:27:06 +0000 |
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#!/usr/bin/env perl use strict; use warnings; use Data::Dumper; BEGIN { unshift( @INC, './lib' ) } $ENV{PATH} .= ":./bin"; BEGIN { use Test::Most; use_ok('Bio::Roary::ContigsToGeneIDsFromGFF'); } ok( my $obj = Bio::Roary::ContigsToGeneIDsFromGFF->new( gff_file => 't/data/query_1.gff' ), 'Initialise contigs to gene ids obj' ); is_deeply( $obj->contig_to_ids, { 'abc|SC|contig000001' => [ '1_1', 'abc_00002', 'abc_00003', 'abc_00004', '1_2', 'abc_00006', '1_3', 'abc_00008', 'abc_00010', 'abc_00011', 'abc_00012', 'abc_00014', '1_6', 'abc_00016' ] }, 'Contigs match expected with standard output' ); ok( $obj = Bio::Roary::ContigsToGeneIDsFromGFF->new( gff_file => 't/data/query_1_alternative_patterns.gff' ), 'Initialise contigs to gene ids obj with alternative ID patterns' ); is_deeply( $obj->contig_to_ids, { 'abc|SC|contig000001' => [ '1_1', 'abc_00002', 'abc_00003', 'abc_00004', '1_2', 'abc_00006' ] }, 'Contigs match expected with alternative output' ); is_deeply( $obj->_genes_annotation, [ { 'database_annotation_exists' => 1, 'product' => 'superantigen-like protein', 'end' => '3337', 'start' => '2621', 'contig' => 'abc|SC|contig000001', 'id_name' => 'abc_00004' }, { 'database_annotation_exists' => 1, 'product' => 'hypothetical protein', 'end' => '4170', 'start' => '3445', 'contig' => 'abc|SC|contig000001', 'id_name' => '1_2' }, { 'database_annotation_exists' => 1, 'product' => 'superantigen-like protein', 'end' => '4990', 'start' => '4265', 'contig' => 'abc|SC|contig000001', 'id_name' => 'abc_00006' } ], 'Product annotation with non standard format' ); done_testing();