Mercurial > repos > dereeper > roary_plots
view Roary/t/Bio/Roary/AnnotateGroups.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; use Moose; use Test::Files; use File::Slurper qw(read_lines); BEGIN { unshift( @INC, './t/lib' ) } with 'TestHelper'; BEGIN { unshift( @INC, './lib' ) } $ENV{PATH} .= ":./bin"; BEGIN { use Test::Most; use_ok('Bio::Roary::AnnotateGroups'); } my $obj; ok( $obj = Bio::Roary::AnnotateGroups->new( gff_files => [ 't/data/query_1.gff', 't/data/query_2.gff', 't/data/query_3.gff' ], groups_filename => 't/data/query_groups', ), 'initalise' ); ok( $obj->reannotate, 'reannotate' ); is_deeply( $obj->_ids_to_gene_size, { 'abc_00012' => 188, '2_3' => 1001, '1_1' => 959, 'abc_00004' => 716, '3_3' => 1001, '3_2' => 725, '2_2' => 725, 'abc_00006' => 725, 'abc_00008' => 935, '1_6' => 134, 'abc_00015' => 134, '3_1' => 959, 'abc_00014' => 134, 'abc_01705' => 1556, 'abc_00013' => 75, 'abc_00010' => 227, '1_2' => 725, 'abc_00011' => 947, 'abc_00016' => 686, '2_7' => 134, '1_3' => 1001, '2_1' => 959, '3_5' => 686, 'abc_00002' => 146, 'abc_00003' => 197 }, 'gene lengths as expected' ); is_deeply( $obj->group_nucleotide_lengths, { 'group_3' => { 'average' => 1001, 'min' => 1001, 'max' => 1001 }, 'group_5' => { 'average' => 686, 'min' => 686, 'max' => 686 }, 'group_7' => { 'average' => 134, 'min' => 134, 'max' => 134 }, 'group_1' => { 'average' => 959, 'min' => 959, 'max' => 959 }, 'group_6' => { 'average' => 134, 'min' => 134, 'max' => 134 }, 'group_2' => { 'average' => 725, 'min' => 725, 'max' => 725 } }, 'group lengths' ); compare_files( 'reannotated_groups_file', 't/data/expected_reannotated_groups_file', 'groups reannotated as expected' ); unlink('reannotated_groups_file'); ok( $obj = Bio::Roary::AnnotateGroups->new( gff_files => [ 't/data/gene_name_field/annotation_1.gff', 't/data/gene_name_field/annotation_2.gff' ], groups_filename => 't/data/gene_name_field/groups', ), 'initalise where gene key is replaced by Name' ); ok( $obj->reannotate, 'reannotate' ); compare_files('reannotated_groups_file', 't/data/gene_name_field/expected_reannotated_groups_file', 'Reannoated groups file has the gene names transferred' ); unlink('reannotated_groups_file'); done_testing();