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#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use Test::Files;
BEGIN { unshift( @INC, './lib' ) }
$ENV{PATH} .= ":./bin";
BEGIN {
use Test::Most;
use_ok('Bio::Roary::PresenceAbsenceMatrix');
use Bio::Roary::AnnotateGroups;
}
my $obj;
my $annotate_groups = 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',
);
my $sorted_file_names = [ 't/data/query_1.fa', 't/data/query_2.fa', 't/data/query_3.fa' ];
my $groups_to_files = {
'group_3' => {
't/data/query_1.fa' => [ '1_3' ],
't/data/query_3.fa' => [ '3_3' ]
},
'group_5' => {
't/data/query_3.fa' => [ '3_5' ]
},
'group_7' => {
't/data/query_2.fa' => [ '2_7' ]
},
'group_4' => {
't/data/query_3.fa' => [ '3_4' ],
't/data/query_2.fa' => [ '2_4' ]
},
'group_1' => {
't/data/query_1.fa' => [ '1_1' ],
't/data/query_3.fa' => [ '3_1' ],
't/data/query_2.fa' => [ '2_1' ]
},
'group_6' => {
't/data/query_1.fa' => [ '1_6' ]
},
'group_2' => {
't/data/query_1.fa' => [ '1_2' ],
't/data/query_2.fa' => [ '2_2' ]
}
};
my $num_files_in_groups = {
'group_3' => 2,
'group_5' => 1,
'group_7' => 1,
'group_4' => 2,
'group_1' => 3,
'group_6' => 1,
'group_2' => 2
};
my $sample_headers = [ 'query_1.fa', 'query_2.fa', 'query_3.fa' ];
ok(
$obj = Bio::Roary::PresenceAbsenceMatrix->new(
annotate_groups_obj => $annotate_groups,
output_filename => 'test_gene_presence_absence.Rtab',
sorted_file_names => $sorted_file_names,
groups_to_files => $groups_to_files,
num_files_in_groups => $num_files_in_groups,
sample_headers => $sample_headers,
),
'initialise object'
);
ok( $obj->create_matrix_file, 'create matrix file' );
ok( -e 'test_gene_presence_absence.Rtab', 'matrix file exists' );
compare_ok( 'test_gene_presence_absence.Rtab', 't/data/expected_gene_presence_and_absence.Rtab', 'Rtab matrix content as expected' );
# one gene one group
$groups_to_files = {'group_1' => {'t/data/query_1.fa' => [ '1_1' ]}};
$num_files_in_groups = {'group_1' => 1};
ok(
$obj = Bio::Roary::PresenceAbsenceMatrix->new(
annotate_groups_obj => $annotate_groups,
output_filename => 'test_gene_presence_absence.Rtab',
sorted_file_names => $sorted_file_names,
groups_to_files => $groups_to_files,
num_files_in_groups => $num_files_in_groups,
sample_headers => $sample_headers,
),
'initialise object one gene one group'
);
ok( $obj->create_matrix_file, 'create matrix file one gene one group' );
compare_ok( 'test_gene_presence_absence.Rtab', 't/data/expected_one_gene_presence_and_absence.Rtab', 'Rtab matrix content as expected for one gene one group' );
unlink('test_gene_presence_absence.Rtab');
done_testing();
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