Mercurial > repos > dereeper > roary_plots

comparison Roary/t/Bio/Roary/ReformatInputGFFs.t @ 0:c47a5f61bc9f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Fri, 14 May 2021 20:27:06 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:c47a5f61bc9f
1 #!/usr/bin/env perl
2 use strict;
3 use warnings;
4 use Data::Dumper;
5 use File::Path qw(remove_tree);
6 use Test::Files;
7
8 BEGIN { unshift( @INC, './lib' ) }
9 $ENV{PATH} .= ":./bin";
10
11 BEGIN {
12 use Test::Most;
13 use_ok('Bio::Roary::ReformatInputGFFs');
14 }
15
16
17 my $obj;
18 remove_tree('fixed_input_files');
19 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff']), 'initialise with one input gff');
20 ok($obj->fix_duplicate_gene_ids, 'fix duplicates with one input gff');
21 is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff'] ,'list of gff files with one input gff, nothing should change');
22 ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist because there arent any fixed input files');
23
24
25 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff', 't/data/reformat_input_gffs/query_2.gff',]), 'initialise with 2 input gffs');
26 ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist before running');
27 is_deeply($obj->_get_ids_for_gff_file('t/data/reformat_input_gffs/query_1.gff'),[
28 '1_1',
29 'abc_00002',
30 'abc_00003',
31 'abc_00004',
32 '1_2'
33 ],'extract ids');
34 is_deeply($obj->_get_ids_for_gff_file('t/data/reformat_input_gffs/query_2.gff'),[
35 '1_1',
36 'abc_00002',
37 'abc_00003',
38 'abc_00004',
39 '1_2'
40 ],'extract ids');
41 ok($obj->fix_duplicate_gene_ids, 'fix duplicates with 2 input gffs');
42 ok(( -d 'fixed_input_files'), 'Directory should exist because there is one gff thats fixed');
43 is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff','fixed_input_files/query_2.gff' ] ,'list of gff files one in the fixed directory');
44 ok(( -e 'fixed_input_files/query_2.gff'), 'fixed file should exist');
45 compare_ok('fixed_input_files/query_2.gff', 't/data/reformat_input_gffs/expected_fixed_query_2.gff', 'fixed file should have expected changes');
46 remove_tree('fixed_input_files');
47
48 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff', 't/data/reformat_input_gffs/query_2.gff', 't/data/reformat_input_gffs/query_3.gff']), 'initialise with 3 input gffs, 2 identical duplicates');
49 ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist before running');
50 ok($obj->fix_duplicate_gene_ids, 'fix duplicates with 3 input gffs');
51 ok(( -d 'fixed_input_files'), 'Directory should exist because there are 2 gffs thats fixed');
52 is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff','fixed_input_files/query_2.gff' ] ,'list of gff files 2 in the fixed directory');
53 ok(( -e 'fixed_input_files/query_2.gff'), 'fixed file should exist');
54 ok(!( -e 'fixed_input_files/query_3.gff'), 'fixed file should exist');
55 compare_ok('fixed_input_files/query_2.gff','t/data/reformat_input_gffs/expected_fixed_query_2.gff', 'fixed file should have expected changes');
56 remove_tree('fixed_input_files');
57
58
59 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/real_1.gff']), 'initialise with 1 gff that has shown to have a bug');
60 ok(my $fixed_file = $obj->_add_suffix_to_gene_ids_and_return_new_file('t/data/reformat_input_gffs/real_1.gff', 'id__'), 'fix duplicates');
61 ok(( -e 'fixed_input_files/real_1.gff'), 'fixed file should exist');
62 compare_ok('fixed_input_files/real_1.gff', 't/data/reformat_input_gffs/expected_real_1.gff', 'fixed file should have expected changes');
63 remove_tree('fixed_input_files');
64
65
66 done_testing();
67