Mercurial > repos > dereeper > roary_plots
comparison Roary/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.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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-1:000000000000 | 0:c47a5f61bc9f |
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1 #!/usr/bin/env perl | |
2 use strict; | |
3 use warnings; | |
4 use Data::Dumper; | |
5 use Test::Files; | |
6 | |
7 BEGIN { unshift( @INC, './lib' ) } | |
8 | |
9 BEGIN { | |
10 use Test::Most; | |
11 use_ok('Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL'); | |
12 } | |
13 | |
14 ok( | |
15 my $core_gene_obj = Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL->new( | |
16 multifasta_files => [ | |
17 't/data/multifasta_files/1.fa.aln', 't/data/multifasta_files/outof_order.fa.aln', | |
18 't/data/multifasta_files/2.fa.aln', 't/data/multifasta_files/3.fa.aln' | |
19 ], | |
20 gene_lengths => { | |
21 't/data/multifasta_files/1.fa.aln' => 1, | |
22 't/data/multifasta_files/outof_order.fa.aln' => 10, | |
23 't/data/multifasta_files/2.fa.aln' => 100, | |
24 't/data/multifasta_files/3.fa.aln' => 1000 | |
25 }, | |
26 output_filename => 'output_name.embl' | |
27 ), | |
28 'initialise core gene obj' | |
29 ); | |
30 | |
31 is('efg',$core_gene_obj->_gene_name_from_filename('t/abc/efg.fa.aln'), 'Get gene name with directory'); | |
32 is('efg',$core_gene_obj->_gene_name_from_filename('efg.fa.aln'), 'Get gene name with no directory'); | |
33 is('efg',$core_gene_obj->_gene_name_from_filename('efg'), 'Get gene name where theres no extension'); | |
34 is('efg',$core_gene_obj->_gene_name_from_filename('efg.fa'), 'Get gene name with partial extension'); | |
35 | |
36 ok($core_gene_obj->create_file,'create the embl header file'); | |
37 compare_ok('output_name.embl', 't/data/multifasta_files/expected_output.embl', 'content of embl file as expected'); | |
38 | |
39 is(1112,$core_gene_obj->_current_coordinate,'next coordinate'); | |
40 unlink('output_name.embl'); | |
41 | |
42 done_testing(); |