Mercurial > repos > dereeper > roary_plots
view 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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#!/usr/bin/env perl use strict; use warnings; use Data::Dumper; use Test::Files; BEGIN { unshift( @INC, './lib' ) } BEGIN { use Test::Most; use_ok('Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL'); } ok( my $core_gene_obj = Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL->new( multifasta_files => [ 't/data/multifasta_files/1.fa.aln', 't/data/multifasta_files/outof_order.fa.aln', 't/data/multifasta_files/2.fa.aln', 't/data/multifasta_files/3.fa.aln' ], gene_lengths => { 't/data/multifasta_files/1.fa.aln' => 1, 't/data/multifasta_files/outof_order.fa.aln' => 10, 't/data/multifasta_files/2.fa.aln' => 100, 't/data/multifasta_files/3.fa.aln' => 1000 }, output_filename => 'output_name.embl' ), 'initialise core gene obj' ); is('efg',$core_gene_obj->_gene_name_from_filename('t/abc/efg.fa.aln'), 'Get gene name with directory'); is('efg',$core_gene_obj->_gene_name_from_filename('efg.fa.aln'), 'Get gene name with no directory'); is('efg',$core_gene_obj->_gene_name_from_filename('efg'), 'Get gene name where theres no extension'); is('efg',$core_gene_obj->_gene_name_from_filename('efg.fa'), 'Get gene name with partial extension'); ok($core_gene_obj->create_file,'create the embl header file'); compare_ok('output_name.embl', 't/data/multifasta_files/expected_output.embl', 'content of embl file as expected'); is(1112,$core_gene_obj->_current_coordinate,'next coordinate'); unlink('output_name.embl'); done_testing();