diff Roary/t/Bio/Roary/PrepareInputFiles.t @ 0:c47a5f61bc9f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/PrepareInputFiles.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,56 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Data::Dumper;
+use File::Basename;
+
+BEGIN { unshift( @INC, './lib' ) }
+$ENV{PATH} .= ":./bin";
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::PrepareInputFiles');
+}
+
+my $obj;
+
+ok(
+    $obj = Bio::Roary::PrepareInputFiles->new(
+        input_files => [
+            't/data/example_annotation.gff',   't/data/example_1.faa',
+            't/data/example_annotation_2.gff', 't/data/example_2.faa','t/data/sequences_with_unknowns.faa'
+        ],
+    ),
+    'initalise'
+);
+
+my @sorted_fasta_files = sort map { basename($_) } sort @{$obj->fasta_files};
+my @expected_fasta_files = sort((
+            'example_1.faa.tmp.filtered.fa',
+            'example_2.faa.tmp.filtered.fa',
+            'example_annotation.gff.proteome.faa',
+            'example_annotation_2.gff.proteome.faa',
+            'sequences_with_unknowns.faa.tmp.filtered.fa'
+));
+
+is_deeply(
+    \@sorted_fasta_files,
+    \@expected_fasta_files,
+    'proteome extracted from gff files, input fasta files filtered'
+);
+
+my @input_files_lookup = sort map { basename($_) } @{$obj->lookup_fasta_files_from_unknown_input_files( [ 't/data/example_annotation_2.gff', 't/data/example_1.faa' ] )};
+is_deeply(
+    \@input_files_lookup,
+    ['example_1.faa.tmp.filtered.fa','example_annotation_2.gff.proteome.faa'],
+    'previously created faa file looked up from gff filename'
+);
+
+unlink('example_annotation.gff.proteome.faa');
+unlink('example_annotation_2.gff.proteome.faa');
+unlink('sequences_with_unknowns.faa.tmp.filtered.fa');
+unlink('example_1.faa.tmp.filtered.fa');
+unlink('example_2.faa.tmp.filtered.fa');
+
+done_testing();
+