From 64e00f69a815961476b7e6d89af3ed26e7dc3cd8 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 15 Jun 2012 13:00:01 +0000
Subject: [PATCH] Updating GFF parser tests
---
modules/t/gffParser.t | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/modules/t/gffParser.t b/modules/t/gffParser.t
index eaf375cafa..427aee3107 100644
--- a/modules/t/gffParser.t
+++ b/modules/t/gffParser.t
@@ -79,4 +79,38 @@ GFF
}
}
+{
+ my $string = <<GFF;
+##gff-version 3
+##sequence-region ctg123 1 1497228
+##taken-from example parsing file with FASTA directive
+ctg123\t.\tgene\t1000\t9000\t.\t+\t.\tID=gene00001;Name=EDEN
+###
+##FASTA
+>ctg123
+AACCTTTGGGCCGGGCCTTAAAA
+AACC
+GFF
+ my $io = IO::String->new(\$string);
+
+ my $gff = Bio::EnsEMBL::Utils::IO::GFFParser->new($io);
+ my $header = $gff->parse_header();
+ is_deeply(
+ $header,
+ [ '##gff-version 3', '##sequence-region ctg123 1 1497228', '##taken-from example parsing file with FASTA directive'],
+ 'Checking headers all parse'
+ );
+ my $actual_gene = $gff->parse_next_feature();
+ my $expected_gene = {
+ seqid => 'ctg123', start => 1000, end => 9000, strand => 1,
+ source => '.', type => 'gene', score => '.', phase => '.',
+ attribute => { ID => 'gene00001', Name => 'EDEN' }
+ };
+ is_deeply($actual_gene, $expected_gene, 'Checking TF record parses');
+ my $id = $gff->parse_next_feature();
+ ok(! defined $id, 'No more features');
+ my $seq = $gff->parse_next_sequence();
+ is_deeply($seq, {header => '>ctg123', sequence => "AACCTTTGGGCCGGGCCTTAAAAAACC"}, "Checking Sequence parses correctly")
+}
+
done_testing();
--
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