From 165c0e682d96693b4cab5239c6eeb8b8ce682cfb Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Wed, 15 Feb 2012 15:28:51 +0000
Subject: [PATCH] New test for veracity of FASTA Serializer class. Tests
custom headers and compares results for SeqDumper and FASTA Serializer.
---
modules/t/fastaSerializer.t | 83 +++++++++++++++++++++++++++++++++++++
1 file changed, 83 insertions(+)
create mode 100644 modules/t/fastaSerializer.t
diff --git a/modules/t/fastaSerializer.t b/modules/t/fastaSerializer.t
new file mode 100644
index 0000000000..eadc6db831
--- /dev/null
+++ b/modules/t/fastaSerializer.t
@@ -0,0 +1,83 @@
+use strict;
+use warnings;
+
+use Test::More;
+use Test::Exception;
+use File::Temp qw/tempfile/;
+
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+use Bio::EnsEMBL::Utils::IO::FASTASerializer;
+use Bio::EnsEMBL::Utils::SeqDumper;
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::Utils::IO qw/work_with_file/;
+
+# Get some basic underpinnings for testing
+
+my $multi_db = Bio::EnsEMBL::Test::MultiTestDB->new;
+my $db = $multi_db->get_DBAdaptor('core');
+
+#
+# TEST - Slice creation from adaptor
+#
+my $slice_adaptor = $db->get_SliceAdaptor;
+my $coord_adaptor = $db->get_CoordSystemAdaptor();
+my $coord_system = $coord_adaptor->fetch_by_name('chromosome');
+
+# instantiate slice
+#SEQ COORD_SYSTEM SEQ_REGION_NAME SEQ_REGION_LENGTH
+# START END STRAND ADAPTOR EMPTY
+
+my $slice = Bio::EnsEMBL::Slice->new(
+ -SEQ_REGION_NAME => "top_banana",
+ -COORD_SYSTEM => $coord_system,
+ -STRAND => 1,
+ -START => 110,
+ -END => 199,
+ -SEQ_REGION_LENGTH => 90,
+ -SEQ => "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGCGCGCGCGGGA",
+);
+
+# ensure Serializer produces output identical to the well-used SeqDumper.
+my $fh_SeqDumper = tempfile();
+
+Bio::EnsEMBL::Utils::SeqDumper->dump_fasta( $slice, $fh_SeqDumper);
+
+my $fh_Serializer = tempfile();
+my $serializer = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($fh_Serializer);
+$serializer->print_Seq($slice);
+
+$fh_SeqDumper->seek(0,0);
+$fh_Serializer->seek(0,0);
+
+local $/ = undef;
+
+my $SeqDumper_output = <$fh_SeqDumper>;
+my $Serializer_output = <$fh_Serializer>;
+
+$fh_SeqDumper->close;
+$fh_Serializer->close;
+
+#print STDERR $Serializer_output."\n";
+
+is ($SeqDumper_output,$Serializer_output,"Outputs should match from both serializers");
+
+# Test custom header capabilities
+
+my $custom_header = sub {
+ my $slice = shift;
+ return ">It's a FASTA header";
+};
+
+$fh_Serializer = tempfile();
+$serializer = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($fh_Serializer, $custom_header);
+$serializer->print_Seq($slice);
+$fh_Serializer->seek(0,0);
+$Serializer_output = <$fh_Serializer>;
+
+print $Serializer_output."\n";
+
+is ($Serializer_output,">It's a FASTA header\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAAAAAAAAAAAAAAAAAAAAA\nAAAAAAAAAAAAAAAAACGCGCGCGCGGGA\n", "Serializer custom header should override correctly.");
+$fh_Serializer->close;
+
+done_testing();
\ No newline at end of file
--
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