New test for veracity of FASTA Serializer class. Tests custom headers and...

New test for veracity of FASTA Serializer class.  Tests custom headers and compares results for SeqDumper and FASTA Serializer.

modules/t/fastaSerializer.t

+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