[Bioperl-guts-l] [15024] bioperl-live/trunk/t: po, not poa

Christopher John Fields cjfields at dev.open-bio.org
Tue Nov 25 18:59:57 EST 2008


Revision: 15024
Author:   cjfields
Date:     2008-11-25 18:59:57 -0500 (Tue, 25 Nov 2008)

Log Message:
-----------
po, not poa

Added Paths:
-----------
    bioperl-live/trunk/t/AlignIO_po.t

Removed Paths:
-------------
    bioperl-live/trunk/t/AlignIO_poa.t

Copied: bioperl-live/trunk/t/AlignIO_po.t (from rev 15022, bioperl-live/trunk/t/AlignIO_poa.t)
===================================================================
--- bioperl-live/trunk/t/AlignIO_po.t	                        (rev 0)
+++ bioperl-live/trunk/t/AlignIO_po.t	2008-11-25 23:59:57 UTC (rev 15024)
@@ -0,0 +1,57 @@
+# -*-Perl-*- Test Harness script for Bioperl
+# $Id: AlignIO.t 14971 2008-10-28 16:08:52Z cjfields $
+
+use strict;
+
+BEGIN {
+	use lib 't/lib';
+    use BioperlTest;
+    
+    test_begin(-tests => 11);
+	
+	use_ok('Bio::AlignIO');
+}
+
+my $DEBUG = test_debug();
+
+my ($str,$aln,$strout,$status);
+
+# POA
+# just skip on perl 5.6.0 and earlier as it causes a crash on 
+# default perl with OS X 10.2
+# fink perl 5.6.0 does not seem to have the problem
+# can't figure out what it is so just skip for now
+SKIP: {
+	skip("skipping due to bug in perl 5.6.0 that comes with OS X 10.2", 10) unless ($^O ne 'darwin' || $] > 5.006);
+	
+	$str = Bio::AlignIO->new(
+			  -file   => test_input_file('testaln.po'),
+			  -format => 'po',
+			  );
+	isa_ok($str, 'Bio::AlignIO');
+	$aln = $str->next_aln();
+	isa_ok($aln,'Bio::Align::AlignI');
+	is $aln->no_sequences, 6;
+	
+	# output is? i.e. does conversion from clustalw to po give the same alignment?
+	$str = Bio::AlignIO->new(
+		  '-file'   => test_input_file('testaln.aln'),
+		  '-format' => 'clustalw');
+	isa_ok($str,'Bio::AlignIO');
+	$aln = $str->next_aln();
+	isa_ok($aln,'Bio::Align::AlignI');
+	$strout = Bio::AlignIO->new(
+		 '-file'   => ">" . test_output_file(),
+		 '-format' => 'po');
+	$status = $strout->write_aln($aln);
+	is $status, 1, "po output test";
+	
+	$str = Bio::AlignIO->new(
+		 '-file'   => test_input_file('testaln.po'),
+		 '-format' => 'po');
+	isa_ok($str,'Bio::AlignIO');
+	my $aln2 = $str->next_aln();
+	isa_ok($aln2,'Bio::Align::AlignI');
+	is $aln2->no_sequences, $aln->no_sequences;
+	is $aln2->length, $aln->length;
+}

Deleted: bioperl-live/trunk/t/AlignIO_poa.t
===================================================================
--- bioperl-live/trunk/t/AlignIO_poa.t	2008-11-25 23:52:55 UTC (rev 15023)
+++ bioperl-live/trunk/t/AlignIO_poa.t	2008-11-25 23:59:57 UTC (rev 15024)
@@ -1,57 +0,0 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id: AlignIO.t 14971 2008-10-28 16:08:52Z cjfields $
-
-use strict;
-
-BEGIN {
-	use lib 't/lib';
-    use BioperlTest;
-    
-    test_begin(-tests => 11);
-	
-	use_ok('Bio::AlignIO');
-}
-
-my $DEBUG = test_debug();
-
-my ($str,$aln,$strout,$status);
-
-# POA
-# just skip on perl 5.6.0 and earlier as it causes a crash on 
-# default perl with OS X 10.2
-# fink perl 5.6.0 does not seem to have the problem
-# can't figure out what it is so just skip for now
-SKIP: {
-	skip("skipping due to bug in perl 5.6.0 that comes with OS X 10.2", 10) unless ($^O ne 'darwin' || $] > 5.006);
-	
-	$str = Bio::AlignIO->new(
-			  -file   => test_input_file('testaln.po'),
-			  -format => 'po',
-			  );
-	isa_ok($str, 'Bio::AlignIO');
-	$aln = $str->next_aln();
-	isa_ok($aln,'Bio::Align::AlignI');
-	is $aln->no_sequences, 6;
-	
-	# output is? i.e. does conversion from clustalw to po give the same alignment?
-	$str = Bio::AlignIO->new(
-		  '-file'   => test_input_file('testaln.aln'),
-		  '-format' => 'clustalw');
-	isa_ok($str,'Bio::AlignIO');
-	$aln = $str->next_aln();
-	isa_ok($aln,'Bio::Align::AlignI');
-	$strout = Bio::AlignIO->new(
-		 '-file'   => ">" . test_output_file(),
-		 '-format' => 'po');
-	$status = $strout->write_aln($aln);
-	is $status, 1, "po output test";
-	
-	$str = Bio::AlignIO->new(
-		 '-file'   => test_input_file('testaln.po'),
-		 '-format' => 'po');
-	isa_ok($str,'Bio::AlignIO');
-	my $aln2 = $str->next_aln();
-	isa_ok($aln2,'Bio::Align::AlignI');
-	is $aln2->no_sequences, $aln->no_sequences;
-	is $aln2->length, $aln->length;
-}




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