[Bioperl-guts-l] [16545] bioperl-live/trunk/t/AlignIO: tests now allow strandedness; add strand check for those seqs that are now changed

[Christopher John Fields]

Revision: 16545
Author:   cjfields
Date:     2009-12-20 01:03:22 -0500 (Sun, 20 Dec 2009)
Log Message:
-----------
tests now allow strandedness; add strand check for those seqs that are now changed

Modified Paths:
--------------
    bioperl-live/trunk/t/AlignIO/stockholm.t
    bioperl-live/trunk/t/AlignIO/xmfa.t

Modified: bioperl-live/trunk/t/AlignIO/stockholm.t
===================================================================
--- bioperl-live/trunk/t/AlignIO/stockholm.t	2009-12-20 05:59:19 UTC (rev 16544)
+++ bioperl-live/trunk/t/AlignIO/stockholm.t	2009-12-20 06:03:22 UTC (rev 16545)
@@ -7,7 +7,7 @@
 	use lib '.';
     use Bio::Root::Test;
     
-    test_begin(-tests => 83);
+    test_begin(-tests => 84);
 	
 	use_ok('Bio::AlignIO::stockholm');
 }
@@ -77,7 +77,8 @@
 $aln = $str->next_aln();
 is($aln->source, 'stockholm');
 isa_ok($aln,'Bio::Align::AlignI');
-is($aln->get_seq_by_pos(1)->get_nse, 'AJ295015.1/1-58');
+is($aln->get_seq_by_pos(1)->get_nse, 'AJ295015.1/58-1');
+is($aln->get_seq_by_pos(1)->strand, -1);
 is($aln->accession, 'RF00008');
 is($aln->id, 'Hammerhead_3');
 is($aln->description,'Hammerhead ribozyme (type III)');

Modified: bioperl-live/trunk/t/AlignIO/xmfa.t
===================================================================
--- bioperl-live/trunk/t/AlignIO/xmfa.t	2009-12-20 05:59:19 UTC (rev 16544)
+++ bioperl-live/trunk/t/AlignIO/xmfa.t	2009-12-20 06:03:22 UTC (rev 16545)
@@ -7,7 +7,7 @@
 	use lib '.';
     use Bio::Root::Test;
     
-    test_begin(-tests => 16);
+    test_begin(-tests => 18);
 	
 	use_ok('Bio::AlignIO::xmfa');
 }
@@ -22,8 +22,10 @@
 		 -format => 'xmfa');
 $aln = $str->next_aln();
 isa_ok($aln,'Bio::Align::AlignI');
-is $aln->get_seq_by_pos(1)->get_nse, 'chrY/1-598', 
+is $aln->get_seq_by_pos(1)->get_nse, 'chrY/598-1', 
   "xmfa input test ";
+is $aln->get_seq_by_pos(1)->strand, -1, 
+  "xmfa strand test";
 is ($aln->get_seq_by_pos(2)->description, undef, 
     "xmfa input test for description");
 is ($aln->get_seq_by_pos(3)->display_id, 'chr7',
@@ -36,8 +38,10 @@
 
 $aln = $str->next_aln();
 isa_ok($aln,'Bio::Align::AlignI');
-is $aln->get_seq_by_pos(1)->get_nse, 'chrY/1000-1059', 
+is $aln->get_seq_by_pos(1)->get_nse, 'chrY/1059-1000', 
   "xmfa input test ";
+is $aln->get_seq_by_pos(1)->strand, -1, 
+  "xmfa strand";
 is ($aln->get_seq_by_pos(2)->description, undef, 
     "xmfa input test for description");
 is ($aln->get_seq_by_pos(3)->display_id, 'chr12',