[Bioperl-guts-l] bioperl commit

[Brian Osborne]

bosborne
Thu May 13 23:18:10 EDT 2004
Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv1590/t

Modified Files:
	Index.t 
Log Message:
Mark's patch to Index.t

bioperl-live/t Index.t,1.28,1.29
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/Index.t,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/bioperl/bioperl-live/t/Index.t	2003/06/10 21:34:57	1.28
+++ /home/repository/bioperl/bioperl-live/t/Index.t	2004/05/14 03:18:10	1.29
@@ -6,13 +6,14 @@
 BEGIN {     
     eval { require Test; };
     use vars qw($NUMTESTS);
-    $NUMTESTS = 32;
+    $NUMTESTS = 35;
     if( $@ ) {
 	use lib 't';
     }
     use Test;
     $exit = 0;
     eval { require Bio::Index::Fasta;
+           require Bio::Index::Qual;
 	   require Bio::Index::SwissPfam;
 	   require Bio::Index::EMBL;
 	   require Bio::Index::GenBank;
@@ -100,6 +101,65 @@
 }
 
 {
+    my $ind = Bio::Index::Fasta->new(-filename => 'multifa_index',
+				     -write_flag => 1,
+				     -verbose => 0);
+    $ind->make_index(Bio::Root::IO->catfile($dir,"t","data","multifa.seq.qual"));
+}
+
+ok ( -e "multifa_index" );
+
+{
+    my $ind = Bio::Index::Qual->new(-filename => 'multifa_qual_index',
+                                    -write_flag => 1,
+                                    -verbose => 0);
+    $ind->make_index(Bio::Root::IO->catfile($dir,"t","data","multifa.seq.qual"));
+}
+
+ok ( -e "multifa_qual_index" );
+
+{
+    my %t_seq = (
+        HSEARLOBE               => 321,
+        HSMETOO                 => 134,
+        MMWHISK                 => 62,
+    );
+
+    my $ind_f = Bio::Index::Fasta->new(-FILENAME => 'multifa_index');
+    my $ind_q = Bio::Index::Qual->new(-FILENAME => 'multifa_qual_index');
+
+    my $ok_3 = 1;
+    my $ok_4 = 1;
+    while (my($name, $length) = each %t_seq) {
+        my $seq = $ind_f->fetch($name);
+	my $qual = $ind_q->fetch($name);
+        if( defined($seq) and $seq->isa('Bio::SeqI') ) {
+            my $r_length = $seq->length;
+	    unless ($r_length == $length) {
+                warn "$name - retrieved seq length '$r_length' doesn't match known length '$length'\n";
+                $ok_3 = 0;
+            }
+        } else {
+            warn "Didn't get sequence '$name' from fasta index\n";
+            $ok_3 = 0;
+        }
+	ok $ok_3;
+	if( defined($qual) and $qual->isa('Bio::Seq::QualI') ) {
+            my $r_length = $qual->length;
+	    unless ($r_length == $length) {
+                warn "$name - retrieved qual length '$r_length' doesn't match known length '$length'\n";
+                $ok_4 = 0;
+            }
+        } else {
+            warn "Didn't get sequence '$name' from qual index\n";
+            $ok_4 = 0;
+        }
+
+	ok $ok_4;
+    }
+}
+
+{
     my $ind = Bio::Index::SwissPfam->new(-filename=>'Wibbl2', 
 					 -write_flag=>1);
     $ind->make_index(Bio::Root::IO->catfile($dir,"t","data","swisspfam.data"));