pyrox.dev
1diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl
2index 72411f3..1deb77b 100755
3--- a/Bio/Ext/Align/test.pl
4+++ b/Bio/Ext/Align/test.pl
5@@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
6 BEGIN {
7 eval { require Test; };
8 use Test;
9- plan tests => 9;
10+ plan tests => 4;
11 }
12
13 use Bio::Ext::Align;
14-use Bio::Tools::dpAlign;
15-use Bio::Seq;
16-use Bio::AlignIO;
17
18 $loaded = 1;
19 ok(1); # modules loaded
20@@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2,
21 $seq2->seq,15,50,STDERR) if $DEBUG;
22
23
24-warn( "Testing Local Alignment case...\n") if $DEBUg;
25-
26-$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);
27-$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",
28- "CAGCCTCGCTTAG",3,-1,3,1,
29- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
30-
31-$out = Bio::SimpleAlign->new();
32-
33-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,
34- -start => $aln->start1,
35- -end => $aln->end1,
36- -id => "one"));
37-
38-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,
39- -start => $aln->start2,
40- -end => $aln->end2,
41- -id => "two"));
42-$alnout->write_aln($out) if $DEBUG;
43-
44-$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,
45- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
46-$out = Bio::SimpleAlign->new();
47-ok($aln);
48-
49-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,
50- -start => $aln->start1,
51- -end => $aln->end1,
52- -id => "one"));
53-
54-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,
55- -start => $aln->start2,
56- -end => $aln->end2,
57- -id => "two"));
58-$alnout->write_aln($out) if $DEBUG;
59-ok(1);
60-
61-warn( "Testing Global Alignment case...\n") if $DEBUG;
62-
63-$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);
64-$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');
65-$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');
66-$aln = $factory->pairwise_alignment($s1, $s2);
67-$alnout->write_aln($aln) if $DEBUG;
68-$factory->align_and_show($s1, $s2) if $DEBUG;
69-
70-ok(1);
71-
72-$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW",
73- -alphabet => 'protein');
74-$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW",
75- -alphabet => 'protein');
76-$aln = $factory->pairwise_alignment($s1, $s2);
77-$alnout->write_aln($aln) if $DEBUG;
78-$factory->align_and_show($s1, $s2) if $DEBUG;
79-ok(1);
80-
81-$prof = $factory->sequence_profile($s1);
82-warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;
83-
84-ok($factory->pairwise_alignment_score($prof,$s2),77);