386d93d06d
Bug: with perl > 5.36, the compiler is more restrictive with errors. This package has implicit function definitions. The fix is to ignore the errors as vep, the main package for that, runs without issue. Also this package is no longer maintained We also add test that were missing from the package. Not all test can be run as they depends on other Perl modules in Bioper.
85 lines
2.7 KiB
Diff
85 lines
2.7 KiB
Diff
diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl
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index 72411f3..1deb77b 100755
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--- a/Bio/Ext/Align/test.pl
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+++ b/Bio/Ext/Align/test.pl
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@@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
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BEGIN {
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eval { require Test; };
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use Test;
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- plan tests => 9;
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+ plan tests => 4;
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}
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use Bio::Ext::Align;
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-use Bio::Tools::dpAlign;
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-use Bio::Seq;
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-use Bio::AlignIO;
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$loaded = 1;
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ok(1); # modules loaded
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@@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2,
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$seq2->seq,15,50,STDERR) if $DEBUG;
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-warn( "Testing Local Alignment case...\n") if $DEBUg;
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-
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-$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);
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-$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",
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- "CAGCCTCGCTTAG",3,-1,3,1,
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- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
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-
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-$out = Bio::SimpleAlign->new();
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-
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-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,
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- -start => $aln->start1,
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- -end => $aln->end1,
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- -id => "one"));
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-
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-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,
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- -start => $aln->start2,
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- -end => $aln->end2,
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- -id => "two"));
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-$alnout->write_aln($out) if $DEBUG;
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-
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-$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,
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- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
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-$out = Bio::SimpleAlign->new();
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-ok($aln);
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-
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-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,
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- -start => $aln->start1,
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- -end => $aln->end1,
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- -id => "one"));
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-
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-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,
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- -start => $aln->start2,
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- -end => $aln->end2,
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- -id => "two"));
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-$alnout->write_aln($out) if $DEBUG;
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-ok(1);
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-
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-warn( "Testing Global Alignment case...\n") if $DEBUG;
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-
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-$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);
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-$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');
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-$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');
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-$aln = $factory->pairwise_alignment($s1, $s2);
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-$alnout->write_aln($aln) if $DEBUG;
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-$factory->align_and_show($s1, $s2) if $DEBUG;
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-
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-ok(1);
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-
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-$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW",
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- -alphabet => 'protein');
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-$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW",
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- -alphabet => 'protein');
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-$aln = $factory->pairwise_alignment($s1, $s2);
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-$alnout->write_aln($aln) if $DEBUG;
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-$factory->align_and_show($s1, $s2) if $DEBUG;
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-ok(1);
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-
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-$prof = $factory->sequence_profile($s1);
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-warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;
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-
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-ok($factory->pairwise_alignment_score($prof,$s2),77);
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