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What happens if I push all of nixpkgs
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2.8 kB · 84 lines
12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.plindex 72411f3..1deb77b 100755--- a/Bio/Ext/Align/test.pl+++ b/Bio/Ext/Align/test.pl@@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0; BEGIN { eval { require Test; }; use Test;- plan tests => 9;+ plan tests => 4; } use Bio::Ext::Align;-use Bio::Tools::dpAlign;-use Bio::Seq;-use Bio::AlignIO; $loaded = 1; ok(1); # modules loaded@@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2, $seq2->seq,15,50,STDERR) if $DEBUG; -warn( "Testing Local Alignment case...\n") if $DEBUg;--$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);-$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",- "CAGCCTCGCTTAG",3,-1,3,1,- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);--$out = Bio::SimpleAlign->new();--$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,- -start => $aln->start1,- -end => $aln->end1,- -id => "one"));--$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,- -start => $aln->start2,- -end => $aln->end2,- -id => "two"));-$alnout->write_aln($out) if $DEBUG;--$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);-$out = Bio::SimpleAlign->new();-ok($aln);--$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,- -start => $aln->start1,- -end => $aln->end1,- -id => "one"));--$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,- -start => $aln->start2,- -end => $aln->end2,- -id => "two"));-$alnout->write_aln($out) if $DEBUG;-ok(1);--warn( "Testing Global Alignment case...\n") if $DEBUG;--$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);-$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');-$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');-$aln = $factory->pairwise_alignment($s1, $s2);-$alnout->write_aln($aln) if $DEBUG;-$factory->align_and_show($s1, $s2) if $DEBUG;--ok(1);--$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW", - -alphabet => 'protein');-$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW", - -alphabet => 'protein');-$aln = $factory->pairwise_alignment($s1, $s2);-$alnout->write_aln($aln) if $DEBUG;-$factory->align_and_show($s1, $s2) if $DEBUG;-ok(1);--$prof = $factory->sequence_profile($s1);-warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;--ok($factory->pairwise_alignment_score($prof,$s2),77);