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perlPackages.BioExtAlign: bug fix and add test (#380488)
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84 changes: 84 additions & 0 deletions
84
pkgs/development/perl-modules/Bio-Ext-Align/disable-other-tests.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl | ||
| index 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); |
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13 changes: 13 additions & 0 deletions
13
pkgs/development/perl-modules/Bio-Ext-Align/no-implicit-function.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| diff --git a/Bio/Ext/Align/Makefile.PL b/Bio/Ext/Align/Makefile.PL | ||
| index cc6c343..ea5cffa 100755 | ||
| --- a/Bio/Ext/Align/Makefile.PL | ||
| +++ b/Bio/Ext/Align/Makefile.PL | ||
| @@ -5,7 +5,7 @@ WriteMakefile( | ||
| 'NAME' => 'Bio::Ext::Align', | ||
| 'VERSION' => '1.5.1', | ||
| 'LIBS' => ['-lm'], # e.g., '-lm' | ||
| - 'DEFINE' => '-DPOSIX -DNOERROR', # e.g., '-DHAVE_SOMETHING' | ||
| + 'DEFINE' => '-DPOSIX -DNOERROR -Wno-implicit-function-declaration', # e.g., '-DHAVE_SOMETHING' | ||
| 'INC' => '-I./libs', # e.g., '-I/usr/include/other' | ||
| 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', | ||
| 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } |