[Bioperl-guts-l] [15000] bioperl-live/trunk/t: Remove redundant test files

Christopher John Fields cjfields at dev.open-bio.org
Mon Nov 17 17:57:51 EST 2008


Revision: 15000
Author:   cjfields
Date:     2008-11-17 17:57:51 -0500 (Mon, 17 Nov 2008)

Log Message:
-----------
Remove redundant test files

Removed Paths:
-------------
    bioperl-live/trunk/t/Exonerate.t
    bioperl-live/trunk/t/RNA_SearchIO.t
    bioperl-live/trunk/t/Sim4.t
    bioperl-live/trunk/t/UCSCParsers.t
    bioperl-live/trunk/t/WABA.t
    bioperl-live/trunk/t/hmmer.t
    bioperl-live/trunk/t/hmmer_pull.t

Deleted: bioperl-live/trunk/t/Exonerate.t
===================================================================
--- bioperl-live/trunk/t/Exonerate.t	2008-11-17 22:57:10 UTC (rev 14999)
+++ bioperl-live/trunk/t/Exonerate.t	2008-11-17 22:57:51 UTC (rev 15000)
@@ -1,69 +0,0 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
-
-use strict;
-
-BEGIN {     
-    use lib 't/lib';
-	use BioperlTest;
-	
-	test_begin(-tests => 45);
-	
-	use_ok('Bio::SearchIO');
-}
-
-my ($searchio, $result,$hit,$hsp);
-
-$searchio = Bio::SearchIO->new(-file => test_input_file('testdat.exonerate'),
-			      -format => 'exonerate');
-my @data = ( [qw(ln27 416 Contig124 939
-		 293 416 -1 
-		 1   124 1 
-		 
-		 107 292 -1 
-		 178 363 1 
-		 
-		 66 106 -1
-		 899 939 1
-		 )],
-	     [qw(ln74 644 Contig275 1296 
-		 601 644 -1
-		 901 944 1
-		 
-		 436 600 -1
-		 998 1162    1
-
-		 386 435 -1
-		 1247 1296 1
-		 
-		 )] );
-
-
-my $val;
-
-while( my $r = $searchio->next_result ) {
-    my $d = shift @data;
-    is($r->query_name, shift @$d);
-	SKIP: {
-		$val = shift @$d;
-		skip('no query length available in default output',1);
-	    is($r->query_length, $val);
-		   };
-    
-    my $h = $r->next_hit;
-    is($h->name, shift @$d);
-	SKIP: {
-		$val = shift @$d;
-		skip( 'no hit length available in default output',1);
-	    is($h->length, $val);
-		   };
-    while( my $hsp = $h->next_hsp ) {
-	is($hsp->query->start, shift @$d);
-	is($hsp->query->end, shift @$d);
-	is($hsp->query->strand, shift @$d);
-	
-	is($hsp->hit->start, shift @$d);
-	is($hsp->hit->end, shift @$d);
-	is($hsp->hit->strand, shift @$d);
-    }
-}

Deleted: bioperl-live/trunk/t/RNA_SearchIO.t
===================================================================
--- bioperl-live/trunk/t/RNA_SearchIO.t	2008-11-17 22:57:10 UTC (rev 14999)
+++ bioperl-live/trunk/t/RNA_SearchIO.t	2008-11-17 22:57:51 UTC (rev 15000)
@@ -1,841 +0,0 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
-
-use strict;
-
-BEGIN {
-    use lib 't/lib';
-    use BioperlTest;
-    
-    test_begin(-tests => 495);
-    
-    use_ok('Bio::SearchIO');
-}
-
-my ($searchio, $result,$iter,$hit,$hsp, $algorithm, $meta);
-
-### Infernal ####
-
-$searchio = Bio::SearchIO->new( -format => 'infernal',
-                                -file   => test_input_file('test.infernal'),
-                                # version is reset to the correct one by parser
-                                -version => 0.7, 
-                                -model => 'Purine',
-                                -query_acc => 'RF00167',
-                                -query_desc => 'Purine riboswitch',
-                                -database => 'b_sub.fas',
-                                -hsp_minscore => 40,
-                                -convert_meta => 0,
-                                -verbose => 2
-                               );
-
-$result = $searchio->next_result;
-isa_ok($result, 'Bio::Search::Result::ResultI');
-$algorithm = $result->algorithm;
-is($result->algorithm, 'CMSEARCH', "Result $algorithm");
-is($result->algorithm_reference, undef, "Result $algorithm reference");
-is($result->algorithm_version, 0.7, "Result $algorithm version");
-is($result->available_parameters, 0, "Result parameters");
-is($result->available_statistics, 0, "Result statistics");
-is($result->database_entries, '', "Result entries");
-is($result->database_letters, '', "Result letters");
-is($result->database_name, 'b_sub.fas', "Result database_name");
-is($result->num_hits, 2, "Result num_hits");
-is($result->program_reference, undef, "Result program_reference");
-is($result->query_accession, 'RF00167', "Result query_accession");
-is($result->query_description, 'Purine riboswitch', "Result query_description");
-is($result->query_length, 102, "Result query_length");
-is($result->query_name, 'Purine', "Result query_name");
-
-$hit = $result->next_hit;
-isa_ok($hit, 'Bio::Search::Hit::HitI');
-is($hit->ncbi_gi, '2239287', "Hit GI");
-is($hit->accession, 'U51115.1', "Hit accession");
-is($hit->algorithm, 'CMSEARCH', "Hit algorithm");
-is($hit->bits, 81.29, "Hit bits");
-is($hit->description, '', "Hit description"); # no hit descs yet
-is($hit->locus, 'BSU51115', "Hit locus");
-is($hit->n, 2, "Hit n");
-is($hit->name, 'gi|2239287|gb|U51115.1|BSU51115', "Hit name");
-is($hit->num_hsps, 2, "Hit num_hsps");
-
-# These Bio::Search::Hit::HitI methods are currently unimplemented in
-# Bio::Search::Hit::ModelHit; they may be integrated over time but will require
-# some reconfiguring for Model-based searches
-
-eval { $hit->length_aln() };
-like($@, qr'length_aln not implemented for Model-based searches',
-     "Hit length_aln() not implemented");
-eval {$hit->num_unaligned_hit};
-like($@, qr'num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches',
-     "Hit num_unaligned_hit() not implemented");
-eval {$hit->num_unaligned_query};
-like($@, qr'num_unaligned_query not implemented for Model-based searches',
-     "Hit num_unaligned_query() not implemented");
-eval {$hit->num_unaligned_sbjct};
-like($@, qr'num_unaligned_hit/num_unaligned_sbjct not implemented for Model-based searches',
-     "Hit num_unaligned_sbjct() not implemented");
-eval {$hit->start};
-like($@, qr'start not implemented for Model-based searches','Hit start not implemented');
-eval {$hit->end};
-like($@, qr'end not implemented for Model-based searches','Hit end not implemented');
-eval {$hit->strand};
-like($@, qr'strand not implemented for Model-based searches','Hit strand not implemented');
-eval {$hit->logical_length};
-like($@, qr'logical_length not implemented for Model-based searches','Hit logical_length not implemented');
-eval {$hit->frac_aligned_hit};
-like($@, qr'frac_aligned_hit not implemented for Model-based searches','Hit frac_aligned_hit not implemented');
-eval{$hit->frac_aligned_query};
-like($@, qr'frac_aligned_query not implemented for Model-based searches','Hit frac_aligned_query not implemented');
-eval {$hit->frac_conserved};
-like($@, qr'frac_conserved not implemented for Model-based searches','Hit frac_conserved not implemented');
-eval{$hit->frac_identical};
-like($@, qr'frac_identical not implemented for Model-based searches','Hit frac_identical not implemented');
-eval{$hit->matches};
-like($@, qr'matches not implemented for Model-based searches','Hit matches not implemented');
-eval{$hit->gaps};
-like($@, qr'gaps not implemented for Model-based searches','Hit gaps not implemented');
-eval{$hit->frame};
-like($@, qr'frame not implemented for Model-based searches','Hit frame not implemented');
-eval {$hit->range};
-like($@, qr'range not implemented for Model-based searches','Hit range not implemented');
-eval {$hit->seq_inds};
-like($@, qr'seq_inds not implemented for Model-based searches','Hit seq_inds not implemented');
-
-# p() works but there are no evalues yet for Infernal output, so catch and check...
-eval {$hit->p};
-like($@, qr'P-value not defined. Using expect\(\) instead',
-     "No p values");
-
-is($hit->length, 0, "Hit length");
-is($hit->overlap, 0, "Hit overlap");
-is($hit->query_length, 102, "Hit query_length");
-is($hit->rank, 1, "Hit rank");
-is($hit->raw_score, 81.29, "Hit raw_score");
-is($hit->score, 81.29, "Hit score");
-is($hit->significance, undef, "Hit significance");
-
-$hsp = $hit->next_hsp;
-isa_ok($hsp, 'Bio::Search::HSP::HSPI');
-is($hsp->algorithm, 'CMSEARCH', "HSP algorithm");
-is($hsp->evalue, undef, "HSP evalue");
-isa_ok($hsp->feature1, 'Bio::SeqFeature::Similarity');
-isa_ok($hsp->feature2, 'Bio::SeqFeature::Similarity');
-($meta) = $hsp->feature1->get_tag_values('meta');
-is($meta, ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,)))).))))::::::::::::::');
-($meta) = $hsp->feature2->get_tag_values('meta');
-is($meta, ':::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<<<<<_______>>>>>>>,,)))).))))::::::::::::::');
-
-is($hsp->frame('query'), 0, "HSP frame");
-is($hsp->gaps, 0, "HSP gaps");
-is($hit->length, 0, "Hit length");
-isa_ok($hsp->get_aln, 'Bio::Align::AlignI');
-isa_ok($hsp->hit, 'Bio::SeqFeature::Similarity', "HSP hit");
-is($hsp->hit_string,
-   'CAUGAAAUCAAAACACGACCUCAUAUAAUCUUGGGAAUAUGGCCCAUAAGUUUCUACCCGGCAACCGUAAAUUGCCGGACUAUGcAGGGAAGUGAUCGAUAAA',
-   "HSP hit_string");
-is($hsp->homology_string,
-   ' A+ A+A+ AAAA A   :CUC:UAUAAU: :GGGAAUAUGGCCC: :AGUUUCUACC:GGCAACCGUAAAUUGCC:GACUA:G AG: AA + ++  +++++',
-   "HSP homology_string");
-is($hsp->hsp_group, undef, "HSP hsp_group");
-is($hsp->hsp_length, 103, "HSP hsp_length");
-is($hsp->length, 103, "HSP length");
-is($hsp->links, undef, "HSP links");
-is($hsp->n, '', "HSP n");
-is($hsp->pvalue, undef, "HSP pvalue");
-isa_ok($hsp->query, 'Bio::SeqFeature::Similarity', "HSP query");
-is($hsp->query_string,
-   'aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaGgcaaCCGUAAAuugcCuGACUAcG.aGuaAauauuaaauauuu',
-   "HSP query_string");
-is($hsp->range, 102, "HSP range");
-is($hsp->rank, 1, "HSP rank");
-is($hsp->seq_inds, 67, "HSP seq_inds");
-is($hsp->significance, undef, "HSP significance");
-is($hsp->end, 102, "HSP end");
-is($hsp->expect, undef, "HSP expect");
-
-# These Bio::Search::HSP::HSPI methods are currently unimplemented in
-# Bio::Search::HSP::ModelHSP; they may be integrated over time but will require
-# some reconfiguring for Model-based searches
-
-eval {$hsp->matches};
-like($@, qr'matches not implemented for Model-based searches','HSP matches not implemented');
-eval {$hsp->frac_conserved};
-like($@, qr'frac_conserved not implemented for Model-based searches','HSP frac_conserved not implemented');
-eval {$hsp->frac_identical};
-like($@, qr'frac_identical not implemented for Model-based searches','HSP frac_identical not implemented');
-eval {$hsp->num_conserved};
-like($@, qr'num_conserved not implemented for Model-based searches','HSP num_conserved not implemented');
-eval {$hsp->num_identical};
-like($@, qr'num_identical not implemented for Model-based searches','HSP num_identical not implemented');
-eval {$hsp->percent_identity};
-like($@, qr'percent_identity not implemented for Model-based searches','HSP percent_identity not implemented');
-eval {$hsp->cigar_string};

@@ Diff output truncated at 10000 characters. @@



More information about the Bioperl-guts-l mailing list