[Bioperl-guts-l] bioperl-live/t rnamotif.t,1.5,1.6

Christopher John Fields cjfields at dev.open-bio.org
Thu Jan 11 09:15:38 EST 2007


Update of /home/repository/bioperl/bioperl-live/t
In directory dev.open-bio.org:/tmp/cvs-serv28224

Modified Files:
	rnamotif.t 
Log Message:
Bug 2182

Index: rnamotif.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/rnamotif.t,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** rnamotif.t	29 Nov 2006 11:38:47 -0000	1.5
--- rnamotif.t	11 Jan 2007 14:15:35 -0000	1.6
***************
*** 17,30 ****
  
      use Test::More;
! 	
! 	eval {
! 		require Bio::Tools::RNAMotif;
! 	};
! 	if ($@) {
! 		plan skip_all => 'Bio::Tools::RNAMotif failed to load, DB_File probably not installed. This means that the module is not usable. Skipping tests';
! 	}
! 	else {
! 		plan tests => 72;
! 	}
  }
  
--- 17,30 ----
  
      use Test::More;
!     
!     eval {
!         require Bio::Tools::RNAMotif;
!     };
!     if ($@) {
!         plan skip_all => 'Bio::Tools::RNAMotif failed to load, DB_File probably not installed. This means that the module is not usable. Skipping tests';
!     }
!     else {
!         plan tests => 72;
!     }
  }
  
***************
*** 36,40 ****
  
  my $parser = new Bio::Tools::RNAMotif(
! 		-verbose => $verbose,
          -file => Bio::Root::IO->catfile('t','data','trna.strict.rnamotif'),
          -motiftag => 'tRNA_gene',
--- 36,40 ----
  
  my $parser = new Bio::Tools::RNAMotif(
!         -verbose => $verbose,
          -file => Bio::Root::IO->catfile('t','data','trna.strict.rnamotif'),
          -motiftag => 'tRNA_gene',
***************
*** 71,75 ****
  
  $parser = Bio::Tools::RNAMotif->new(
! 			-verbose => $verbose,
              -file => Bio::Root::IO->catfile('t','data','sprintf.rnamotif'),
              -motiftag => 'term',
--- 71,75 ----
  
  $parser = Bio::Tools::RNAMotif->new(
!             -verbose => $verbose,
              -file => Bio::Root::IO->catfile('t','data','sprintf.rnamotif'),
              -motiftag => 'term',
***************
*** 119,147 ****
  
  $parser = Bio::Tools::ERPIN->new(
! 			-verbose => $verbose,
              -file => Bio::Root::IO->catfile('t','data','testfile.erpin'),
              -motiftag => 'protein_bind',
! 			-desctag =>  'pyrR_BL');
  
  while( my $gene = $parser->next_prediction ) {
! 	my @stats = @{ shift @erpinstats };
! 	is($gene->display_name, 'pyrR_BL','ERPIN::display_name()');
! 	is($gene->seq_id, shift @stats,'ERPIN::seq_id()');
! 	is($gene->primary_tag, 'protein_bind','ERPIN::primary_tag()');
! 	is($gene->start, shift @stats,'ERPIN::start()');
! 	is($gene->end, shift @stats,'ERPIN::end()');
! 	is($gene->strand, shift @stats,'ERPIN::strand()');
! 	is($gene->get_Annotations('sequence'), shift @stats,
! 	   "ERPIN::get_Annotations('sequence')");
! 	is($gene->get_Annotations('descfile'), shift @stats,
! 	   "ERPIN::get_Annotations('descfile')");
! 	is($gene->get_Annotations('descline'), shift @stats,
! 	   "ERPIN::get_Annotations('descline')");
! 	is($gene->get_Annotations('secstructure'), shift @stats,
! 	   "ERPIN::get_Annotations('secstructure')");
! 	is($gene->score, shift @stats,'ERPIN::score()');
! 	is($gene->source_tag, 'ERPIN','ERPIN::source_tag()');
  }
  
  ### Infernal.pm tests ###
  ### FASTR.pm tests ###
\ No newline at end of file
--- 119,209 ----
  
  $parser = Bio::Tools::ERPIN->new(
!             -verbose => $verbose,
              -file => Bio::Root::IO->catfile('t','data','testfile.erpin'),
              -motiftag => 'protein_bind',
!             -desctag =>  'pyrR_BL');
  
  while( my $gene = $parser->next_prediction ) {
!     my @stats = @{ shift @erpinstats };
!     is($gene->display_name, 'pyrR_BL','ERPIN::display_name()');
!     is($gene->seq_id, shift @stats,'ERPIN::seq_id()');
!     is($gene->primary_tag, 'protein_bind','ERPIN::primary_tag()');
!     is($gene->start, shift @stats,'ERPIN::start()');
!     is($gene->end, shift @stats,'ERPIN::end()');
!     is($gene->strand, shift @stats,'ERPIN::strand()');
!     is($gene->get_Annotations('sequence'), shift @stats,
!        "ERPIN::get_Annotations('sequence')");
!     is($gene->get_Annotations('descfile'), shift @stats,
!        "ERPIN::get_Annotations('descfile')");
!     is($gene->get_Annotations('descline'), shift @stats,
!        "ERPIN::get_Annotations('descline')");
!     is($gene->get_Annotations('secstructure'), shift @stats,
!        "ERPIN::get_Annotations('secstructure')");
!     is($gene->score, shift @stats,'ERPIN::score()');
!     is($gene->source_tag, 'ERPIN','ERPIN::source_tag()');
  }
  
  ### Infernal.pm tests ###
+ 
+ # Infernal 0.70
+ $parser = Bio::Tools::Infernal->new(
+             -verbose => $verbose,
+             -file => Bio::Root::IO->catfile('t','data','test2.infernal'),
+             -motiftag => 'protein_bind',
+             -desctag =>  'pyrR_BL',
+ 	    -cm => 'pyrR.cm',
+ 	    -rfam => 'RF01234',
+ 	    );
+ 
+ while( my $gene = $parser->next_prediction ) {
+     my @stats = @{ shift @erpinstats };
+     is($gene->display_name, 'pyrR_BL','ERPIN::display_name()');
+     is($gene->seq_id, shift @stats,'ERPIN::seq_id()');
+     is($gene->primary_tag, 'protein_bind','ERPIN::primary_tag()');
+     is($gene->start, shift @stats,'ERPIN::start()');
+     is($gene->end, shift @stats,'ERPIN::end()');
+     is($gene->strand, shift @stats,'ERPIN::strand()');
+     is($gene->get_Annotations('sequence'), shift @stats,
+        "ERPIN::get_Annotations('sequence')");
+     is($gene->get_Annotations('descfile'), shift @stats,
+        "ERPIN::get_Annotations('descfile')");
+     is($gene->get_Annotations('descline'), shift @stats,
+        "ERPIN::get_Annotations('descline')");
+     is($gene->get_Annotations('secstructure'), shift @stats,
+        "ERPIN::get_Annotations('secstructure')");
+     is($gene->score, shift @stats,'ERPIN::score()');
+     is($gene->source_tag, 'ERPIN','ERPIN::source_tag()');
+ }
+ 
+ # Infernal 0.71
+ 
+ $parser = Bio::Tools::Infernal->new(
+             -verbose => $verbose,
+             -file => Bio::Root::IO->catfile('t','data','test2.infernal'),
+             -motiftag => 'protein_bind',
+             -desctag =>  'pyrR_BL',
+ 	    -cm => 'pyrR.cm',
+ 	    -rfam => 'RF01234',
+ 	    );
+ 
+ while( my $gene = $parser->next_prediction ) {
+     my @stats = @{ shift @erpinstats };
+     is($gene->display_name, 'pyrR_BL','ERPIN::display_name()');
+     is($gene->seq_id, shift @stats,'ERPIN::seq_id()');
+     is($gene->primary_tag, 'protein_bind','ERPIN::primary_tag()');
+     is($gene->start, shift @stats,'ERPIN::start()');
+     is($gene->end, shift @stats,'ERPIN::end()');
+     is($gene->strand, shift @stats,'ERPIN::strand()');
+     is($gene->get_Annotations('sequence'), shift @stats,
+        "ERPIN::get_Annotations('sequence')");
+     is($gene->get_Annotations('descfile'), shift @stats,
+        "ERPIN::get_Annotations('descfile')");
+     is($gene->get_Annotations('descline'), shift @stats,
+        "ERPIN::get_Annotations('descline')");
+     is($gene->get_Annotations('secstructure'), shift @stats,
+        "ERPIN::get_Annotations('secstructure')");
+     is($gene->score, shift @stats,'ERPIN::score()');
+     is($gene->source_tag, 'ERPIN','ERPIN::source_tag()');
+ }
+ 
  ### FASTR.pm tests ###
\ No newline at end of file



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