[Bioperl-guts-l] bioperl-live/t seqwithquality.t,1.8,1.9

Heikki Lehvaslaiho heikki at pub.open-bio.org
Mon Jul 11 10:40:51 EDT 2005


Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv10732/t

Modified Files:
	seqwithquality.t 
Log Message:
add deprecated warning


Index: seqwithquality.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/seqwithquality.t,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** seqwithquality.t	7 Jul 2005 16:41:22 -0000	1.8
--- seqwithquality.t	11 Jul 2005 14:40:49 -0000	1.9
***************
*** 25,28 ****
--- 25,30 ----
  open (STDERR, ">&STDOUT");
  
+ my $verbosity = -1;
+ 
  print("Checking if the Bio::Seq::SeqWithQuality module could be used...\n") if $DEBUG;
          # test 1
***************
*** 41,50 ****
                              -id  => 'QualityFragment-12',
                              -accession_number => 'X78121',
                              );
  ok(!$@);
  
  
- 
- 
  # create some random quality object with the same number of qualities and the same identifiers
  my $string_quals = "10 20 30 40 50 40 30 20 10";
--- 43,51 ----
                              -id  => 'QualityFragment-12',
                              -accession_number => 'X78121',
+                             -verbose => $verbosity
                              );
  ok(!$@);
  
  
  # create some random quality object with the same number of qualities and the same identifiers
  my $string_quals = "10 20 30 40 50 40 30 20 10";
***************
*** 55,68 ****
                              -id  => 'QualityFragment-12',
                              -accession_number => 'X78121',
                              );
  };
  ok(!$@);
  
       # check to see what happens when you construct the SeqWithQuality object
  my $swq1 = Bio::Seq::SeqWithQuality->new( -seq	=>	$seqobj,
  					-qual		=>	$qualobj);
  ok(!$@);
! 
! 
  
  print("Testing various weird constructors...\n") if $DEBUG;
--- 56,71 ----
                              -id  => 'QualityFragment-12',
                              -accession_number => 'X78121',
+                             -verbose => $verbosity
                              );
  };
  ok(!$@);
  
+ 
       # check to see what happens when you construct the SeqWithQuality object
  my $swq1 = Bio::Seq::SeqWithQuality->new( -seq	=>	$seqobj,
+                                          -verbose => $verbosity,
  					-qual		=>	$qualobj);
  ok(!$@);
! no warnings;
  
  print("Testing various weird constructors...\n") if $DEBUG;
***************
*** 72,83 ****
  eval {
  	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq  =>	$seqobj,
  						-qual	=>	"");
  };
  ok(!$@);
  
- 
  print("\tb) No ids, no sequence, quality object...\n") if $DEBUG;
  	# note that you must provide a alphabet for this one.
  $wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
  					-qual => $qualobj,
  					-alphabet => 'dna'
--- 75,87 ----
  eval {
  	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq  =>	$seqobj,
+                                                 -verbose => $verbosity,
  						-qual	=>	"");
  };
  ok(!$@);
  
  print("\tb) No ids, no sequence, quality object...\n") if $DEBUG;
  	# note that you must provide a alphabet for this one.
  $wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
+                                         -verbose => $verbosity,
  					-qual => $qualobj,
  					-alphabet => 'dna'
***************
*** 86,89 ****
--- 90,94 ----
  eval {
  	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
+                                                 -verbose => $verbosity,
  						-qual => "",
  						-alphabet => 'dna'
***************
*** 94,97 ****
--- 99,103 ----
  eval {
  	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
+                                                 -verbose => $verbosity,
  						-qual => "",
  						-alphabet => 'dna',
***************
*** 105,108 ****
--- 111,115 ----
  eval {
  	$wswq1 = Bio::Seq::SeqWithQuality->new( -seq  =>	"",
+                                                 -verbose => $verbosity,
  							-qual	=>	"");
  };
***************
*** 180,194 ****
  $swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
                                        -qual => '0',
                                       );
  my $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
                                           -qual => '65',
                                       );
  ok  $swq1->length, $swq2->length;
  
  $swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'GC',
                                        -qual => '0 0',
                                       );
  $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'GT',
!                                          -qual => '65 0',
                                       );
  ok  $swq1->length, $swq2->length;
--- 187,205 ----
  $swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
                                        -qual => '0',
+                                       -verbose => $verbosity,
                                       );
  my $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'G',
                                           -qual => '65',
+                                          -verbose => $verbosity,
                                       );
  ok  $swq1->length, $swq2->length;
  
  $swq1 = Bio::Seq::SeqWithQuality->new(-seq =>  'GC',
+                                       -verbose => $verbosity,
                                        -qual => '0 0',
                                       );
  $swq2 = Bio::Seq::SeqWithQuality->new(-seq =>  'GT',
!                                       -verbose => $verbosity,
!                                       -qual => '65 0',
                                       );
  ok  $swq1->length, $swq2->length;



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