[Bioperl-guts-l] bioperl-run/t Clustalw.t,1.35,1.36

Senduran Balasubramaniam sendu at dev.open-bio.org
Fri Jun 1 04:04:23 EDT 2007


Update of /home/repository/bioperl/bioperl-run/t
In directory dev.open-bio.org:/tmp/cvs-serv7334/t

Modified Files:
	Clustalw.t 
Log Message:
tidy up; test that score is set on the alignment

Index: Clustalw.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/Clustalw.t,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** Clustalw.t	13 Dec 2006 19:08:15 -0000	1.35
--- Clustalw.t	1 Jun 2007 08:04:21 -0000	1.36
***************
*** 6,14 ****
  
  BEGIN {
-   # Things to do ASAP once the script is run
-   # even before anything else in the file is parsed
-   #use vars qw($NUMTESTS $DEBUG $error);
-   #$DEBUG = $ENV{'BIOIPERLDEBUG'} || 0;
-   
    # Use installed Test module, otherwise fall back
    # to copy of Test.pm located in the t dir
--- 6,9 ----
***************
*** 18,30 ****
    }
  
-   # Currently no errors
-   #$error = 0;
- 
    # Setup Test::More and plan the number of tests
!   use Test::More tests=>42;
    
-   # Use modules that are needed in this test that are from
-   # any of the Bioperl packages: Bioperl-core, Bioperl-run ... etc
-   # use_ok('<module::to::use>');
    use_ok('Bio::Tools::Run::Alignment::Clustalw');
    use_ok('Bio::SimpleAlign');
--- 13,19 ----
    }
  
    # Setup Test::More and plan the number of tests
!   use Test::More tests => 43;
    
    use_ok('Bio::Tools::Run::Alignment::Clustalw');
    use_ok('Bio::SimpleAlign');
***************
*** 43,56 ****
  ok( -e $profile2, 'Found profile2 file' );
  
- # setup output files etc
- # none in this test
- 
  # setup global objects that are to be used in more than one test
  # Also test they were initialised correctly
! my @params = (
!          'ktuple' => 3,
! 	 'quiet'  => 1,
! 	 #-verbose => $verbose,
! );
  my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  isa_ok( $factory, 'Bio::Tools::Run::Alignment::Clustalw');
--- 32,38 ----
  ok( -e $profile2, 'Found profile2 file' );
  
  # setup global objects that are to be used in more than one test
  # Also test they were initialised correctly
! my @params = ('ktuple' => 3, 'quiet'  => 1);
  my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  isa_ok( $factory, 'Bio::Tools::Run::Alignment::Clustalw');
***************
*** 65,79 ****
  is( $factory->program_name(), 'clustalw',                'Correct exe default name' );
  
- # block of tests to skip if you know the tests will fail
- # under some condition. E.g.:
- #   Need network access,
- #   Wont work on particular OS,
- #   Cant find the exectuable
- # DO NOT just skip tests that seem to fail for an unknown reason
  SKIP: {
!   # condition used to skip this block of tests
!   #skip($why, $how_many_in_block);
!   skip("Couldn't find the executable", 16)
!     unless defined $factory->executable();
    
    # test all factory methods dependent on finding the executable
--- 47,52 ----
  is( $factory->program_name(), 'clustalw',                'Correct exe default name' );
  
  SKIP: {
!   skip("Couldn't find the executable", 16) unless defined $factory->executable();
    
    # test all factory methods dependent on finding the executable
***************
*** 91,100 ****
    isa_ok( $aln, 'Bio::SimpleAlign');
    is( $aln->no_sequences, 7,                               'Correct number of seqs returned' );
    
    # test execution using an array of Seq objects
!   my $str = Bio::SeqIO->new(
!                         '-file' => $inputfilename,
! 			'-format' => 'Fasta',
!   );
    my @seq_array =();
    while ( my $seq = $str->next_seq() ) {
--- 64,71 ----
    isa_ok( $aln, 'Bio::SimpleAlign');
    is( $aln->no_sequences, 7,                               'Correct number of seqs returned' );
+   is $aln->score, 16047, 'Score';
    
    # test execution using an array of Seq objects
!   my $str = Bio::SeqIO->new('-file' => $inputfilename, '-format' => 'Fasta');
    my @seq_array =();
    while ( my $seq = $str->next_seq() ) {



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