[Bioperl-guts-l] bioperl-run/t Pseudowise.t,1.3,1.4

[Jason Stajich]

Update of /home/repository/bioperl/bioperl-run/t
In directory pub.open-bio.org:/tmp/cvs-serv12915/t

Modified Files:
	Pseudowise.t 
Log Message:
an hour of my life gone... pseudowise wrapper is now better suited to actually work and separate parsing from running


Index: Pseudowise.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/t/Pseudowise.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Pseudowise.t	5 Jan 2003 17:24:15 -0000	1.3
--- Pseudowise.t	25 Sep 2005 19:06:40 -0000	1.4
***************
*** 1,7 ****
! #!/usr/local/bin/perl
  # -*-Perl-*-
  ## Bioperl Test Harness Script for Modules
  
  use strict;
  BEGIN {
      eval { require Test; };
--- 1,8 ----
! # $Id$
  # -*-Perl-*-
  ## Bioperl Test Harness Script for Modules
  
  use strict;
+ my $DEBUG = $ENV{BIOPERLDEBUG};
  BEGIN {
      eval { require Test; };
***************
*** 11,15 ****
      use Test;
      use vars qw($NTESTS);
!     $NTESTS = 13;
      plan tests => $NTESTS;
  }
--- 12,16 ----
      use Test;
      use vars qw($NTESTS);
!     $NTESTS = 15;
      plan tests => $NTESTS;
  }
***************
*** 25,74 ****
  use Bio::Seq;
  
- #ok(1);
  my $verbose = -1;
  #my @params = ('dymem', 'linear', 'kbyte', '5000','erroroffstd'=>1);
! my @params = ('dymem'=> 'linear','kbyte'=>'5000','erroroffstd'=>1);
  my  $factory = Bio::Tools::Run::Pseudowise->new(@params);
! ok $factory->isa('Bio::Tools::Run::Pseudowise');
! my $bequiet = 1;
! $factory->quiet($bequiet);  # Suppress pseudowise messages to terminal
  
  
! #test with one file with 2 sequences
  my $inputfilename = Bio::Root::IO->catfile("t","data","ps1.fa");
! my $seq1 = Bio::Seq->new();
! my $seq2 = Bio::Seq->new();
! my $seq3 = Bio::Seq->new();
! my $seqstream = Bio::SeqIO->new(-file => $inputfilename, -fmt => 'Fasta');
! $seq1 = $seqstream->next_seq();
! $seq2 = $seqstream->next_seq();
! $seq3 = $seqstream->next_seq();
  
  
- unless ($factory->executable) {
-     warn("Pseudowise program not found. Skipping tests $Test::ntest to $NTESTS.\n");
-     exit 0;
- }
  my @feat = $factory->predict_genes($seq1, $seq2, $seq3);
  my $geneno = scalar(@feat);
! my @subfeat = $feat[0]->sub_SeqFeature();
  my $exonno = scalar(@subfeat);
  
  ok($geneno, 1);
! ok($exonno, 1);
  ok($feat[0]->isa("Bio::SeqFeatureI"));
  ok($subfeat[0]->isa("Bio::SeqFeatureI"));
  ok($feat[0]->primary_tag, 'pseudogene');
  ok($subfeat[0]->primary_tag, 'exon');
! ok($feat[0]->start, 865);
! ok($subfeat[0]->start, 865);
! ok($feat[0]->end, 897);
! ok($subfeat[0]->end, 897);
! ok($feat[0]->score, 1.67);
! ok($subfeat[0]->score, 1.67);
! 
! 
! 
! 
! 
! 
--- 26,69 ----
  use Bio::Seq;
  
  my $verbose = -1;
  #my @params = ('dymem', 'linear', 'kbyte', '5000','erroroffstd'=>1);
! my @params = ('erroroffstd'=>1,'-verbose' => $DEBUG, 
! 	      quiet => $DEBUG);
  my  $factory = Bio::Tools::Run::Pseudowise->new(@params);
! my $executable = $factory->executable;
! ok($executable);
! if( ! $executable ) {
!     warn("Pseudowise program not found. Skipping tests $Test::ntest to $NTESTS.\n");
!     exit 0;
! }
  
+ warn("$executable\n") if $DEBUG; 
+ ok $factory->isa('Bio::Tools::Run::Pseudowise');
  
! #test with one file with 3 sequences
  my $inputfilename = Bio::Root::IO->catfile("t","data","ps1.fa");
! my $seqstream = Bio::SeqIO->new(-file   => $inputfilename, 
! 				-format => 'fasta');
! my $seq1 = $seqstream->next_seq();
! my $seq2 = $seqstream->next_seq();
! my $seq3 = $seqstream->next_seq();
  
  
  my @feat = $factory->predict_genes($seq1, $seq2, $seq3);
  my $geneno = scalar(@feat);
! ok($geneno,1);
! my @subfeat = $feat[0]->sub_SeqFeature;
  my $exonno = scalar(@subfeat);
  
  ok($geneno, 1);
! ok($exonno, 2);
  ok($feat[0]->isa("Bio::SeqFeatureI"));
  ok($subfeat[0]->isa("Bio::SeqFeatureI"));
  ok($feat[0]->primary_tag, 'pseudogene');
  ok($subfeat[0]->primary_tag, 'exon');
! ok($feat[0]->start, 163);
! ok($subfeat[0]->start, 163);
! ok($feat[0]->end, 626);
! ok($subfeat[0]->end, 213);
! ok($subfeat[1]->start,585);
! ok($subfeat[1]->end, 626);