[Bioperl-guts-l] bioperl-live/t scf.t,1.12,1.13

Christopher John Fields cjfields at dev.open-bio.org
Mon Jan 29 09:40:32 EST 2007


Update of /home/repository/bioperl/bioperl-live/t
In directory dev.open-bio.org:/tmp/cvs-serv30448/t

Modified Files:
	scf.t 
Log Message:
Bug 2197

Index: scf.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/scf.t,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** scf.t	4 Nov 2006 04:41:39 -0000	1.12
--- scf.t	29 Jan 2007 14:40:30 -0000	1.13
***************
*** 13,22 ****
      # we include the t dir (where a copy of Test.pm is located)
      # as a fallback
!     eval { require Test; };
      if( $@ ) {
!         use lib 't';
      }
!     use Test;
!     plan tests => 17;
  }
  
--- 13,25 ----
      # we include the t dir (where a copy of Test.pm is located)
      # as a fallback
!     eval { require Test::More; };
      if( $@ ) {
!         use lib 't/lib';
      }
!     use Test::More;
!     plan tests => 33;
! 	use_ok('Bio::SeqIO::scf');
! 	use_ok('Bio::Seq::SequenceTrace');
! 
  }
  
***************
*** 35,41 ****
  $dumper->veryCompact(1) if $DEBUG;
  
- use Bio::SeqIO::scf;
- use Bio::Seq::SequenceTrace;
- 
  my $in_scf = Bio::SeqIO->new(-file => Bio::Root::IO->catfile
  									  ("t","data","chad100.scf"),
--- 38,41 ----
***************
*** 46,70 ****
  my $swq = $in_scf->next_seq();
  
! ok (ref($swq) eq "Bio::Seq::SequenceTrace");
  
! ok (length($swq->seq())>10);
  my $qualities = join(' ',@{$swq->qual()});
  
! ok (length($qualities)>10);
  my $id = $swq->id();
! ok ($swq->id() eq "ML4942R");
  
  my $a_channel = $swq->trace("a");
! ok (scalar(@$a_channel) > 10);
  my $c_channel = $swq->trace("c");
! ok (length($c_channel) > 10);
  my $g_channel = $swq->trace("g");
! ok (length($g_channel) > 10);
  my $t_channel = $swq->trace("t");
! ok (length($t_channel) > 10);
  
  my $ref = $swq->peak_indices();
  my @indices = @$ref;
! ok (scalar(@indices), 761);
  
  warn("Now checking version3...\n") if $DEBUG;
--- 46,70 ----
  my $swq = $in_scf->next_seq();
  
! isa_ok($swq,"Bio::Seq::SequenceTrace");
  
! cmp_ok (length($swq->seq()), '>', 10);
  my $qualities = join(' ',@{$swq->qual()});
  
! cmp_ok (length($qualities), '>', 10);
  my $id = $swq->id();
! is ($swq->id(), "ML4942R");
  
  my $a_channel = $swq->trace("a");
! cmp_ok (scalar(@$a_channel), '>', 10);
  my $c_channel = $swq->trace("c");
! cmp_ok (scalar(@$c_channel), '>', 10);
  my $g_channel = $swq->trace("g");
! cmp_ok (scalar(@$g_channel), '>', 10);
  my $t_channel = $swq->trace("t");
! cmp_ok (scalar(@$t_channel), '>', 10);
  
  my $ref = $swq->peak_indices();
  my @indices = @$ref;
! is (scalar(@indices), 761);
  
  warn("Now checking version3...\n") if $DEBUG;
***************
*** 75,114 ****
  
  my $v3 = $in_scf_v3->next_seq();
  my $ind = $v3->peak_indices();
  my @ff = @$ind;
  
  @indices = @{$v3->peak_indices()};
! ok (scalar(@indices) == 1106);
  
  my %header = %{$in_scf_v3->get_header()};
! ok $header{bases}, 1106;
! ok $header{samples},  14107;
  
! my $ac = $in_scf_v3->get_comments();
  
! ok (ref($ac) eq "Bio::Annotation::Collection");
  
  my @name_comments = grep {$_->tagname() eq 'NAME'} 
    $ac->get_Annotations('comment');
  
! ok $name_comments[0]->as_text(), 'Comment: IIABP1D4373';
  
  my @conv_comments = grep {$_->tagname() eq 'CONV'} 
    $ac->get_Annotations('comment');
  
! ok $conv_comments[0]->as_text(), 'Comment: phred version=0.990722.h';
  
  # is the SequenceTrace object annotated?
  my $st_ac = $swq->annotation();
  
! ok (ref($st_ac) eq "Bio::Annotation::Collection");
  
! warn("Now testing the _writing_ of scfs\n") if $DEBUG;
  
  my $out_scf = Bio::SeqIO->new(-file => ">write_scf.scf",
  										-format => 'scf',
  										-verbose => $verbose);
  exit;	# the new way
  
  $out_scf->write_seq(-target	=>	$v3,
  						  -MACH		=>	'CSM sequence-o-matic 5000',
--- 75,163 ----
  
  my $v3 = $in_scf_v3->next_seq();
+ isa_ok($v3, 'Bio::Seq::SequenceTrace');
  my $ind = $v3->peak_indices();
  my @ff = @$ind;
  
  @indices = @{$v3->peak_indices()};
! is (scalar(@indices), 1106);
  
  my %header = %{$in_scf_v3->get_header()};
! is $header{bases}, 1106;
! is $header{samples},  14107;
  
! # is the Bio::Seq::SequenceTrace AnnotatableI?
! my $ac = $v3->annotation();
  
! isa_ok($ac,"Bio::Annotation::Collection");
  
  my @name_comments = grep {$_->tagname() eq 'NAME'} 
    $ac->get_Annotations('comment');
  
! is $name_comments[0]->as_text(), 'Comment: IIABP1D4373';
! 
! # also get comments this way...
! $ac = $in_scf_v3->get_comments();
! 
! isa_ok($ac,"Bio::Annotation::Collection");
! 
! @name_comments = grep {$_->tagname() eq 'NAME'} 
!   $ac->get_Annotations('comment');
! 
! is $name_comments[0]->as_text(), 'Comment: IIABP1D4373';
  
  my @conv_comments = grep {$_->tagname() eq 'CONV'} 
    $ac->get_Annotations('comment');
  
! is $conv_comments[0]->as_text(), 'Comment: phred version=0.990722.h';
  
  # is the SequenceTrace object annotated?
  my $st_ac = $swq->annotation();
  
! isa_ok ($st_ac, "Bio::Annotation::Collection");
  
! my @ann =   $st_ac->get_Annotations();
! 
! is $ann[0]->tagname, 'SIGN';
! is $ann[2]->text, 'SRC3700';
! is $ann[5]->tagname, 'LANE';
! is $ann[5]->text, 89;
! is $ann[6]->text, 'phred version=0.980904.e';
! is $ann[8]->text, 'ABI 373A or 377';
  
  my $out_scf = Bio::SeqIO->new(-file => ">write_scf.scf",
  										-format => 'scf',
  										-verbose => $verbose);
+ 
+ # Bug 2196 - commentless scf
+ 
+ my $in = Bio::SeqIO->new(-file => Bio::Root::IO->catfile
+ 							  qw(t data 13-pilE-F.scf),
+ 							  -format => 'scf',
+ 							  -verbose => $verbose);
+ 
+ my $seq = $in->next_seq;
+ 
+ ok ($seq);
+ 
+ isa_ok($seq, 'Bio::Seq::SequenceTrace');
+ 
+ $ac = $seq->annotation;
+ 
+ isa_ok($ac, 'Bio::Annotation::Collection');
+ 
+ @name_comments = grep {$_->tagname() eq 'NAME'} 
+   $ac->get_Annotations('comment');
+ 
+ is $name_comments[0], undef;
+ 
+ @conv_comments = grep {$_->tagname() eq 'CONV'} 
+   $ac->get_Annotations('comment');
+ 
+ is $conv_comments[0], undef;
+ 
  exit;	# the new way
  
+ warn("Now testing the _writing_ of scfs\n") if $DEBUG;
+ 
  $out_scf->write_seq(-target	=>	$v3,
  						  -MACH		=>	'CSM sequence-o-matic 5000',
***************
*** 152,157 ****
  my $sub_v3 = $v3->sub_trace_object(5,50);
  
! warn("The subtrace object is this:\n") if $DEBUG;
! $dumper->dumpValue($sub_v3) if $DEBUG;
  
  $out_scf->write_seq(-target => $sub_v3 );
--- 201,206 ----
  my $sub_v3 = $v3->sub_trace_object(5,50);
  
! #warn("The subtrace object is this:\n") if $DEBUG;
! #$dumper->dumpValue($sub_v3) if $DEBUG;
  
  $out_scf->write_seq(-target => $sub_v3 );
***************
*** 169,171 ****
                       -version => 2 );
  
! # now some version 2 things.
--- 218,220 ----
                       -version => 2 );
  
! # now some version 2 things...



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