[Bioperl-guts-l] bioperl-live/t StandAloneBlast.t, 1.31, 1.32 qual.t, 1.10, 1.11 Perl.t, 1.12, 1.13

Senduran Balasubramaniam sendu at dev.open-bio.org
Wed Jun 27 06:59:01 EDT 2007


Update of /home/repository/bioperl/bioperl-live/t
In directory dev.open-bio.org:/tmp/cvs-serv27622/t

Modified Files:
	StandAloneBlast.t qual.t Perl.t 
Log Message:
corrected in/outfile problem

Index: qual.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/qual.t,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** qual.t	27 Jun 2007 10:16:38 -0000	1.10
--- qual.t	27 Jun 2007 10:58:59 -0000	1.11
***************
*** 46,50 ****
                      -qual =>   \@quals,
                      -header   =>   "Hank is a good cat. I gave him a bath yesterday.");
! my $out = Bio::SeqIO->new(-file  =>   '>write_qual2.qual',
                           -format   =>   'qual');
  # yes, that works
--- 46,50 ----
                      -qual =>   \@quals,
                      -header   =>   "Hank is a good cat. I gave him a bath yesterday.");
! my $out = Bio::SeqIO->new(-file  =>   ">".test_output_file(),
                           -format   =>   'qual');
  # yes, that works

Index: StandAloneBlast.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/StandAloneBlast.t,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** StandAloneBlast.t	27 Jun 2007 10:16:38 -0000	1.31
--- StandAloneBlast.t	27 Jun 2007 10:58:59 -0000	1.32
***************
*** 70,78 ****
  
  # dashed parameters should work
  ok my $factory = Bio::Tools::Run::StandAloneBlast->new(-verbose     => $verbose,
  													   -program     => 'blastn',
  													   -database    => $nt_database , 
  													   -_READMETHOD => 'SearchIO', 
! 													   -output      => 'blastreport.out',
  													   -verbose     => 0);
  is $factory->database, $nt_database;
--- 70,79 ----
  
  # dashed parameters should work
+ my $outfile = test_output_file();
  ok my $factory = Bio::Tools::Run::StandAloneBlast->new(-verbose     => $verbose,
  													   -program     => 'blastn',
  													   -database    => $nt_database , 
  													   -_READMETHOD => 'SearchIO', 
! 													   -output      => $outfile,
  													   -verbose     => 0);
  is $factory->database, $nt_database;
***************
*** 83,87 ****
  			  'database'    => $nt_database , 
  			  '_READMETHOD' => 'SearchIO', 
! 			  'output'      => 'blastreport.out',
  			  'verbose'     => 0 );
  ok $factory = Bio::Tools::Run::StandAloneBlast->new('-verbose' => $verbose, @params);
--- 84,88 ----
  			  'database'    => $nt_database , 
  			  '_READMETHOD' => 'SearchIO', 
! 			  'output'      => $outfile,
  			  'verbose'     => 0 );
  ok $factory = Bio::Tools::Run::StandAloneBlast->new('-verbose' => $verbose, @params);

Index: Perl.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/Perl.t,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Perl.t	27 Jun 2007 10:16:37 -0000	1.12
--- Perl.t	27 Jun 2007 10:58:59 -0000	1.13
***************
*** 34,38 ****
  isa_ok $seq_object_array[1], 'Bio::SeqI';
  
! $filename = 'Perltmp';
  ok write_sequence(">$filename",'genbank',$seq_object);
  ok ($seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232"));
--- 34,38 ----
  isa_ok $seq_object_array[1], 'Bio::SeqI';
  
! $filename = test_output_file();
  ok write_sequence(">$filename",'genbank',$seq_object);
  ok ($seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232"));



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