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revision 1.6, Wed Jul 20 13:32:14 2011 UTC revision 1.7, Fri Jul 22 19:12:45 2011 UTC
# Line 56  Line 56 
56  directory, it is treated as a directory of directories, and all the sub-directories  directory, it is treated as a directory of directories, and all the sub-directories
57  are processed.  are processed.
58    
59    =item passive
60    
61    If specified, then no change will be made to the expression directory if the
62    pearson coefficients are already computed.
63    
64  =item h  =item h
65    
66  Display this command's parameters and options.  Display this command's parameters and options.
# Line 70  Line 75 
75    
76  # Get the command-line options and parameters.  # Get the command-line options and parameters.
77  my ($options, @parameters) = StandardSetup([qw() ],  my ($options, @parameters) = StandardSetup([qw() ],
78                                             { recursive => ["", "if specified, all child directories will be processed"] },                                             {
79                                                recursive => ["", "if specified, all child directories will be processed"],
80                                                passive => ["", "if specified, coefficients will only be computed if they don't already exist"],
81                                               },
82                                             "<expressionDirectory>",                                             "<expressionDirectory>",
83                                             @ARGV);                                             @ARGV);
84  # Get the expression directory.  # Get the expression directory.
# Line 95  Line 103 
103      }      }
104      # Process all the directories.      # Process all the directories.
105      for my $expDataDirectory (@dirs) {      for my $expDataDirectory (@dirs) {
106            # Only proceed if we are NOT passive OR there is no pearson file.
107            if ($options->{passive} && -f "$expDataDirectory/pearson.tbl") {
108                Trace("Directory $expDataDirectory skipped due to passive mode.") if T(2);
109            } else {
110          # Get the raw data file.          # Get the raw data file.
111          my $raw_data_file = "$expDataDirectory/rma_normalized.tab";          my $raw_data_file = "$expDataDirectory/rma_normalized.tab";
112          if (! -f $raw_data_file) {          if (! -f $raw_data_file) {
# Line 148  Line 160 
160          }          }
161      }      }
162  }  }
163    }
164    
165  =head3 compute_pc  =head3 compute_pc
166    

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