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revision 1.2, Tue Jul 19 19:59:05 2011 UTC revision 1.3, Wed Jul 20 13:09:35 2011 UTC
# Line 74  Line 74 
74                                             "<expressionDirectory>",                                             "<expressionDirectory>",
75                                             @ARGV);                                             @ARGV);
76  # Get the expression directory.  # Get the expression directory.
77  my $expDataDirectory = $parameters[0];  my $mainDirectory = $parameters[0];
78  if (! -d $expDataDirectory) {  if (! -d $mainDirectory) {
79      # It wasn't found, so complain.      # It wasn't found, so complain.
80      Trace("Directory $expDataDirectory not found.") if T(0);      Trace("Directory $mainDirectory not found.") if T(0);
81  } else {  } else {
82      # Get the list of directories to process.      # Get the list of directories to process.
83      my @dirs;      my @dirs;
84      if ($options->{recursive}) {      if ($options->{recursive}) {
85          # Direct mode. Process the incoming directory.          # Direct mode. Process the incoming directory.
86          push @dirs, $expDataDirectory;          push @dirs, $mainDirectory;
87      } else {      } else {
88          # Recursive mode. Process the subdirectories.          # Recursive mode. Process the subdirectories.
89          if (opendir(my $dh, $expDataDirectory)) {          if (opendir(my $dh, $mainDirectory)) {
90              my @genomes = grep { $_ =~ /^\d+$/ } readdir $dh;              my @genomes = grep { $_ =~ /^\d+$/ } readdir $dh;
91              push @dirs, map { "$expDataDirectory/$_" } @genomes;              push @dirs, map { "$mainDirectory/$_" } @genomes;
92          }          }
93      }      }
94        # Process all the directories.
95        for my $expDataDirectory (@dirs) {
96      # Get the raw data file.      # Get the raw data file.
97      my $raw_data_file = "$expDataDirectory/rma_normalized.tab";      my $raw_data_file = "$expDataDirectory/rma_normalized.tab";
98      if (! -f $raw_data_file) {      if (! -f $raw_data_file) {
# Line 143  Line 145 
145          }          }
146      }      }
147  }  }
148    }
149    
150  =head3 compute_pc  =head3 compute_pc
151    

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