* Fix genecard and harvester parsers

[function2gene.git] / bin / function2gene

diff --git a/bin/function2gene b/bin/function2gene
index 922deac9ca044b09f37998fe0e50eec3870ec28c..ed9a38ca23a3b948c7c07913c62efde34d1949a5 100755 (executable)
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -56,7 +56,8 @@ databases.]
 =item B<--restart-at>
 
 If you need to restart the process at a particular state (which has
-already been completed) specify this option.
+already been completed) specify this option. Valid values are get,
+parse, or combine.
 
 =item B<--debug, -d>
 
@@ -78,6 +79,10 @@ Display this manual.
    echo 'transferrin' > keywords.txt
    function2gene --keywords keywords.txt --results keyword_results
 
+   # reparse the results
+   function2gene --keywords keywords.txt --results keyword_results \
+       --restart-at parse
+
 =cut
 
 
@@ -281,13 +286,17 @@ if ($actions{combine}) {
                           @parsed_results,
                          );
      for my $result (@parsed_results) {
-         s/^parsed_results_//;
-         s/\.txt$//;
-         my ($db,$keyword) = split /_/, $_, 2;
+         $result =~ s/^parsed_results_//;
+         $result =~ s/\.txt$//;
+         my ($db,$keyword) = split /_/, $result, 2;
          $state{done_keywords}{combined}{$db}{$keyword} = 1;
      }
      save_state(\%state);
-     ADVISE("Finished; results in $options{results}/combined_results");
+     write_command_to_file('combined_results_table.txt',
+                          "$base_dir/results_to_table",
+                          'combined_results.txt',
+                         );
+     ADVISE("Finished; results in $options{results}/combined_results.txt");
 }
 else {
      ADVISE('Nothing to do. [Perhaps you wanted --restart-at?]');