X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Ffunction2gene;h=c407047418332d93c80fac96b7712dae31a611e3;hp=07dd2aed5f40500c9c7fc59fbae01c8d58444b28;hb=d8245a8bd7b77af4cdb72418346e52d8834e94a6;hpb=0486e6434cd182e8b30ba008d98ad3d3f008d2ab

diff --git a/bin/function2gene b/bin/function2gene
index 07dd2ae..c407047 100755
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -28,6 +28,7 @@ use Storable;
   --results directory to store results in
   --database databases to search
   --restart-at mode to start searching at
+  --invalidate-state state to invalidate
   --debug, -d debugging level (Default 0)
   --help, -h display this help
   --man, -m display manual
@@ -56,7 +57,16 @@ 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<--invalidate-state>
+
+This is a more powerful version of --restart-at, which can
+specifically invalidate a certain method,database,keyword combination.
+
+For example, you can request that the keyword foo be retreived again
+from ncbi using --invalidate-state 'get,ncbi,foo'
 
 =item B<--debug, -d>
 
@@ -78,6 +88,10 @@ 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
 
 
@@ -94,10 +108,12 @@ my %options = (databases       => [],
 	       help            => 0,
 	       man             => 0,
 	       results         => '',
+	       invalidate_state => [],
 	       );
 
 GetOptions(\%options,'keywords=s@','databases=s@',
 	   'restart_at|restart-at=s','results=s',
+	   'invalidate_state|invalidate-state=s@',
 	   'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -201,6 +217,24 @@ if (exists $options{restart_at} and length $options{restart_at}) {
      }
 }
 
+if (exists $options{invalidate_state}) {
+     for my $invalidate_state (@{$options{invalidate_state}}) {
+	  my ($method,$database,$keyword) = split /,/, $invalidate_state;
+	  if (not exists $state{done_keywords}{$method}) {
+	       print STDERR "Method '$method' does not exist, and cannot be invalidated\n";
+	  }
+	  elsif (not exists $state{done_keywords}{$method}{$database}) {
+	       print STDERR "Database '$database' does not exist for method '$method', and cannot be invalidated\n";
+	  }
+	  elsif (not exists $state{done_keywords}{$method}{$database}{$keyword}) {
+	       print STDERR "Keyword '$keyword' does not exist for database '$database' and method '$method', and cannot be invalidated\n";
+	  }
+	  else {
+	       delete $state{done_keywords}{$method}{$database}{$keyword};
+	  }
+     }
+}
+
 # now we need to figure out what has to happen
 # for each keyword, we check to see if we've got results, parsed
 # results, and combined it. If not, we queue up those actions.
@@ -287,7 +321,11 @@ if ($actions{combine}) {
 	  $state{done_keywords}{combined}{$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?]');