X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Ffunction2gene;h=b6810e2be8c8ed4eab05cedd73ca50b99e3d6719;hp=f3bd3ddfd7364a89afac2c4d391e43b3787e8b8d;hb=ad648ff8ab8c675513d4ae80be9cd73ee0c64551;hpb=364cd5a25c2bb985b587a6b0b5d2e23de18d9c10

diff --git a/bin/function2gene b/bin/function2gene
index f3bd3dd..b6810e2 100755
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -192,6 +192,7 @@ if (@{$options{keywords}}) {
 	       next if /^\s*[#;]/;
 	       next unless /\w+/;
 	       chomp;
+	       s/\r$//;
 	       my ($keyword,$weight) = split /\t/, $_;
 	       $weight = 1 if not defined $weight;
 	       $state{keyword_weight}{$keyword} = $weight;
@@ -339,13 +340,18 @@ if ($actions{combine}) {
 			   } keys %{$state{done_keywords}{parse}};
 
      # create temporary file to store keyword weights
-
-     write_command_to_file('combined_results.txt',
-			   "$base_dir/combine_results",
-			   '--keywords',
-			   
-			   @parsed_results,
-			  );
+     my $file = IO::File->new('combined_keywords.txt','w') or
+	  die "Unable to open combined_keywords.txt for writing: $!";
+     for my $keyword (keys %{$state{keyword_weight}}) {
+	  print {$file} "$keyword\t$state{keyword_weight}{$keyword}\n";
+     }
+     system("$base_dir/combine_results",
+	    '--keywords','combined_keywords.txt',
+	    '--results','combined_results.txt',
+	    '--results-table','combined_results_table.txt',
+	    @parsed_results,
+	   ) == 0
+		or die "combine_results failed with ".($?>>8);
      for my $result (@parsed_results) {
 	  $result =~ s/^parsed_results_//;
 	  $result =~ s/\.txt$//;
@@ -353,10 +359,6 @@ if ($actions{combine}) {
 	  $state{done_keywords}{combined}{$db}{$keyword} = 1;
      }
      save_state(\%state);
-     write_command_to_file('combined_results_table.txt',
-			   "$base_dir/results_to_table",
-			   'combined_results.txt',
-			  );
      ADVISE("Finished; results in $options{results}/combined_results.txt");
 }
 else {