X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bin%2Ffunction2gene;h=66b02bb51ca6e48ed400a5e40abc3b7f325761fb;hb=b7fa49b314e0844bbca5ed06cbe5f7e6bfa651c4;hp=f3bd3ddfd7364a89afac2c4d391e43b3787e8b8d;hpb=364cd5a25c2bb985b587a6b0b5d2e23de18d9c10;p=function2gene.git

diff --git a/bin/function2gene b/bin/function2gene
index f3bd3dd..66b02bb 100755
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -130,7 +130,7 @@ $ERRORS.="restart-at must be one of get, parse or combine\n" if
 
 $ERRORS.="unknown database(s)" if
      @{$options{databases}} and
-     grep {$_ !~ /^(?:ncbi|genecard|harvester)$/i} @{$options{databases}};
+     grep {$_ !~ /^(?:ncbi|genecard|harvester|ensembl|uniprot)$/i} @{$options{databases}};
 
 if (not length $options{results}) {
      $ERRORS.="results directory not specified";
@@ -142,7 +142,7 @@ elsif (not -d $options{results} or not -w $options{results}) {
 pod2usage($ERRORS) if length $ERRORS;
 
 if (not @{$options{databases}}) {
-     $options{databases} = [qw(ncbi genecard harvester)]
+     $options{databases} = [qw(ncbi genecard harvester ensembl uniprot)]
 }
 
 $DEBUG = $options{debug};
@@ -192,6 +192,7 @@ if (@{$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 {