add todo

[function2gene.git] / bin / function2gene

diff --git a/bin/function2gene b/bin/function2gene
index de4915bc4f95ecbdd9c564ffb7de88938658d4c0..a89207267a9d19473d37fa243f9feacc211e5905 100755 (executable)
--- 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)$/i} @{$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)]
 }
 
 $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;