Add results to table; modify the search parssers to work better. Fix error in get_ncb...

[function2gene.git] / bin / parse_harvester_results

diff --git a/bin/parse_harvester_results b/bin/parse_harvester_results
index 29d07194a8a4e7c830fe7af55bdaa4d9e873a15d..30fc0113271433674f6f178a5da882334d533c4f 100755 (executable)
--- a/bin/parse_harvester_results
+++ b/bin/parse_harvester_results
@@ -77,9 +77,12 @@ my %options = (debug    => 0,
               man      => 0,
               dir      => '.',
               keyword  => undef,
+              keywords => 0,
              );
 
-GetOptions(\%options,'keyword|k=s','dir|D=s','debug|d+','help|h|?','man|m');
+GetOptions(\%options,'keyword|k=s','dir|D=s','debug|d+','help|h|?','man|m',
+          'keywords',
+         );
 
 
 pod2usage() if $options{help};
@@ -99,6 +102,15 @@ use constant {NAME        => 0,
              FILENAME    => 8,
             };
 
+if ($options{keywords}) {
+     if (@ARGV != 1) {
+         pod2usage("If the --keywords option is used, exactly one argument (the keyword) must be passed");
+     }
+     $options{dir} = "$ARGV[0]_results_harvester";
+}
+
+
+
 if (not -d $options{dir}) {
      die "$options{dir} does not exist or is not a directory";
 }
@@ -132,6 +144,7 @@ while ($_ = $dir->read) {
      }
 
      $results[NAME] ||= 'NO NAME';
+     $results[NAME] =~ s/_HUMAN//;
 
      # Find REF SEQ number
      ($results[REFSEQ]) = $result =~ m&<a\s+href="http://www.ncbi.nlm.nih.gov/entrez/