X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Fparse_harvester_results;h=e52066127ceab16107b04bfc68c919ee150adb86;hp=a35c9b902f5a9ff840d6bb3450862ae0989cd9e1;hb=50e9739109c91b53ab620b462255f71a0b870f95;hpb=79c0f28d89ba108bcfca68a8b5d4f0e3855455dc

diff --git a/bin/parse_harvester_results b/bin/parse_harvester_results
index a35c9b9..e520661 100755
--- a/bin/parse_harvester_results
+++ b/bin/parse_harvester_results
@@ -80,7 +80,9 @@ my %options = (debug    => 0,
 	       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 $options{help};
@@ -104,7 +106,7 @@ if ($options{keywords}) {
      if (@ARGV != 1) {
 	  pod2usage("If the --keywords option is used, exactly one argument (the keyword) must be passed");
      }
-     $option{dir} = "$ARGV[0]_results_harvester";
+     $options{dir} = "$ARGV[0]_results_harvester";
 }
 
 
@@ -140,8 +142,16 @@ while ($_ = $dir->read) {
 	  ($results[NAME]) = $result =~ m&<TR>\s*<TD\s*BGCOLOR="\#FEFE99"\s*VALIGN="top"\s*NOWRAP>Entry\s*name</TD>\s*
 					  <TD\s*VALIGN="top"\s*COLSPAN="5">\s*<b>\s*([^<]+?)\s*</b></TD>\s*</TR>&xis;
      }
+     if (not defined $results[NAME]) {
+	  ($results[NAME]) = $result =~ m{<TITLE>[^:]+:\s*[^\*]+\*[^\*]+\*\s*([^-]+)}xis;
+	  $results[NAME] =~ s/\s*$// if defined $results[NAME];
+	  $results[NAME] =~ s/^\s*$// if defined $results[NAME];
+	  $results[NAME] =~ s/\d+\s*kDa\s*protein// if defined $results[NAME];
+	  $results[NAME] =~ s/\s*similar to .+// if defined $results[NAME];
+     }
 
      $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/