X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Fparse_harvester_results;h=e52066127ceab16107b04bfc68c919ee150adb86;hp=29d07194a8a4e7c830fe7af55bdaa4d9e873a15d;hb=27d14c1110035a9e8425c100f587792517d1f19b;hpb=d09b67e0af77d6f2818e41d6b4d648cff651c79d

diff --git a/bin/parse_harvester_results b/bin/parse_harvester_results
index 29d0719..e520661 100755
--- 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";
 }
@@ -130,8 +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/