f9e3913d0a717429adb9e7ce395a80886e1253f0
chinhli
  Fri Sep 23 09:33:55 2011 -0700
Finished geneReviews for hg19 and hg18
diff --git src/utils/geneReviews/addGeneReviewToBed.pl src/utils/geneReviews/addGeneReviewToBed.pl
new file mode 100755
index 0000000..d1f8946
--- /dev/null
+++ src/utils/geneReviews/addGeneReviewToBed.pl
@@ -0,0 +1,53 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+sub usage() {
+    print "usage: ./addGRtoBed.pl dbName > outputFile\n";
+}
+my $argc=scalar(@ARGV);
+if ($argc != 1) {
+    usage; die "ERROR: Please supply a database name for results.\n";
+}
+#get the list of (unique) of gene symbols form geneReviews table
+my @geneReviews = split('\n',
+ `hgsql -N -e "select chrom, chromStart, chromEnd, name from geneReviews;" $ARGV[0]`);
+my $grBed;
+my $clickMsg = " (Click links below to search GeneReviews or GeneTests)";
+my $firstTime = 1;
+my $field;
+my $details;
+foreach $grBed(@geneReviews) {
+   $details = "";
+   my @col = split(/\t/, $grBed);
+   #print "Processing name: ", $col[3], " <BR>";
+   my @grShort = split('\n',
+    `hgsql -N -e 'select  grShort, diseaseID, diseaseName from geneReviewsRefGene where geneSymbol="$col[3]"' $ARGV[0]`);
+   $firstTime = 1;
+   my $count = scalar(@grShort);
+   my $i;
+   my $j;
+   for ($i=0; $i < $count; $i++) {
+       my @f5 = split(/\t/, $grShort[$i]);
+   if ($firstTime == 1) {
+      $firstTime=0;
+      $details = "";
+      $details = "<BR><B>GeneReview available for " . $col[3] .  ": </B> " . $clickMsg . "<BR>";
+      $details .= "<PRE><TT>";
+      $details .= "Short name    Disease ID     GeneTests disease name<BR>";
+      $details .= "-----------------------------------------------------------";
+      $details .= "-----------------------------------------------------------";
+      $details .= "----------------------------------<BR>";
+      }
+      $details .= "<A HREF=\"http://www.ncbi.nlm.nih.gov/books/n/gene/" . $f5[0] . "\" TARGET=_blank><B>" . $f5[0] . "</B></A>";
+      if (length($f5[0]) <= 15) {
+        for ($j = 0; $j <  15-length($f5[0]); $j ++ )
+           {
+              $details .= " ";
+           }
+         }
+       $details .=  $f5[1] . "       ";
+       $details .= "<A HREF=\"http://www.ncbi.nlm.nih.gov/sites/GeneTests/review/disease/" . $f5[2] . "?db=genetests&search_param==begins_with\" TARGET=_blank>" . $f5[2]  ."<BR>";
+     }
+       $details .= "</TT></PRE><BR>";
+       print $col[0], "\t", $col[1], "\t", $col[2], "\t", $col[3], "\t", $details, "\n";
+  }