--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/disease_ontology_gene_fuzzy_selector.pl	Tue Aug 20 10:55:38 2013 -0400
@@ -0,0 +1,64 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+##################################################################
+# Select genes that are associated with the diseases listed in the
+# disease ontology.
+# ontology: http://do-wiki.nubic.northwestern.edu/index.php/Main_Page
+# gene associations by FunDO: http://projects.bioinformatics.northwestern.edu/do_rif/
+# Sept 2010, switch to doLite
+# input: build outfile sourceFileLoc.loc term or partial term
+##################################################################
+
+if (!@ARGV or @ARGV < 3) { 
+   print "usage: disease_ontology_gene_selector.pl build outfile.txt sourceFile.loc [list of terms]\n";
+   exit;
+}
+
+my $build = shift @ARGV;
+my $out = shift @ARGV;
+my $in = shift @ARGV;
+my $term = shift @ARGV;
+$term =~ s/^'//; #remove quotes protecting from shell
+$term =~ s/'$//; 
+my $data;
+open(LOC, $in) or die  "Couldn't open $in, $!\n";
+while (<LOC>) {
+   chomp;
+   if (/^\s*#/) { next; }
+   my @f = split(/\t/);
+   if ($f[0] eq $build) { 
+      if ($f[1] eq 'disease associated genes') { 
+         $data = $f[2]; 
+      }
+   }
+}
+close LOC or die "Couldn't close $in, $!\n";
+if (!$data) { 
+   print "Error $build not found in $in\n";
+   exit; 
+}
+if (!defined $term) { 
+   print "No disease term entered\n";
+   exit;
+}
+
+#start with just fuzzy term matches
+open(OUT, ">", $out) or die "Couldn't open $out, $!\n";
+open(FH, $data) or die "Couldn't open data file $data, $!\n";
+$term =~ s/\s+/|/g; #use OR between words
+while (<FH>) {
+   chomp;
+   my @f = split(/\t/); #chrom start end strand geneName geneID disease
+   if ($f[6] =~ /($term)/i) { 
+      print OUT join("\t", @f), "\n";
+   }elsif ($term eq 'disease') { #print all with disease
+      print OUT join("\t", @f), "\n";
+   }
+}
+close FH or die "Couldn't close data file $data, $!\n";
+close OUT or die "Couldn't close $out, $!\n";
+
+exit;