new

src/gard/align2best.pl

@@ -0,0 +1,45 @@
+#!/usr/bin/perl -w
+use strict;
+my %maph = ();
+my %nh = ();
+my $num = 0;
+while(<>) {
+    chomp;
+    my ($id,$n,$x,$xn,$stem) = split(/\t/,$_);
+
+    if ($id =~ m@GARD@) {
+        $num++;
+        my $s = $x;
+        $s =~ s@:.*@@;
+        my $tuple = [$s, $x,$xn,$stem];
+        if (!$maph{$id}) {
+            $maph{$id} = $tuple;
+        }
+        else {
+            my $curr = $maph{$id};
+            my $replace = 0;
+            if ($stem eq 'true' && $curr->[3] eq 'false') {
+                # never replace a non-stem with a stemmed
+                $replace = 0;
+            }
+            elsif ($stem eq 'false' && $curr->[3] eq 'true' && $s eq $curr->[0]) {
+                # prioritize non-stem
+                $replace = 1;
+            }
+            elsif ($s eq 'OMIM') {
+                $replace = 1;
+            }
+            elsif ($s eq 'MESH') {
+                $replace = 0;
+            }
+            if ($replace) {
+                $maph{$id} = $tuple;
+            }
+        }
+    }
+}
+print STDERR "DONE: $num\n";
+foreach my $k (keys %maph) {
+    my ($s, $x, $xn) = @{$maph{$k}};
+    print "$k\thttps://monarchinitiative.org/disease/$x\n";
+}