--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/snpFreq2.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,107 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+#expected input: path to file, cols of counts (2 sets of 3), threshold
+if (!@ARGV or scalar @ARGV != 9) {
+   print "usage snpFreq.pl /path/to/snps.txt <6 column numbers(1 based) with counts for alleles, first one group then another> #threshold outfile\n";
+   exit 1;
+}
+
+#get and verify inputs
+my $file = shift @ARGV;
+my $a1 = shift @ARGV;
+if ($a1 =~ /\D/ or $a1 < 1) {
+   print "Error the column number, must be an integer greater than or equal to 1. Got $a1\n";
+   exit 1;
+}
+my $a2 = shift @ARGV;
+if ($a2 =~ /\D/ or $a2 < 1) {
+   print "Error the column number, must be an integer greater than or equal to 1. Got $a2\n";
+   exit 1;
+}
+my $a3 = shift @ARGV;
+if ($a3 =~ /\D/ or $a3 < 1) {
+   print "Error the column number, must be an integer greater than or equal to 1. Got $a3\n";
+   exit 1;
+}
+my $b1 = shift @ARGV;
+if ($b1 =~ /\D/ or $b1 < 1) {
+   print "Error the column number, must be an integer greater than or equal to 1. Got $b1\n";
+   exit 1;
+}
+my $b2 = shift @ARGV;
+if ($b2 =~ /\D/ or $b2 < 1) {
+   print "Error the column number, must be an integer greater than or equal to 1. Got $b2\n";
+   exit 1;
+}
+my $b3 = shift @ARGV;
+if ($b3 =~ /\D/ or $b3 < 1) {
+   print "Error the column number, must be an integer greater than or equal to 1. Got $b3\n";
+   exit 1;
+}
+my $thresh = shift @ARGV;
+if ($thresh !~ /^\d*\.?\d+$/) {
+   print "Error the threshold must be a number. Got $thresh\n"; 
+   exit 1;
+}elsif ($thresh > .3) {
+   print "Error the threshold can not be greater than 0.3 got $thresh\n";
+   exit 1;
+}
+my $outfile = shift @ARGV;
+
+#run a fishers exact test (using R) on whole table
+my $cmd = qq|options(warn=-1)
+           tab <- read.table('$file', sep="\t")
+           size <- length(tab[,1])
+           width <- length(tab[1,])
+           x <- 1:size
+           y <- matrix(data=0, nr=size, nc=6)
+           for(i in 1:size) {
+              m <- matrix(c(tab[i,$a1], tab[i,$b1], tab[i,$a2], tab[i,$b2], tab[i,$a3], tab[i,$b3]), nrow=2)
+              t <- fisher.test(m)
+              x[i] <- t\$p.value
+              if (x[i] >= 1) {
+                  x[i] <- .999
+              }
+              n <- (tab[i,$a1] + tab[i,$a2] + tab[i,$a3] + tab[i,$b1] + tab[i,$b2] + tab[i,$b3])
+              n_a <- (tab[i,$a1] + tab[i,$a2] + tab[i,$a3])
+              y[i,1] <- ((tab[i,$a1] + tab[i,$b1])*(n_a))/n
+              y[i,1] <- round(y[i,1],3)
+              y[i,2] <- ((tab[i,$a2] + tab[i,$b2])*(n_a))/n
+              y[i,2] <- round(y[i,2],3)
+              y[i,3] <- ((tab[i,$a3] + tab[i,$b3])*(n_a))/n
+              y[i,3] <- round(y[i,3],3)
+              n_b <- (tab[i,$b1] + tab[i,$b2] + tab[i,$b3])
+              y[i,4] <- ((tab[i,$a1] + tab[i,$b1])*(n_b))/n
+              y[i,4] <- round(y[i,4],3)
+              y[i,5] <- ((tab[i,$a2] + tab[i,$b2])*(n_b))/n
+              y[i,5] <- round(y[i,5],3)
+              y[i,6] <- ((tab[i,$a3] + tab[i,$b3])*(n_b))/n
+              y[i,6] <- round(y[i,6],3)
+           }|;
+           #results <- data.frame(tab[1:size,1:width], x[1:size])
+           #write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
+           #q()|;
+
+my $cmd2 = qq|suppressPackageStartupMessages(library(qvalue))
+              qobj <- qvalue(x[1:size], lambda=seq(0,0.90,$thresh), pi0.method="bootstrap", fdr.level=0.1, robust=FALSE, smooth.log.pi0 = FALSE)
+              q <- qobj\$qvalues
+              results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size], q[1:size])
+              write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
+              q()|;
+
+#for TESTING
+my $pr = qq|results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size])
+            write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
+              q()|;
+
+open(FT, "| R --slave --vanilla") 
+   or die "Couldn't call fisher.text, $!\n";
+print FT $cmd, "\n"; #fisher test
+print FT $cmd2, "\n"; #qvalues and results
+#print FT $pr, "\n";
+close FT or die "Couldn't finish fisher.test, $!\n";
+
+exit;