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1 #!/usr/bin/env perl
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2
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3 use strict;
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4 use warnings;
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5
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6 #expected input: path to file, cols of counts (2 sets of 3), threshold
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7 if (!@ARGV or scalar @ARGV != 9) {
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8 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";
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9 exit 1;
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10 }
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11
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12 #get and verify inputs
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13 my $file = shift @ARGV;
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14 my $a1 = shift @ARGV;
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15 if ($a1 =~ /\D/ or $a1 < 1) {
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16 print "Error the column number, must be an integer greater than or equal to 1. Got $a1\n";
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17 exit 1;
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18 }
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19 my $a2 = shift @ARGV;
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20 if ($a2 =~ /\D/ or $a2 < 1) {
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21 print "Error the column number, must be an integer greater than or equal to 1. Got $a2\n";
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22 exit 1;
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23 }
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24 my $a3 = shift @ARGV;
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25 if ($a3 =~ /\D/ or $a3 < 1) {
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26 print "Error the column number, must be an integer greater than or equal to 1. Got $a3\n";
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27 exit 1;
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28 }
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29 my $b1 = shift @ARGV;
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30 if ($b1 =~ /\D/ or $b1 < 1) {
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31 print "Error the column number, must be an integer greater than or equal to 1. Got $b1\n";
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32 exit 1;
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33 }
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34 my $b2 = shift @ARGV;
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35 if ($b2 =~ /\D/ or $b2 < 1) {
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36 print "Error the column number, must be an integer greater than or equal to 1. Got $b2\n";
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37 exit 1;
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38 }
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39 my $b3 = shift @ARGV;
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40 if ($b3 =~ /\D/ or $b3 < 1) {
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41 print "Error the column number, must be an integer greater than or equal to 1. Got $b3\n";
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42 exit 1;
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43 }
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44 my $thresh = shift @ARGV;
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45 if ($thresh !~ /^\d*\.?\d+$/) {
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46 print "Error the threshold must be a number. Got $thresh\n";
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47 exit 1;
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48 }elsif ($thresh > .3) {
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49 print "Error the threshold can not be greater than 0.3 got $thresh\n";
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50 exit 1;
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51 }
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52 my $outfile = shift @ARGV;
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53
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54 #run a fishers exact test (using R) on whole table
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55 my $cmd = qq|options(warn=-1)
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56 tab <- read.table('$file', sep="\t")
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57 size <- length(tab[,1])
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58 width <- length(tab[1,])
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59 x <- 1:size
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60 y <- matrix(data=0, nr=size, nc=6)
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61 for(i in 1:size) {
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62 m <- matrix(c(tab[i,$a1], tab[i,$b1], tab[i,$a2], tab[i,$b2], tab[i,$a3], tab[i,$b3]), nrow=2)
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63 t <- fisher.test(m)
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64 x[i] <- t\$p.value
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65 if (x[i] >= 1) {
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66 x[i] <- .999
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67 }
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68 n <- (tab[i,$a1] + tab[i,$a2] + tab[i,$a3] + tab[i,$b1] + tab[i,$b2] + tab[i,$b3])
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69 n_a <- (tab[i,$a1] + tab[i,$a2] + tab[i,$a3])
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70 y[i,1] <- ((tab[i,$a1] + tab[i,$b1])*(n_a))/n
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71 y[i,1] <- round(y[i,1],3)
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72 y[i,2] <- ((tab[i,$a2] + tab[i,$b2])*(n_a))/n
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73 y[i,2] <- round(y[i,2],3)
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74 y[i,3] <- ((tab[i,$a3] + tab[i,$b3])*(n_a))/n
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75 y[i,3] <- round(y[i,3],3)
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76 n_b <- (tab[i,$b1] + tab[i,$b2] + tab[i,$b3])
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77 y[i,4] <- ((tab[i,$a1] + tab[i,$b1])*(n_b))/n
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78 y[i,4] <- round(y[i,4],3)
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79 y[i,5] <- ((tab[i,$a2] + tab[i,$b2])*(n_b))/n
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80 y[i,5] <- round(y[i,5],3)
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81 y[i,6] <- ((tab[i,$a3] + tab[i,$b3])*(n_b))/n
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82 y[i,6] <- round(y[i,6],3)
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83 }|;
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84 #results <- data.frame(tab[1:size,1:width], x[1:size])
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85 #write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
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86 #q()|;
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87
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88 my $cmd2 = qq|suppressPackageStartupMessages(library(qvalue))
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89 qobj <- qvalue(x[1:size], lambda=seq(0,0.90,$thresh), pi0.method="bootstrap", fdr.level=0.1, robust=FALSE, smooth.log.pi0 = FALSE)
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90 q <- qobj\$qvalues
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91 results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size], q[1:size])
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92 write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
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93 q()|;
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94
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95 #for TESTING
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96 my $pr = qq|results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size])
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97 write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
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98 q()|;
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99
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100 open(FT, "| R --slave --vanilla")
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101 or die "Couldn't call fisher.text, $!\n";
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102 print FT $cmd, "\n"; #fisher test
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103 print FT $cmd2, "\n"; #qvalues and results
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104 #print FT $pr, "\n";
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105 close FT or die "Couldn't finish fisher.test, $!\n";
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106
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107 exit;
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