Mercurial > repos > xuebing > sharplabtool

comparison tools/human_genome_variation/snpFreq2.pl @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5
6 #expected input: path to file, cols of counts (2 sets of 3), threshold
7 if (!@ARGV or scalar @ARGV != 9) {
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";
9 exit 1;
10 }
11
12 #get and verify inputs
13 my $file = shift @ARGV;
14 my $a1 = shift @ARGV;
15 if ($a1 =~ /\D/ or $a1 < 1) {
16 print "Error the column number, must be an integer greater than or equal to 1. Got $a1\n";
17 exit 1;
18 }
19 my $a2 = shift @ARGV;
20 if ($a2 =~ /\D/ or $a2 < 1) {
21 print "Error the column number, must be an integer greater than or equal to 1. Got $a2\n";
22 exit 1;
23 }
24 my $a3 = shift @ARGV;
25 if ($a3 =~ /\D/ or $a3 < 1) {
26 print "Error the column number, must be an integer greater than or equal to 1. Got $a3\n";
27 exit 1;
28 }
29 my $b1 = shift @ARGV;
30 if ($b1 =~ /\D/ or $b1 < 1) {
31 print "Error the column number, must be an integer greater than or equal to 1. Got $b1\n";
32 exit 1;
33 }
34 my $b2 = shift @ARGV;
35 if ($b2 =~ /\D/ or $b2 < 1) {
36 print "Error the column number, must be an integer greater than or equal to 1. Got $b2\n";
37 exit 1;
38 }
39 my $b3 = shift @ARGV;
40 if ($b3 =~ /\D/ or $b3 < 1) {
41 print "Error the column number, must be an integer greater than or equal to 1. Got $b3\n";
42 exit 1;
43 }
44 my $thresh = shift @ARGV;
45 if ($thresh !~ /^\d*\.?\d+$/) {
46 print "Error the threshold must be a number. Got $thresh\n";
47 exit 1;
48 }elsif ($thresh > .3) {
49 print "Error the threshold can not be greater than 0.3 got $thresh\n";
50 exit 1;
51 }
52 my $outfile = shift @ARGV;
53
54 #run a fishers exact test (using R) on whole table
55 my $cmd = qq|options(warn=-1)
56 tab <- read.table('$file', sep="\t")
57 size <- length(tab[,1])
58 width <- length(tab[1,])
59 x <- 1:size
60 y <- matrix(data=0, nr=size, nc=6)
61 for(i in 1:size) {
62 m <- matrix(c(tab[i,$a1], tab[i,$b1], tab[i,$a2], tab[i,$b2], tab[i,$a3], tab[i,$b3]), nrow=2)
63 t <- fisher.test(m)
64 x[i] <- t\$p.value
65 if (x[i] >= 1) {
66 x[i] <- .999
67 }
68 n <- (tab[i,$a1] + tab[i,$a2] + tab[i,$a3] + tab[i,$b1] + tab[i,$b2] + tab[i,$b3])
69 n_a <- (tab[i,$a1] + tab[i,$a2] + tab[i,$a3])
70 y[i,1] <- ((tab[i,$a1] + tab[i,$b1])*(n_a))/n
71 y[i,1] <- round(y[i,1],3)
72 y[i,2] <- ((tab[i,$a2] + tab[i,$b2])*(n_a))/n
73 y[i,2] <- round(y[i,2],3)
74 y[i,3] <- ((tab[i,$a3] + tab[i,$b3])*(n_a))/n
75 y[i,3] <- round(y[i,3],3)
76 n_b <- (tab[i,$b1] + tab[i,$b2] + tab[i,$b3])
77 y[i,4] <- ((tab[i,$a1] + tab[i,$b1])*(n_b))/n
78 y[i,4] <- round(y[i,4],3)
79 y[i,5] <- ((tab[i,$a2] + tab[i,$b2])*(n_b))/n
80 y[i,5] <- round(y[i,5],3)
81 y[i,6] <- ((tab[i,$a3] + tab[i,$b3])*(n_b))/n
82 y[i,6] <- round(y[i,6],3)
83 }|;
84 #results <- data.frame(tab[1:size,1:width], x[1:size])
85 #write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
86 #q()|;
87
88 my $cmd2 = qq|suppressPackageStartupMessages(library(qvalue))
89 qobj <- qvalue(x[1:size], lambda=seq(0,0.90,$thresh), pi0.method="bootstrap", fdr.level=0.1, robust=FALSE, smooth.log.pi0 = FALSE)
90 q <- qobj\$qvalues
91 results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size], q[1:size])
92 write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
93 q()|;
94
95 #for TESTING
96 my $pr = qq|results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size])
97 write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
98 q()|;
99
100 open(FT, "| R --slave --vanilla")
101 or die "Couldn't call fisher.text, $!\n";
102 print FT $cmd, "\n"; #fisher test
103 print FT $cmd2, "\n"; #qvalues and results
104 #print FT $pr, "\n";
105 close FT or die "Couldn't finish fisher.test, $!\n";
106
107 exit;