root/galaxy-central/tools/human_genome_variation/snpFreq2.pl

リビジョン 2, 4.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

  • 属性 svn:executable の設定値 *
行番号 
1#!/usr/bin/env perl
2
3use strict;
4use warnings;
5
6#expected input: path to file, cols of counts (2 sets of 3), threshold
7if (!@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
13my $file = shift @ARGV;
14my $a1 = shift @ARGV;
15if ($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}
19my $a2 = shift @ARGV;
20if ($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}
24my $a3 = shift @ARGV;
25if ($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}
29my $b1 = shift @ARGV;
30if ($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}
34my $b2 = shift @ARGV;
35if ($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}
39my $b3 = shift @ARGV;
40if ($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}
44my $thresh = shift @ARGV;
45if ($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}
52my $outfile = shift @ARGV;
53
54#run a fishers exact test (using R) on whole table
55my $cmd = qq|options(warn=-1)
56           tab <- read.table('$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
88my $cmd2 = qq|suppressPackageStartupMessages(library(qvalue))
89              qobj <- qvalue(x[1:size], lambda=seq(0,0.90,$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
96my $pr = qq|results <- data.frame(tab[1:size,1:width], y[1:size,1:6], x[1:size])
97            write.table(results, file="$outfile", row.names = FALSE ,col.names = FALSE,quote = FALSE, sep="\t")
98              q()|;
99
100open(FT, "| R --slave --vanilla")
101   or die "Couldn't call fisher.text, $!\n";
102print FT $cmd, "\n"; #fisher test
103print FT $cmd2, "\n"; #qvalues and results
104#print FT $pr, "\n";
105close FT or die "Couldn't finish fisher.test, $!\n";
106
107exit;
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。