cth

#!/usr/bin/ruby 

if ARGV.length != 1
        puts "Usage: ./average_experiments experiment_directory\n\n"
        puts "Computes the average over a number of experiment data files"
        puts "located in the directory given as first argument. "
        puts "The experiment files are expected to contain an equal number lines  "
        puts "with an equal number of entries. Each entry is expected to be a number"
        puts "and entries are expected to be separated by space."
        exit

cth

#!/usr/bin/env ruby
# Simple utility to remove trailing space in the end of lines
# Takes as first argument the file to be processed.

lines = []
File.open(ARGV[0]).each do |line|
        line.reverse =~ /\s*(.*)/
        lines << $1.reverse
end

cth

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% A simple script to create a visual report of PRISM parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% May 2011, Christian Theil Have
% 
% usage: prism_switch_html(PRISM_SWITCH_FILE, HTML_OUTPUT_FILE).
%

:- table int_to_hex/2.

cth

import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Rectangle;
import javax.swing.JComponent;

public class RectangleComponent extends JComponent {
	public void paintComponent(Graphics g) {
	
		// Recover Graphics2D
		Graphics2D g2 = (Graphics2D)g;

cth

function nth() {
  target=$1
  shift
  idx=1
  for symbol in $@; do
    if [ $symbol == $target ]; then
      echo $idx
      return
    fi
    idx=$(($idx+1))

cth

# Script to swap alleles in imputed .gprobs files (genotype likelihoods), e.g., from IMPUTE2
# ruby swapgeno.rb genotypes.gprobs swap_snps.txt swapped.gprobs
# swap_snps.txt is a list of SNPs for which genotypes should be swapped (one per line in file)

# Read list of snps to swap
swap_snps = {}
File.open(ARGV[1]) { |sf| sf.each { |l| swap_snps[l.chomp] = true } }

File.open(ARGV[2],"w") do |outfile|
        File.open(ARGV[0]) do |file|

cth

Markdown based testing of files

This is a markdown based language for specification of testcases for files in a filesystem. Ideally a set of files may be described and at the same time formal specifications about the files can be specified using test cases written in, e.g., shell scripts embedded as code-blocks.

Overview

cth

def mean_std_dev(arr,n)
	sum=0
	mean = arr.inject{|sum,x| sum + x } / n.to_f 
	total=0
	[mean, Math.sqrt(arr.inject{|total,x| total + ((mean-x)*(mean-x)) } / n.to_f) ]
end

def percentile_depths(arr,n,pct)
	samples_in_percentile = (n * pct).floor
	(arr.sort.reverse.slice(0,samples_in_percentile)).min

cth

require 'rinruby'
require 'bio-samtools'
require 'rake'

plink_stems = {
	:lucamp => "/eva/brutus/J8/data/deepExom/burden5/clean/lrt24qibin7R2BeagleV2",
#	:metabochip => "/eva/brutus/J8/data/metaboChip/clean/metaboChipAll",
	:exomchip => "/eva/brutus/J8/data/exomChip/clean/exomChipAll"
}

cth

#!/bin/sh
#$ -S /bin/bash
#$ -cwd
# Christian Theil HAve, 2015

# Modify this to be the final report directory of interest 
# Note that final reports must contain LRR and BAF
FINAL_REPORTS_DIR=target_final_reports

# This is where