johandahlberg’s gists

johandahlberg / ReplaceSampleNameInReadGroup.java

Created September 11, 2012 12:46

A Picard class for switching read names according to a translation table in a white space separated file.

	package net.sf.picard.sam;

	import java.io.BufferedReader;
	import java.io.DataInputStream;
	import java.io.File;
	import java.io.FileInputStream;
	import java.io.InputStreamReader;
	import java.util.HashMap;
	import java.util.List;
	import java.util.Map;

johandahlberg / gist:4058394

Created November 12, 2012 09:42

Working document for Scala/GATK/Queue setup guide.

	*----------------------------------
	* Setting up git
	*----------------------------------

	Clone gatk git repo

	Add the main gatk repo as a upstream remote repo:
	git remote add upstream https://github.com/broadgsa/gatk.git

	Change the remote of the master branch to upstream. .git/config should look like this.

johandahlberg / fixPipelineSetup-py

Created November 21, 2012 13:43

	#!/usr/bin/python

	import os

	def get_immediate_subdirectories(dir):
	return [name for name in os.listdir(dir)
	if os.path.isdir(os.path.join(dir, name))]

	# Get runfolder name from file and return as list.
	def get_runfolders_already_run(file):

johandahlberg / SimpleBWT

Last active December 12, 2015 04:49

Naive functional implementation of Burrows-Wheels transform in scala

	import scala.math.Ordering

	object SimpleBW extends App {

	def bwt(s: String): String = {
	def tranformString(string: String): List[String] = { transformString(string, string.length) }

	def transformString(string: String, splitIndex: Int): List[String] = {
	if (splitIndex == 0) {
	// Recursion base case

johandahlberg / PlayWithURLs.scala

Created April 12, 2013 08:28

Playing with getting source from URL, to get gene names from refseq-ids and converting them into R if-statements. Mostly an experiment in using Scalas parallel collections. NOTE: This should under no circumstances be used in production, then you need to be using some API instead. You have been warned.

	object PlayWithURLs extends App {

	// Some ids for the BRCA1 gene
	val refseqids = List("uc010whl.1", "uc002icp.3", "uc010whp.1")

	def queryRefSeqId(refSeqId: String): String = {
	def read(url: String): String = io.Source.fromURL(url).mkString
	val document = read("http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=" + refSeqId + "&org=human")

	val regexp = """.Genetic Association Database:\s\<A HREF=.\>(\w+)\<.*""".r

johandahlberg / gist:5459321

Last active December 16, 2015 15:58

Ugly code example for slides on Best practices in scientific computing.

	object UglyCodeExample extends App {
	def m(stringToTransform: String): String = {
	def t(string: String): List[String] = {
	def th(string: String, si: Int): List[String] = {
	if (si == 0) Nil
	else {
	val (firstString, secondString) = string.splitAt(si); val newString = secondString + firstString
	newString :: th(string, si - 1)}}
	th(string, string.length)
	}

johandahlberg / BetterCodeExample.scala

Last active December 16, 2015 15:59

A better code example for slides on best practice in scientific computing.

	object BetterCodeExample extends App {

	/**
	* Burrows-Wheeler transform of string
	*
	* Perform the Burrows-Wheeler transform on a string. See http://en.wikipedia.org/wiki/Burrows%E2%80%93Wheeler_transform
	* for a introduction to the algorithm.
	*
	* This particular implementation is recursive.
	*

johandahlberg / BetterCodeExampleUnitTests.scala

Created April 25, 2013 13:33

Unit test example for the BetterCodeExample burrows wheeler functions

	import org.scalatest.FunSuite

	import BetterCodeExample._

	class BetterCodeExampleUnitTests extends FunSuite {

	test("Burrow wheelers transform of ^BANANA\|") {
	assert(BetterCodeExample.burrowsWheelersTransform("^BANANA\|") === """BNN^AA\|A""")
	}

johandahlberg / GCCounter.scala

Last active December 17, 2015 12:39

GCCounter in Scala inspired by http://saml.rilspace.org/moar-languagez-gc-content-in-python-d-fpc-c-and-c. This is no match performance wise for the C/D/C++ etc solutions, but I think that it makes a nice point of showing how Scalas parallel collections can be used to with very little extra effort parallelize operations. Test file available for …

	import scala.io.Source
	import java.io.File

	object GCCounter extends App {

	val file = new File("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa")

	// The actual GC counting function
	def countGCOnLine(line: String): (Long, Long) = {
	if (line.startsWith(">"))

johandahlberg / plotCoverageProportions.R

Created June 27, 2013 16:35

A R script to plot cumulative coverage based on GATK DepthOfCoverage output files. Not very pretty, but perhaps helpful to somebody.

	library(ggplot2)

	setwd("<my working directory>")

	removeExtraLine <- function(x) {
	x[,2:length(x)]
	}

	createInitialDataset <- function(x, sampleName) {
	extraLineRemoved <- t(removeExtraLine(x))

Johan Dahlberg johandahlberg