johandahlberg

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

*----------------------------------
* 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

#!/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

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

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

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

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

import org.scalatest.FunSuite

import BetterCodeExample._

class BetterCodeExampleUnitTests extends FunSuite {

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

johandahlberg

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

library(ggplot2)

setwd("<my working directory>")

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

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