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

package molmed

import net.sf.samtools.util.SortingCollection
import net.sf.samtools.BAMRecordCodec
import net.sf.picard.fastq.FastqRecord
import java.util.Comparator
import java.io.InputStream
import java.io.PrintStream
import net.sf.picard.fastq.FastqConstants

johandahlberg

# Licence:
# https://creativecommons.org/licenses/by/3.0/

library(ggplot2)
library(reshape2)
library(dplyr)

# Data:
# Downloaded at: http://www.statistikdatabasen.scb.se/pxweb/sv/ssd/START__HE__HE0110__HE0110A/SamForvInk2/?rxid=c58583e1-7fc3-418a-9395-0300e138fe7f
# Sammanräknad förvärvsinkomst, medianinkomst för boende i Sverige den 31/12, tkr efter region, kön, ålder och år

johandahlberg

#!/bin/bash -l
#SBATCH -A b2010028
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 10:00:00
#SBATCH -J prepare_ref
#SBATCH -o prepare_ref-%j.out
#SBATCH -e prepare_ref-%j.error

# Author: Johan D

johandahlberg

echo "Time in container"
for i in $(seq 1 5)
do
    /usr/bin/time -f "time: %e" proot -S debian-sid --bind=/proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/ samtools mpileup -r 22:1-23096112  /proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/CEP-13-3.clean.dedup.recal.bam 2>&1 > test.pileup | grep time
done

echo "Time outside container"
for i in $(seq 1 5)
do
    /usr/bin/time -f "time: %e" samtools mpileup -r 22:1-23096112  /proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/CEP-13-3.clean.dedup.recal.bam 2>&1 > test.pileup | grep time

johandahlberg

  def rawbuffer2JsValue(rawBuffer: RawBuffer): Option[JsValue] = {
    for {
      bytes <- rawBuffer.asBytes()
    } yield {
      Json.parse(bytes.utf8String)
    }
  }

  def receiveFacebookMessages = withVerifiedPayload {
    Action (parse.raw) {