johandahlberg

from pathlib import Path
from queue import Queue


def bf_search(search_for, root, max_depth):

    class PathLevel():
        def __init__(self, path, level):
            self.path = path
            self.level = level

johandahlberg

# CC BY-SA 4.0
# http://creativecommons.org/licenses/by-sa/4.0/

import json
import time
import datetime

import requests
from bs4 import BeautifulSoup

johandahlberg

library(ggplot2)

setwd("<my working directory>")

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

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

johandahlberg

package controllers

import java.nio.charset.StandardCharsets
import javax.crypto.Mac
import javax.crypto.spec.SecretKeySpec

import models.RegisterFacebook
import org.apache.commons.codec.binary.Hex
import play.api.Logger
import play.api.libs.concurrent.Execution.Implicits.defaultContext

johandahlberg

case class FacebookPostingMessages(`object`: String, entry: Seq[MessagePostEntry]) {
  def messages(): Seq[Message] = {
    entry.flatMap(_.messaging).map(_.message)
  }
}
case class Correspondent(id: String)
case class MessagePostEntry(id: String, time: Long, messaging: Seq[Messaging])
case class Messaging(sender: Correspondent, recipient: Correspondent, timestamp: Long, message: Message)
case class Message(mid: String, seq: Long, text: String)

johandahlberg

class SHA1VerificationService {

  private val secret = "<your key>"

  private def computeSHA1Hash(payloadBytes: Array[Byte], secret: String): String = {
    val HMAC_SHA1_ALGORITHM = "HmacSHA1"

    val secretKeySpec = new SecretKeySpec(secret.getBytes(StandardCharsets.UTF_8), HMAC_SHA1_ALGORITHM)
    val mac = Mac.getInstance(HMAC_SHA1_ALGORITHM)
    mac.init(secretKeySpec)

johandahlberg

val verificationService = new SHA1VerificationService()

  def withVerifiedPayload[A](action: Action[RawBuffer])= Action.async(parse.raw) { request =>
    val xHubSignatureOption = request.headers.get("X-Hub-Signature")

    Logger.debug("Attempting to verify payload signature.")

    val verified =
      for {
        signature <- xHubSignatureOption

johandahlberg

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

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

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

#!/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