Ino de Bruijn inodb

Generate reads with deletions of arbitrary length using ensembl rest api

for del_size in 10 30 50 70 90 150 300 600
do
  chr=17
  start_pos=4126000
  read_length=100
  ens_url="http://grch37.rest.ensembl.org/sequence/region/human/"
  qual=$(python -c "print 'A'*${read_length}")
  (

20161002 Frontend dev workshop

Set up cbioportal-frontend

Check out the README at https://github.com/cBioPortal/cbioportal-frontend/ for up to date info

Install with npm
Try to view new patient view at this link (make sure to change routing to patient): http://localhost:3000/?cancer_study_id=lgg_ucsf_2014&case_id=P04

Try to make a component

Make a new component that show the Patient Information on a single line, instead of in a table. We would like that line to be in the PatientHeader component. You could name it PatientInline similar to SampleInline.

Gene lenghts from ENSEMBL REST API

Use inside notebook (uses ! syntax):

import json
import pandas as pd

def get_gene_length(gene):
    gene_info = \
        !curl -s "http://grch37.rest.ensembl.org/xrefs/symbol/homo_sapiens/"{gene} -H 'Content-type:application/json' | \
 jq '.[0].id' | tr -d '"' | \

	#!/bin/bash
	# Deduplicates all .txt files in sudirs
	# creates file with .dedup postfix
	# keeps one header line if file does not contains comments
	# keeps two header lines if file contains comments
	find . -name '*.txt' \| parallel -k "f=$(mktemp -t mskimpact) &&" sort {} '\|' uniq -d '>' '$f' '&&' test -s '$f' '&&' '('grep -q '^#' {} '&&' '('head -2 {} '>' {}.dedup '&&' tail -n +3 {} '\|' sort '\|' uniq '>>' {}.dedup')' '\|\|' '('head -1 {} '>' {}.dedup '&&' tail -n +2 {} '\|' sort '\|' uniq '>>' {}.dedup'))'
	# to replace all files run:
	#find . -name '*.dedup' \| parallel -k 'f='{} '&&' mv {} '${f/.dedup/}'

	#!/usr/bin/env ruby

	grep = `git grep -n #{ARGV[0]} #{ARGV[1]}`

	puts "\n-----------------------------------------------------------"
	puts "GREP RESULT"
	puts '-----------------------------------------------------------'
	puts grep

	files = grep.scan /.*\:\d+/

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="utf-8">
	<title>Bokeh Plot</title>

	<style>
	/* BEGIN /Users/debruiji/anaconda/lib/python2.7/site-packages/bokeh/server/static/css/bokeh.min.css */

	/**
	* Python-like string format function
	* @param {String} str - Template string.
	* @param {Object} data - Data to insert strings from.
	* @returns {String}
	*/
	var format = function(str, data) {
	var re = /{([^{}]+)}/g;

	return str.replace(/{([^{}]+)}/g, function(match, val) {

	color_grep_file() {
	COLOR_CMD="cat $1"
	echo $COLOR_CMD
	local i=31;
	while read line; do
	echo $line
	COLOR_CMD="$COLOR_CMD \| GREP_COLOR='01;$i' grep --color=always -E '$line\|$'"
	i=$(( $i + 1 ))
	done < $2
	COLOR_CMD="$COLOR_CMD \| less -RS"

	#!/bin/bash
	DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
	export PORTAL_HOME=$DIR