Daniel Klevebring dakl

💌

ML Engineer @ Epidemic Sound

Hacker, gamer, geek, father of two. Staff MLE at @epidemicsound

dakl / gist:15be59836f7c1e37a89ec390feb2e99d

Created October 27, 2024 15:34

pip install git+https://github.com/QuirkyCort/pgzhelper.git

dakl / gist:439837959f57a08f28a18044f738d88a

Created October 7, 2024 13:17

I like super mario.

dakl / tensorboard_logging.py

Created December 20, 2017 14:16 — forked from gyglim/tensorboard_logging.py

Logging to tensorboard with manually generated summaries (not relying on summary ops)

	"""Simple example on how to log scalars and images to tensorboard without tensor ops.

	License: Copyleft
	"""
	__author__ = "Michael Gygli"

	import tensorflow as tf
	from StringIO import StringIO
	import matplotlib.pyplot as plt
	import numpy as np

dakl / gist:40ac776ac3b7d7928dd360ad2997f27f

Created April 22, 2016 07:52

	Sample HS_LIBRARY_SIZE HS_PENALTY_50X PCT_TARGET_BASES_10X OFF_BAIT_BASES ON_BAIT_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED HS_PENALTY_30X PCT_TARGET_BASES_30X READ_GROUP
	HS_PENALTY_40X TOTAL_READS ON_TARGET_BASES MEAN_TARGET_COVERAGE ZERO_CVG_TARGETS_PCT PCT_PF_UQ_READS BAIT_TERRITORY PCT_USABLE_BASES_ON_TARGET PCT_PF_READS LIBRARY PF_READS PCT_TARGET_BASES_2X GC_DROPOUT AT_DROPOUT PCT_TARGET_BASES_50X GENOME_SIZE PCT_PF_UQ_READS_ALIGNED FOLD_80_BASE_PENALTY HS_PENALTY_10X PCT_USABLE_BASES_ON_BAIT HS_PENALTY_20X PF_UNIQUE_READS PCT_TARGET_BASES_20X SAMPLE NEAR_BAIT_BASES TARGET_TERRITORY FOLD_ENRICHMENT PCT_TARGET_BASES_40X PCT_TARGET_BASES_100X BAIT_DESIGN_EFFICIENCY BAIT_SET HS_PENALTY_100X PCT_SELECTED_BASES MEAN_BAIT_COVERAGE PF_UQ_BASES_ALIGNED PF_UQ_READS_ALIGNED
	P-00017852-N-03021179-TD2-CB1 0.0 0.0 899777371.0 524812.0 0.997626 0.245107 0.0 0.0
	0.0 9609180.0 524812.0 0.899072 0.836774 1.0 1689097.0 0.000543 1.0 9609180.0 0.045124 2.779323 2.431879 0.0 3137454505.0 0.938492 ? 0.0 0.000543 0.0 960918

dakl / reportcreatormahcine.Vagrantfile

Last active October 6, 2015 11:12

	#Define the list of machines
	machines = {
	:reportcreatormahcine => {
	:hostname => "reportcreatormahcine",
	:ipaddress => "10.10.10.99" #gretzky
	},
	}

	#--------------------------------------
	# General provisioning inline script

dakl / tcga-vcfs-to-pancan19.sh

Last active November 23, 2015 14:30

Merge VCFs from 19 TCGA projects to a pancan19 VCF

	#!/bin/bash

	REF=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta
	DICT=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.dict
	GATKJAR=/home/daniel.klevebring/projects/tcga-maf-to-vcf/GenomeAnalysisTK.jar

	WORKDIR=$HOME/Crisp/dakl/tcga-maf-to-vcf
	mkdir -p $WORKDIR
	cd $WORKDIR

dakl / tcga-maf-to-vcf.sh

Last active February 12, 2021 14:06

Convert TCGA MAFs to VCFs to use to annotate other VCF files with variant frequency in the various TCGA projects (including pancan12).

	REF=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.fasta
	DICT=/proj/b2010040/private/nobackup/autoseqer-genome/genome/human_g1k_v37_decoy.dict
	GATKJAR=/home/daniel.klevebring/projects/tcga-maf-to-vcf/GenomeAnalysisTK.jar

	WORKDIR=$HOME/Crisp/dakl/tcga-maf-to-vcf
	mkdir -p $WORKDIR
	cd $WORKDIR

	#unpack maf to workdir
	tar xvfz ~/projects/tcga-maf-to-vcf/pancan_cleaned_mafs.tar.gz

dakl / vcfsorter.pl

Created February 11, 2015 14:56

	#!/usr/bin/perl
	use strict;

	######################################################
	# vcfsorter.pl
	#
	# Copyright (C) 2011 German Gaston Leparc
	#
	# sorts VCF by reference genome
	#

dakl / hg19.rRNA.interval_list

Last active March 14, 2018 09:36 — forked from slowkow/hg19.rRNA.interval_list

dakl / basicOncoPrint.R

Last active August 29, 2015 14:10 — forked from armish/basicOncoPrint.R

	# This function sorts the matrix for better visualization of mutual exclusivity across genes
	memoSort <- function(M) {
	geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix;
	scoreCol <- function(x) {
	score <- 0;
	for(i in 1:length(x)) {
	if(x[i]) {
	score <- score + 2^(length(x)-i);
	}
	}