indraniel’s gists

indraniel / 4-identify-and-cleanup-corrupt-cadd-jobs.py

Last active June 8, 2017 21:37

scripts to undo/expunge and redo postvqsr38 pipeline steps (BIO-2310)

	#!/usr/bin/env python

	from __future__ import print_function, division
	import os, sys, re, subprocess, time, datetime, shutil

	def log(msg):
	timestamp = datetime.datetime.now().strftime("%Y-%m-%d %T")
	print('[-- {} --] {}'.format(timestamp, msg), file=sys.stderr)

	def touch(fname, times=None):

indraniel / download-1000-genomes-vcf.py

Created May 26, 2017 23:08

Python example to download files from an anonymous FTP server (example case from 1000 Genomes)

	#!/usr/bin/env python

	from __future__ import print_function
	import ftplib, datetime, sys

	# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr14.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

	def log(msg):
	timestamp = datetime.datetime.now().strftime("%Y-%m-%d %T")
	print('[-- {} --] {}'.format(timestamp, msg), file=sys.stderr)

indraniel / b37-annotate-w-gnomAD.sh

Last active June 30, 2023 03:45

A bash script to annotate a large VCF (i.e. containing many samples) with gnomAD (build 37 edition)

	#!/bin/bash

	# Usage:
	# bash b37-annotate-w-gnomAD.sh </path/to/input.vcf.gz> </path/to/output.vcf.gz>
	#
	# Note:
	# 1. This script with create a "scratch" directory to hold intermediate file
	# states created during the annotation process. The scratch directory will
	# be created next to the /path/to/outvcf.vcf.gz .
	#

indraniel / run-postvqsr-pipeline-template.sh

Last active April 18, 2017 21:22

	#!/bin/bash

	BASE=/gscmnt/gc2802/halllab/idas/laboratory/yaps2-cadd-vep-test

	VIRTUALENV=${BASE}/test-venv
	source ${VIRTUALENV}/bin/activate

	# see confluence
	export BMETRICA_DSN="mysql://USER:PASSWORD@hostname:port/database"

indraniel / cadd-score.sh

Last active April 18, 2017 19:48

An example of using bash subshells (http://tldp.org/LDP/abs/html/subshells.html) in CADD (http://cadd.gs.washington.edu/)

	#!/bin/bash
	AWK=/usr/bin/awk
	CADDpath="`dirname \"$0\"`"
	CADDpath="`( cd \"$CADDpath/..\" && pwd )`"
	if [ -z "$VEPpath" ] ; then source ${CADDpath}/bin/config.sh; fi
	${CADDpath}/bin/src/annotateVEP.py \
	--all \
	--vep=<( zcat ${1} \
	\| ${CADDpath}/bin/src/VCF2vepVCF.py \
	\| sort -k1,1 -k2,2n -k3,3 -k4,4 \

indraniel / sample-vcfs.sh

Created April 14, 2017 18:25

sample a large vcf for testing purposes

	#!/bin/bash

	BASE=/gscmnt/gc2802/halllab/idas/laboratory/yaps2-cadd-vep-test
	BCFTOOLS=/gscmnt/gc2719/halllab/bin/bcftools
	BGZIP=/gscmnt/gc2802/halllab/idas/software/vep/local/htslib-1.3.2/bin/bgzip
	TABIX=/gscmnt/gc2802/halllab/idas/software/vep/local/htslib-1.3.2/bin/tabix

	mkdir -p ${BASE}/data/derived/1-create-test-postvqsr-input-data-file/test-vcfs

	# cat /gscmnt/gc2802/halllab/idas/jira/BIO-2197/data/derived/7-create-postvqsr-input-data-file/dataset.tsv \

indraniel / ocaml-install.sh

Last active March 31, 2017 03:33

	#!/bin/bash

	OPAM_VERSION="1.2.2"
	OCAML_VERSION="4.04.0"
	BASE=/home/archive/ocaml-${OCAML_VERSION}

	ARCH=$(uname -m)
	OS=$(uname -s)

	INSTALL_ROOT=${BASE}/root # generally this value is "$HOME/.opam"

indraniel / application.conf

Last active August 19, 2024 12:48

Example Cromwell / WDL usage at the MGI

	webservice {
	port = 8000
	interface = 0.0.0.0
	instance.name = "reference"
	}

	akka {
	loggers = ["akka.event.slf4j.Slf4jLogger"]
	actor {
	default-dispatcher {

indraniel / test.cpp

Created December 12, 2016 02:46

Example Simple C++ logging (w/o C++11 or later)

	#include <iostream>
	#include <ctime>

	void logMsg( const std::string& msg ) {
	time_t rawtime;
	struct tm * timeinfo;
	char buffer[80];

	time (&rawtime);
	timeinfo = localtime(&rawtime);

indraniel / simple-tsv-parsing.clj

Created November 28, 2016 23:49

simple tsv parsing experiments in clojure

	user=> (->> (line-seq (io/reader "test-data.tsv"))
	#_=> (map #(string/split % #"\t"))
	#_=> (map #(nth % 0))
	#_=> (map #(Integer/parseInt %))
	#_=> (+))
	ClassCastException Cannot cast clojure.lang.LazySeq to java.lang.Number java.lang.Class.cast (Class.java:3369)

	user=> (->> (line-seq (io/reader "test-data.tsv"))
	#_=> (map #(string/split % #"\t"))
	#_=> (map #(nth % 0))

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