Paul Hoffman mojaveazure

mojaveazure / fakeHeader.sh

Last active October 16, 2018 21:57

A simple script to add the `@HD` header line to a SAM or BAM file in case it wasn't added at the time of creation.

	#!/bin/bash

	set -e
	set -u
	set -o pipefail

	# Define the usage message
	function usage() {
	echo -e "\
	Usage: ./fakeHeader.sh <option> <file> \n\

mojaveazure / soNeedy.sh

Last active April 29, 2019 18:20

A simple script to copy files defined by a list in parallel

	#!/bin/bash

	set -e
	set -u
	set -o pipefail

	# A simple script to find files listed in a text file and copy them elsewhere
	# Written for Chaochih Liu
	# Written by Paul Hoffman

mojaveazure / .gitignore

Last active August 29, 2015 14:24 — forked from octocat/.gitignore

Nearly-universal .gitignore

mojaveazure / lineCount.py

Last active August 29, 2015 14:25

A simple Python script to get the line count of a file

	#!/usr/bin/env python

	import sys
	try:
	import argparse
	except ImportError:
	sys.exit("Failed to import the argparse library. Please install for Python 2.6 or use Python 2.7 or higher")

	Arguments = argparse.ArgumentParser(add_help=True)
	Arguments.add_argument('-f',

mojaveazure / regionsExtracter.sh

Last active February 29, 2016 18:53

Extract a list of regions defined listed in a BAM file using SAMTools

	#!/bin/bash

	set -e
	set -o pipefail

	# Extract regions from a BAM file

	# Make sure SAMTools is installed
	if ! `command -v samtools > /dev/null 2> /dev/null`
	then

mojaveazure / basename.py

Created August 6, 2015 20:19

Basename in Python

	#!/usr/bin/env python

	# A script to get the basename of a file in Python

	# Import modules from the standard Python library
	import sys
	import os
	try:
	import argparse
	except ImportError:

mojaveazure / UpdateSettings.sh

Last active June 30, 2017 16:00

My settings files for things

	#!/bin/bash

	set -eo pipefail


	read -p "Choose settings to link: " -a SETTINGS
	declare -a SETTINGS=($(echo ${SETTINGS[@]} \| tr -d '[:space:]' \| grep -o . \| sort -u \| tr '\n' ' '))
	declare -a SETTINGS=($(echo ${SETTINGS[@]} \| tr '[:upper:]' '[:lower:]'))

	for setting in ${SETTINGS[@]}; do

mojaveazure / myFuncs.R

Last active August 29, 2015 14:27

Some R functions that I've found useful

	#!/usr/bin/env Rscript

	# bootstrap
	# A function to bootstrap some data
	bootstrap <- function(tmp.data) {
	boot.rep <- sample(x = tmp.data, replace = T)
	return(mean(boot.rep))
	}

	# push

mojaveazure / singSong.sh

Last active May 9, 2016 03:49

A few ways to make a Mac sing.

	#!/binb/bash

	# Pomp and Circumstance
	say -v Good oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo \
	oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo \
	oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo \
	oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo \
	oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

	# In the Hall of the Mountain King

mojaveazure / getCoverage.sh

Last active June 3, 2016 13:06

Calculate the coverage for multiple samples in parallel from histograms generated by BEDTools

	#!/bin/bash

	set -e
	set -u
	set -o pipefail

	# A simple script to calculate coverage depth
	# from the text files from BEDTools coverage

	function Usage() { # Display a usage message and exit