Nick Crawford ngcrawford

Modify the sample_info.txt appropriately. I'd recommend doing this in excel and exporting the sheet as a CSV file. The first lane is a header and cannot be changed.
Run the bowtie2 commands with python run_bowtie2.py

	"""""""""""""""""VIMRC"""""""""""""""
	""" Nick Crawford (mod from Ben Pote)
	"""Last updated 5.28.14
	"""""""""""""""""""""""""""""""""""""

	""""""Vundle!

	set nocompatible " be iMproved, required
	filetype off " required

	import pysam
	import argparse
	from collections import Counter

	def get_args():
	"""Parse sys.argv"""
	parser = argparse.ArgumentParser()

	parser.add_argument('--bam',
	required=True,

	require 'formula'

	class Openblas64Julia < Formula
	homepage 'http://xianyi.github.com/OpenBLAS/'
	# Maintainers, remember to update the LAPACK url in OpenblasLapack above.
	# See the "LAPACK_URL" in the openblas Makefile for the right version.
	url 'http://github.com/xianyi/OpenBLAS/zipball/v0.2.8'
	sha1 'c62ab98dae8ac6d49c367235033180ef72dd7bbd'
	head "https://github.com/xianyi/OpenBLAS.git", :branch => "develop"

	import os
	import sys
	import shlex
	import argparse
	import multiprocessing
	from subprocess import Popen, PIPE

	def get_args():
	"""Processes arguements"""
	parser = argparse.ArgumentParser()

	#!/usr/bin/env python
	# encoding: utf-8

	"""
	removeFaFromFasta.py

	Created by Nick Crawford on 2012-31-07.

	The author may be contacted at [email protected]

	import os
	import sys
	import glob
	import pysam
	import argparse
	import multiprocessing

	def get_args():
	'''Parse sys.argv'''
	parser = argparse.ArgumentParser()

	#!/usr/bin/env python
	# encoding: utf-8

	import multiprocessing
	from textwrap import dedent
	from itertools import izip_longest

	def process_chunk(d):
	"""Replace this with your own function
	that processes data one line at a