ngcrawford

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

""""""Vundle!

set nocompatible              " be iMproved, required
filetype off                  " required

ngcrawford

import pysam
import argparse
from collections import Counter

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

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

ngcrawford

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"

ngcrawford

1. 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.
2. Run the bowtie2 commands with python run_bowtie2.py

ngcrawford

ngcrawford

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

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

ngcrawford

ngcrawford

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

"""
removeFaFromFasta.py

Created by Nick Crawford on 2012-31-07.

The author may be contacted at ngcrawford@gmail.com

ngcrawford

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

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

ngcrawford

#!/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