- 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
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"""""""""""""""""VIMRC""""""""""""""" | |
""" Nick Crawford (mod from Ben Pote) | |
"""Last updated 5.28.14 | |
""""""""""""""""""""""""""""""""""""" | |
""""""Vundle! | |
set nocompatible " be iMproved, required | |
filetype off " required |
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def topology_test(tree, query_tree, symmetric_distance=False): | |
"""Given a tree and a query tree this function tests if the query tree is present or identical to the | |
tree. If 'symmetric_distance' is set to True the symmetric distance of the query tree to the relavent taxa in the | |
tree is returned. | |
Both trees should be tree objects and contain idential taxon labels. | |
Examples: | |
-------- |
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#!/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 |
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import os | |
import sys | |
import shlex | |
import argparse | |
import multiprocessing | |
from subprocess import Popen, PIPE | |
def get_args(): | |
"""Processes arguements""" | |
parser = argparse.ArgumentParser() |
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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" |
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import pysam | |
import argparse | |
from collections import Counter | |
def get_args(): | |
"""Parse sys.argv""" | |
parser = argparse.ArgumentParser() | |
parser.add_argument('--bam', | |
required=True, |
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import os | |
import sys | |
import glob | |
import pysam | |
import argparse | |
import multiprocessing | |
def get_args(): | |
'''Parse sys.argv''' | |
parser = argparse.ArgumentParser() |
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