timoast

bookdown::gitbook:
  css: style.css
  config:
    toc:
      before: |
        <li><strong><a href="./">Lab notebook</a></strong></li>
    edit:
      link: https://github.com/timoast/notebook/edit/master/%s
      text: "Edit"
    search: yes

timoast

#! /bin/sh


usage="$(basename "$0") -- build bookdown book
          -h show help and exit
          -a upload book to aws"

amazon=false # check options
while getopts "ah" opt; do
    case $opt in

timoast

#! /usr/bin/env python

import MySQLdb
from argparse import ArgumentParser
import gzip


def add_table(options):
    link = MySQLdb.connect(options.host, options.user, options.password)
    cursor = link.cursor()

timoast

#! /usr/bin/env python

"""
extract_reads.py
Created by Tim Stuart
"""

import pysam

timoast

#! /usr/local/bin/python2.7
"""
mean_size.py
Created by Tim Stuart
"""

import numpy as np


def get_data(inp):