nhoffman

#!/usr/bin/env python

import sqlite3
from random import choice
from timeit import timeit
from itertools import chain

con = sqlite3.connect('test_cast.db', isolation_level=None)  # autocommit
cur = con.cursor()

nhoffman

#!/bin/bash

set -e

REQFILE="${1-requirements.txt}"
WHEELSTREET="${2-wheelstreet}"  # base dir for wheel dirs

if [[ ! -f "$REQFILE" ]]; then
    echo "Cannot find requirements file named $REQFILE"
    echo "Usage: $(basename $0) [requirements.txt] [wheelstreet]"

nhoffman

#!/usr/bin/env Rscript

suppressPackageStartupMessages(library(lattice, quietly = TRUE))
suppressPackageStartupMessages(library(latticeExtra, quietly = TRUE))
suppressPackageStartupMessages(library(argparse, quietly = TRUE))

main <- function(arguments){

    parser <- ArgumentParser()
    parser$add_argument('infile')

nhoffman

sshmount () {
	# Usage: sshmount host directory
	host=$1
	pth=$2
	mountpoint=~/mnt/${host}+$(basename $pth)
	mkdir -p $mountpoint
	sshfs $host:$pth $mountpoint -oauto_cache,reconnect,defer_permissions,negative_vncache,volname=${host}+$(basename $pth)
	cd $mountpoint
	echo "unmount using: umount $mountpoint"
}

nhoffman

## Extends Wang, et al, 2007 Fig 1 (pmid 17600086) to show detection threshold at higher coverage
##
                          
library(lattice)

## mu = error rate
mu_hp <- 0.0044
mu_nhp <- 0.0007

thresh <- function(N, mu, p=0.001){

nhoffman

## Use mutual information to define a value separating two
## distributions.

entropy <- function(x,y){
  ## shannon entropy of x or joint entropy of x and y
  if(missing(y)){
    freqs <- table(x)/length(x)
  }else{
    stopifnot(length(x) == length(y))
    freqs <- table(paste(x,y))/length(x)

nhoffman

;; gist.el
;; https://github.com/defunkt/gist.el
;; added as a submodule:
;; % git submodule add https://github.com/defunkt/gist.el.git
;; now, to clone .emacs.d elsewhere:
;; % git clone git@github.com:nhoffman/.emacs.d.git
;; % cd .emacs.d
;; % git submodule init && git submodule update
(condition-case nil
    (require 'gist "~/.emacs.d/gist.el/gist.el")

nhoffman

import os
import sys
import ConfigParser
from os import path, environ
import glob
import itertools

venv = environ.get('VIRTUAL_ENV')
if not venv:
    sys.exit('--> an active virtualenv is required'.format(venv))

nhoffman

#!/bin/bash

# try me out:
# two processors
# $ echo {1..9} | xargs -n1 -P2 ./ps.sh
# four processors
# $ echo {1..9} | xargs -n1 -P4 ./ps.sh

# sleeptime set to a random integer between 2 and 5
sleeptime=$(shuf -i 2-5 -n 1)

nhoffman

#!/usr/bin/env python

import re
import sys

rexp = re.compile(r'|'.join([
            r'\bactinomycete\b',
            r'\bcrenarchaeote\b',
            r'\bculture\b',
            r'\bchimeric\b',