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 [email protected]: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 itertools

from openpyxl.reader.excel import load_workbook

def getrows(sheet, cols):
    headers = [c.value for c in sheet.rows[0] if c.value]
    for row in sheet.rows[1:]:
        d = dict(zip(headers, [c.value for c in row]))
        yield dict((k2, d[k1]) for k1,k2 in cols)
        

nhoffman

#!/bin/sh

# Converts a mysqldump file into a Sqlite 3 compatible file. It also extracts the MySQL `KEY xxxxx` from the
# CREATE block and create them in separate commands _after_ all the INSERTs.

# Awk is choosen because it's fast and portable. You can use gawk, original awk or even the lightning fast mawk.
# The mysqldump file is traversed only once.

# Usage: $ ./mysql2sqlite mysqldump-opts db-name | sqlite3 database.sqlite
# Example: $ ./mysql2sqlite --no-data -u root -pMySecretPassWord myDbase | sqlite3 database.sqlite

nhoffman

gist () {
	gid=${1:-2968328}
	curl -s https://api.github.com/gists/$gid | python3 -c 'import json, sys; print(next(iter(json.load(sys.stdin)["files"].items()))[1]["content"])'
}

nhoffman

#!/usr/bin/env python3

"""A simple python script template.

"""

import os
import sys
import argparse

nhoffman

#########################################
##  Set prompt, iTerm2 window and tabs ##
#########################################

# Color constants used in the prompt
BLACK="%{%}"
BOLD_BLACK="%{%}"
RED="%{%}"
BOLD_RED="%{%}"
GREEN="%{%}"

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',