brentp

"""
Reads a FastQ file from stdin and writes a file with unique records to sdout
usage:
    %s < in.fastq > out.unique.fastq

see: http://hackmap.blogspot.com/2010/10/bloom-filter-ing-repeated-reads.html
"""
from bloomfaster import Elf
import collections
import sys

hrldcpr

One-line Tree in Python

Using Python's built-in defaultdict we can easily define a tree data structure:

def tree(): return defaultdict(tree)

That's it!

btoone

Introduction

An introduction to curl using GitHub's API.

The Basics

Makes a basic GET request to the specifed URI

curl https://api.github.com/users/caspyin

MohamedAlaa

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

earthgecko

#!/bin/bash
# bash generate random alphanumeric string
#

# bash generate random 32 character alphanumeric string (upper and lowercase) and 
NEW_UUID=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 32 | head -n 1)

# bash generate random 32 character alphanumeric string (lowercase only)
cat /dev/urandom | tr -dc 'a-z0-9' | fold -w 32 | head -n 1

brandonb927

#!/bin/sh

###
# SOME COMMANDS WILL NOT WORK ON macOS (Sierra or newer)
# For Sierra or newer, see https://github.com/mathiasbynens/dotfiles/blob/master/.macos
###

# Alot of these configs have been taken from the various places
# on the web, most from here
# https://github.com/mathiasbynens/dotfiles/blob/5b3c8418ed42d93af2e647dc9d122f25cc034871/.osx

schmurfy

# Install MacTex: http://mirror.ctan.org/systems/mac/mactex/mactex-basic.pkg

$ sudo chown -R `whoami` /usr/local/texlive
$ tlmgr update --self
$ tlmgr install ucs
$ tlmgr install etoolbox

# Install pandoc view homebrew

christophergandrud

#####################
# R function for downloading plain-text data from GitHub
# Christopher Gandrud
# 7 January 2013
#####################

# source_GitHubData is directly based on source_url from the Hadley Wickham's devtools package

source_GitHubData <-function(url, sep = ",", header = TRUE)
{

dergachev

OS X Screencast to animated GIF

This gist shows how to create a GIF screencast using only free OS X tools: QuickTime, ffmpeg, and gifsicle.

Instructions

To capture the video (filesize: 19MB), using the free "QuickTime Player" application:

avrilcoghlan

#!/usr/local/bin/perl 
#
# 
# Perl script find_closest_worm_paralogs4.pl
# Written by Avril Coghlan (alc@sanger.ac.uk)
# 16-Feb-09.   
#
# This perl script finds the bootstrap value for the
# clade containing a pair of C. elegans paralogs in a family (where
# there is no other gene in that clade, ie. they are each other's