Bede Constantinides bede

SAM and BAM filtering one-liners

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

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.

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

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

def tree(): return defaultdict(tree)

That's it!

	# This was the order I installed things for a working scientific computing environment on my Mac.

	brew install python
	pip install virtualenv virtualenvwrapper

	# Also add these to your ~/.bash_profile:
	export PATH=/usr/local/bin:/usr/bin:$PATH
	source /usr/local/bin/virtualenvwrapper.sh

	# Not necessary, but quite nice

	<!doctype html>
	<html lang="en">
	<head>
	<meta charset="utf-8">
	<title></title>
	<meta name="author" content="">
	<meta name="description" content="">
	<meta name="viewport" content="width=device-width, initial-scale=1">
	<link rel="icon" href="/favicon.png" />
	<link rel="apple-touch-icon-precomposed" href="/apple-touch-icon.png" />

	loadings = pca.components_

	# I've omitted the code to create ind; a list of the indexes of the
	# loadings ordered by distance from origin.

	plt.scatter(*loadings, alpha=0.3, label="Loadings");
	plt.scatter(*loadings[:, ind[:3]], c='r', marker='o',
	s=80, linewidths=1, facecolors="none",
	edgecolors='r',
	label="Contributes most\nto variance");

	#!/bin/bash
	# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
	#
	# Deinterleaves a FASTQ file of paired reads into two FASTQ
	# files specified on the command line. Optionally GZip compresses the output
	# FASTQ files using pigz if the 3rd command line argument is the word "compress"
	#
	# Can deinterleave 100 million paired reads (200 million total
	# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
	#

	<!--
	A button bar is a set of buttons at the bottom of an activity.
	An example is an AlertDialog with OK/Cancel buttons.

	Note that something similar can be accomplished using a
	split action bar and text-only action buttons, but this is an
	alternate presentation that's often preferred.
	-->
	<LinearLayout xmlns:android="http://schemas.android.com/apk/res/android"
	android:orientation="vertical"

	#!/usr/bin/env sh

	##
	# This is script with usefull tips taken from:
	# https://github.com/mathiasbynens/dotfiles/blob/master/.osx
	#
	# install it:
	# curl -sL https://raw.github.com/gist/2108403/hack.sh \| sh
	#

	git fetch upstream
	git reset --hard upstream/master