Olga Botvinnik olgabot

Prereq:

apt-get install zsh
apt-get install git-core

Getting zsh to work in ubuntu is weird, since sh does not understand the source command. So, you do this to install zsh

wget https://github.com/robbyrussell/oh-my-zsh/raw/master/tools/install.sh -O - | zsh

Locate the section for your github remote in the .git/config file. It looks like this:

[remote "origin"]
	fetch = +refs/heads/*:refs/remotes/origin/*
	url = [email protected]:joyent/node.git

Now add the line fetch = +refs/pull/*/head:refs/remotes/origin/pr/* to this section. Obviously, change the github url to match your project's URL. It ends up looking like this:

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:

Update HISTORY.md
Commit the changes:

git add HISTORY.md
git commit -m "Changelog for upcoming release 0.1.1."

Update version number (can also be minor or major)

bumpversion patch

Creating a Conda development environment

We recommend that you set up a Python environment for developing quantecon that is separate from the "default" Python environment that you use in your own research. This will allow you to contribute to quantecon without worrying about corrupting the Python environment on which your other work depends.

Below are instructions for building a separate development environment for contributing to the quantecon package using the Conda package management system which comes bundled with the Anaconda Python distribution provided by Continuum Analytics.

Step 1:

Fork and clone a copy of the quant-econ repository on to your local machine.

Step 2:

Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.

Extracting paired FASTQ read data from a BAM mapping file

Sometimes FASTQ data is aligned to a reference and stored as a BAM file, instead of the normal FASTQ read files. This is okay, because it is possible to recreate raw FASTQ files based on the BAM file. The following outlines this process. The useful software samtools and bedtools are both required.

From each bam, we need to extract:

reads that mapped properly as pairs
reads that didn’t map properly as pairs (both didn’t map, or one didn’t map)

	#!/usr/bin/env python
	# numpy and biopython are required -- pip install numpy biopython

	from Bio import Entrez
	from Bio import Medline

	MAX_COUNT = 10
	TERM = 'Tuberculosis'

	print('Getting {0} publications containing {1}...'.format(MAX_COUNT, TERM))

	package main

	import (
	"errors"
	"log"
	)

	func getDistance(s1, s2 string) (int, error) {
	if len(s1) != len(s2) {
	return 0, errors.New("ERROR: Strings are of different lengths")

	Last login: Mon Aug 14 16:42:56 on ttys007
	~ source activate maca-dash
	(maca-dash) ➜ ~ conda install --yes phat
	Fetching package metadata ...............

	PackageNotFoundError: Package missing in current osx-64 channels:
	- phat

	Close matches found; did you mean one of these?