nathanhaigh

#!/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)
# 

mikeyk

#! /usr/bin/env python

import redis
import random
import pylibmc
import sys

r = redis.Redis(host = 'localhost', port = 6389)
mc = pylibmc.Client(['localhost:11222'])

taoliu

#!/bin/bash

# check commands: slopBed, bedGraphToBigWig and bedClip

which bedtools &>/dev/null || { echo "bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
which bedGraphToBigWig &>/dev/null || { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
which bedClip &>/dev/null || { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

# end of checking

max-sixty

// This Zellij config offers a more modal experience than the default. There are
// very few keybindings in the mode that you spend most of your time in, and we
// need to hit `C-space` to go into a mode where we navigate.

// The only keybindings in the normal mode are:
// - `C-space` to go into the tmux mode
// - `C-n` for a new pane
// - `C-t` for a new tab
// - `A-[` & `A-]` to go to the previous/next tab
// - `S-arrow` to navigate between panes

cridenour

Setting up Vim as your Go IDE

Intro

I've been wanting to do a serious project in Go. One thing holding me back has been a my working environment. As a huge PyCharm user, I was hoping the Go IDE plugin for IntelliJ IDEA would fit my needs. However, it never felt quite right. After a previous experiment a few years ago using Vim, I knew how powerful it could be if I put in the time to make it so. Luckily there are plugins for almost anything you need to do with Go or what you would expect form and IDE. While this is no where near comprehensive, it will get you writing code, building and testing with the power you would expect from Vim.

Getting Started

I'm assuming you're coming with a clean slate. For me this was OSX so I used MacVim. There is nothing in my config files that assumes this is the case.

aurora

function clone(object)
    local dict = {}
    
    local function clone(object)
        if (type(object) ~= "table") then
            return object
        elseif (dict[object]) then
            return dict[object]
        end

stevedonovan

-----------------
-- Microlight - a very compact Lua utilities module
--
-- Steve Donovan, 2012; License MIT
-- @module ml

local ml = {}

--- String utilties.
-- @section string

lh3

This is a small experiment on the alignment of ~50bp INDELs. The query sequences are shown in 0.01.fq below, where seq_ori is a 204bp sequence extracted from the human reference genome, seq_del54 contains a 54bp deletion in the middle, seq_del84 contains a 84bp deletion in a 120bp read, and seq_ins40 contains a 40bp insertion in a 140bp read. These four short sequences were mapped to the human reference genome with Bowtie2, BWA-MEM, LAST, Novoalign, SNAP and Stampy with default settings. Non-default scoring functions were also tested for Bowtie2 (--rdg 5,1 --rfg 5,1), BWA-MEM (-A2 -E1) and LAST (-r2 -q4). The output by various mappers/settings can be found in this gist. The following table gives my summary:

Mapper	Setting	-84bp	-54bp	+40bp
BBMAP	default	Yes	Yes	Yes
Bowtie2	default	No	No	No
Bowtie2	--rdg 5,1 --rfg 5,1	as insertion	as insertion	Yes
BWA-MEM	default	as split	Yes	Yes
BWA-MEM	-A2 -E1	Yes	Yes	Yes
LAST	default	as split	as split

jmarshall

ARG  ubuntu_version=latest
FROM ubuntu:${ubuntu_version}

USER root

RUN apt-get update && apt-get install -y \
	build-essential \
	curl \
	git \
	libbz2-dev \

arq5x

dad	mom	kid	Inheritance description
HOM_REF	HOM_REF	HOM_REF	Expected
HOM_REF	HOM_REF	HET	Mendelian violation (plausible de novo)
HOM_REF	HOM_REF	HOM_ALT	Mendelian violation (implausible de novo)
HOM_REF	HOM_ALT	HOM_REF	Mendelian violation (uniparental disomy)
HOM_REF	HOM_ALT	HET	Expected
HOM_REF	HOM_ALT	HOM_ALT	Mendelian violation (uniparental disomy)
HOM_REF	HET	HOM_REF	Expected
HOM_REF	HET	HET	Expected