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

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

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

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

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:

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

elowy01

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

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

nevesnunes

#!/usr/bin/env python2.7

"""
Extract title from PDF file.

Dependencies:
    pip install --user unidecode pyPDF PDFMiner

Usage:
    find . -name "*.pdf" | xargs -I{} pdftitle -d tmp --rename {}

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!

andy-thomason

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com