Thiago Britto Borges tbrittoborges

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

Installation:

A quick installation does not require root access, as shown:

(wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash

A "Best of the Best Practices" (BOBP) guide to developing in Python.

	library(plyranges)

	set.seed(1)
	x <- data.frame(seqnames=1, start=0:9 * 100 + 1,
	width=20, id=1:10) %>%
	as_granges()

	y <- data.frame(seqnames=1, start=round(runif(4,100,900)),
	width=10, id=letters[1:4]) %>%
	as_granges() %>%

	"""
	Simple example to demostrate the embedding visualization for word embeddings in tensorflow / tensorboard
	https://www.tensorflow.org/how_tos/embedding_viz/
	"""

	import tensorflow as tf
	import os
	assert tf.__version__ == '1.0.0-rc0' # if code breaks, check tensorflow version
	from tensorflow.contrib.tensorboard.plugins import projector

	"""
	Learning Task:
	Given a sequence, predict a label based on the first value of the sequence

	Explanation of stateful LSTM and setup:
	http://philipperemy.github.io/keras-stateful-lstm/

	Exmple:
	given a sequence [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], predict 1
	given a sequence [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], predict 0

	import asyncio
	import aiohttp
	import bs4
	import tqdm


	@asyncio.coroutine
	def get(args, *kwargs):
	response = yield from aiohttp.request('GET', args, *kwargs)
	return (yield from response.read_and_close(decode=True))