brentp

library(SNPRelate)
library(FDb.UCSC.snp137common.hg19)
library(hash)

args = commandArgs(TRUE)

vcf.fn = args[1]


gds.fn = paste0(args[1], ".gds")

arq5x

Genome arithmetic for data exploration

The goal of today's practical session is to get your hands dirty with bedtools. We will be studying ChiP-seq data from three different cell types. Each cell type was assayed for H3K27ac. Our research goal is to understand and explore the similarities and differences between the ChIP peaks observed in the 3 different cell types.

arq5x

# 1. Get the ENCODE segmentations from EBI.
# consensus
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/gm12878.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/h1hesc.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/helas3.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/hepg2.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/huvec.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/k562.combined.bb

# Segway (ahem; https://twitter.com/michaelhoffman/status/246679147164880897)

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)
# 

arq5x

##########################################
# Step 0. setup a list of sample names.  
# Assume that each of your gzipped
# FASTQ files is named as follows:
# sample1.1.fq.gz
# sample1.2.fq.gz
# sample2.1.fq.gz
# sample2.2.fq.gz
# ...
# sampleN.1.fq.gz

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

stevedonovan

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

local ml = {}

--- String utilties.
-- @section string

drio

What's this?

I was/am in the process of adding multithreading capabilities to a tool I am working on (more on that soon). The tool is written in C/C++. My first option was using POSIX threads (pthreads) before going into higher level options like boost.

I first read this

taoliu

#!/usr/bin/env python

import subprocess
import sys
import os
import time

#time_stamp=time.strftime("%y-%m-%d_%H-%M-%S")
time_stamp=str(time.time())

brantfaircloth

class FullPaths(argparse.Action):
    """Expand user- and relative-paths"""
    def __call__(self, parser, namespace, values, option_string=None):
        setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))

def is_dir(dirname):
    """Checks if a path is an actual directory"""
    if not os.path.isdir(dirname):
        msg = "{0} is not a directory".format(dirname)
        raise argparse.ArgumentTypeError(msg)