chad-m

import base64
import os
import json
import pickle
import uuid
import re

import streamlit as st
import pandas as pd

vidboda

zcat file1.vcf.gz | awk -F"\t" '{if ($0 !~ /^#/) {print "chr"$0} else{print $0}}' | bgzip -c >file1chr.vcf.gz

nloadholtes

from setuptools import setup, find_packages
import subprocess

def _get_version_hash():
  """Talk to git and find out the tag/hash of our latest commit"""
  try:
        p = subprocess.Popen(["git", "describe",
                              "--tags", "--dirty", "--always"],
                             stdout=subprocess.PIPE)
    except EnvironmentError:

davfre

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (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)

obazoud

#!/bin/bash
sudo docker stop $(docker ps -a -q)
sudo docker rm $(docker ps -a -q)
sudo docker ps -a | grep 'months ago' | awk '{print $1}' | xargs sudo docker rm
sudo docker images | grep "\<none\>" | awk '{ print $3 }' | xargs sudo docker rmi

hopsoft

#!/usr/bin/env ruby

# checkout the readme from the master branch
`git checkout gh-pages; git checkout master README.md`

path = `pwd`.gsub(/\n/, "")
readme_path = File.join(path, "README.md")
index_path = File.join(path, "index.md")

# write the index readme file