mattions

Your Vision

What is a vision?

Your vision answers the question "What do I want?" A clear vision help you communicate why you're here and what impact you're going to have.

Your vision should be aligned with the company vision, with your manager's V2MOM, and it should be personal. It should be an honest reflection of your own vision for your own work.

If you manage a team, it should be reflective of the purpose of the team and your collective impact.

mattions

# Upgrade your requirements
# - Finds outdated package with pip
# - install latest stable version
# - Update the requirements with the latest

pip list --outdated | cut -d' ' -f1 | xargs pip install --upgrade
pip freeze > requirements.txt

mattions

# blackkiwi - production app

FROM mattions/webber:1.0
MAINTAINER  mattions "[email protected]"

ENV DEBIAN_FRONTEND noninteractive
ENV PYTHONUNBUFFERED 1

RUN apt-get update && apt-get -qy install\
    python3 \

mattions

from pysam import VariantFile
import time
def count_oldvar_reg(vcffile_reg, labels=["OLDVARS", "OLDVARS_A", "OLDVARS_B"]):
    t_start = time.time()
    
    bcf_in = VariantFile(vcffile_reg)
    total = 0
    reg = 0
    
    for rec in bcf_in:

mattions

Handy commands

Extract bam according to a bed file

bedtools intersect -abam path/to/input.bam -b path/to/regions.bed > out.bam

Extract region of a VCF

mattions

def _save_more_extensions(filename, extensions=['png', 'svg', 'pdf']):
    for ext in extensions:
        comp_filename = "{0}.{1}".format(filename, ext) 
        plt.savefig(comp_filename, dpi=300)
        print "Saved plot: {0}".format(comp_filename)

mattions

#!/bin/sh
#
#    purge-old-kernels - remove old kernel packages
#    Copyright (C) 2012 Dustin Kirkland <[email protected]>
#
#    Authors: Dustin Kirkland <[email protected]>
#             Kees Cook <[email protected]>
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by

mattions

hardstatus alwayslastline '%{= G}[ %{G}%H %{g}][%= %{= w}%?%-Lw%?%{= R}%n*%f %t%?%{= R}(%u)%?%{= w}%+Lw%?%= %{= g}][ %{y}Load: %l %{g}][%{B}%Y-%m-%d %{W}%c:%s %{g}]'
startup_message off
termcapinfo xterm* ti@:te@
backtick 1 5 5 true
termcapinfo rxvt* 'hs:ts=\E]2;:fs=\007:ds=\E]2;\007'

mattions

/*!
 * Bootstrap v3.2.0 (http://getbootstrap.com)
 * Copyright 2011-2014 Twitter, Inc.
 * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
 *//*! normalize.css v3.0.1 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background:0}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:cont

mattions

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import time

data = []
for n_elements in [100, 1000, 10000, 100000]:
    a = range(n_elements)
    sa = set(a)
    b = np.array(a) + 50