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| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <title></title> | |
| <meta name="author" content=""> | |
| <meta name="description" content=""> | |
| <meta name="viewport" content="width=device-width, initial-scale=1"> | |
| <link rel="icon" href="/favicon.png" /> | |
| <link rel="apple-touch-icon-precomposed" href="/apple-touch-icon.png" /> |
| # This was the order I installed things for a working scientific computing environment on my Mac. | |
| brew install python | |
| pip install virtualenv virtualenvwrapper | |
| # Also add these to your ~/.bash_profile: | |
| export PATH=/usr/local/bin:/usr/bin:$PATH | |
| source /usr/local/bin/virtualenvwrapper.sh | |
| # Not necessary, but quite nice |
| class Node(object): | |
| def __init__(self, val): | |
| self.val = val | |
| self.left = None | |
| self.right = None | |
| def __lt__(self, val): | |
| return self.val < val | |
| def __gt__(self, val): |
| #!/usr/bin/env python3 | |
| import io | |
| import sys | |
| import time | |
| import datetime | |
| import requests | |
| from Bio import SeqIO |
| import numpy as np | |
| def array_for_sliding_window(x, wshape): | |
| """Build a sliding-window representation of x. | |
| The last dimension(s) of the output array contain the data of | |
| the specific window. The number of dimensions in the output is | |
| twice that of the input. | |
| Parameters |
| # | |
| # This script calculates the depth of coverage and breadth of coverage for a given bam. | |
| # Outputs a dictionary containing the contig/chromosome names and the depth and breadth of coverage for each | |
| # and for the entire genome. | |
| # | |
| # If you optionally specify the name of the mitochondrial chromosome (e.g. mtDNA, chrM, chrMT) | |
| # The script will also generate breadth and depth of coverage for the nuclear genome AND the ratio | |
| # of mtDNA:nuclearDNA; which can act as a proxy in some cases for mitochondrial count within an individual. | |
| # | |
| # Author: Daniel E. Cook |
| import re | |
| def replace(string, substitutions): | |
| substrings = sorted(substitutions, key=len, reverse=True) | |
| regex = re.compile('|'.join(map(re.escape, substrings))) | |
| return regex.sub(lambda match: substitutions[match.group(0)], string) |
| # functions for plotting garden of forking data plots | |
| library(rethinking) | |
| polar2screen <- function( dist, origin, theta ) { | |
| ## takes dist, angle and origin and returns x and y of destination point | |
| vx <- cos(theta) * dist; | |
| vy <- sin(theta) * dist; | |
| c( origin[1]+vx , origin[2]+vy ); | |
| } |
This procedure results in a computer that runs both Mac OS X and Ubuntu in a dual-boot configuration, each operating system using full (whole) disk encryption, and with the Ubuntu root file system stored on a ZFS pool encrypted using LUKS. The specific hardware and software versions used to document this procedure are:
