jrjhealey

#Copy to a script and run in a terminal to see the codes and their results (this is not an exhaustive list)
print("\033[0;37;40m Normal text\n")
print("\033[2;37;40m Underlined text\033[0;37;40m \n")
print("\033[1;37;40m Bright Colour\033[0;37;40m \n")
print("\033[3;37;40m Negative Colour\033[0;37;40m \n")
print("\033[5;37;40m Negative Colour\033[0;37;40m\n")
 
print("\033[1;37;40m \033[2;37:40m TextColour BlackBackground          TextColour GreyBackground                WhiteText ColouredBackground\033[0;37;40m\n")
print("\033[1;30;40m Dark Gray      \033[0m 1;30;40m            \033[0;30;47m Black      \033[0m 0;30;47m               \033[0;37;41m Black      \033[0m 0;37;41m")
print("\033[1;31;40m Bright Red     \033[0m 1;31;40m            \033[0;31;47m Red        \033[0m 0;31;47m               \033[0;37;42m Black      \033[0m 0;37;42m")

jrjhealey

#!/usr/bin/env python

# Slice subregions out of a genbank between 2 genes.
# Usage:
#   slice_genes.py infile.gbk gene1:gene2:strand

from Bio import SeqIO
import sys, argparse

def get_args():

jrjhealey

# Extract fasta files by their descriptors stored in a separate file.
# Requires biopython

from Bio import SeqIO
import sys
import argparse

def getKeys(args):
	"""Turns the input key file into a list. May be memory intensive."""

jrjhealey

#!/bin/bash
set -eo pipefail

# A small script to generate artemis comparison files (nucleic acid comparison)
# since all the webservers are apparently defunct!

# Script requires blastn (NOT LEGACY BLAST) and makeblastdb in path - check for existence:

command -v makeblastdb >/dev/null 2>&1 || { echo >&2 "makeblastdb doesn't appear to be installed. Aborting."; exit 1; }
command -v blastn >/dev/null 2>&1 || { echo >&2 "BLAST+ doesn't appear to be installed. Aborting."; exit 1; }

jrjhealey

# This script will calculate Shannon entropy from a MSA.

# Dependencies:

# Biopython, Matplotlib [optionally], Math

"""
Shannon's entropy equation (latex format):
    H=-\sum_{i=1}^{M} P_i\,log_2\,P_i
    Entropy is a measure of the uncertainty of a probability distribution (p1, ..... , pM)

jrjhealey

#!/usr/bin/ruby
# Create display override file to force Mac OS X to use RGB mode for Display
# see http://embdev.net/topic/284710

require 'base64'

data=`ioreg -l -d0 -w 0 -r -c AppleDisplay`

edids=data.scan(/IODisplayEDID.*?<([a-z0-9]+)>/i).flatten
vendorids=data.scan(/DisplayVendorID.*?([0-9]+)/i).flatten

jrjhealey

# Step 1
# Add the user with
sudo adduser username
# Ensure a temporary password is given to the account else it remains locked
# other options can be left blank

# Add the username to the AllowedUsers field in /etc/ssh/sshd_config (on the server)

# Next step is often easier to do as the new user to avoid messing up file ownership
sudo -i -u newuser

jrjhealey

"""
This script pulls in homologs of proteins from PDB
as determined by HHSuite. It then employs pychimera and
UCSF Chimera to structurally match them and get an
indication of how well they score (RMSD) in order
to pick the best simulation.
"""
import os
import subprocess
import sys

jrjhealey

\documentclass[a4paper, oneside, 11pt]{memoir} % Doc Setup
\usepackage[left=1cm, right=1cm, top=1cm, bottom=1cm]{geometry}  % Doc Geometry

\usepackage{texshade}
\usepackage{lscape}
\usepackage[active, tightpage]{preview}

\begin{document}
\begin{landscape}
\begin{preview}

jrjhealey

# This gist contains 10 randomly selected kmers (9mers) from the reference human genome (GRCh38).
The following code was used to generate the output:

import re, sys
from Bio import SeqIO
import random
import time

k = 9
n = 10