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

#!/usr/bin/env Rscript

# Perform cell-wise averaging of matrices (ignoring headers and row names)

# Standard install if missing
list.of.packages <- c("argparse", "abind")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
for(i in list.of.packages){suppressMessages(library(i, character.only = TRUE))}

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

#!/usr/bin/env python

"""
Using products of primes to work out whether 2 strings are anagrams of one another.
Inspired by: https://twitter.com/fermatslibrary/status/958700402647674880

Map each of the 26 english characters (A, B, C, ...) to a (unique) prime number.
Multiply the values mapped to each character together (A x B x C x ...).
Since every integer is a prime, or a unique product of primes, according to the
fundamental theorem of arithmetic), two words are anagrams of one another if their

jrjhealey

#!/usr/bin/env Rscript

# Plotting surface plots via ggplot2/plotly
# Usage:
# $ Rscript CDmeltplot.R -i data.csv -o filename


############################################################
# General purpose heatmap plotting script for consistency. #
# This script can be slow as it was designed to be pretty  #

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

#!/bin/bash


#### Print out all fastas ending in a certain string. ####
# Change *"$string" to *"$string"* to find containing,
# or "$string"* to find starts with.

file="$1"
string="$2"

jrjhealey

# Getting python logging info output in a colour coded and customised manner.
# Stolen from M. Galardini and https://stackoverflow.com/questions/384076/how-can-i-color-python-logging-output/2532931#2532931

import logging
import sys

BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE = range(8)

COLORS = {
    'WARNING'  : YELLOW,

jrjhealey

#!/bin/bash

# Script to retrieve PDBs via the command line from the PDB HTTP/FTP

# Capture inputs

usage()
{
cat << EOF
usage: $0 options

jrjhealey

#!/bin/bash
ethernet=$(ifconfig en0 | awk '/ether/{print $2}')
wifi=$(ifconfig en1 | awk '/ether/{print $2}')
echo "Ethernet MAC Address: $ethernet"
echo "Wifi MAC Address: $wifi"