jrjhealey

# -*- coding: utf-8 -*-

"""
This script takes the .hhr files output by HHSuite and
turns the quite verbose file in to a fully tabulated
version with all the fields separated one, one line per
file. Thus, the file can be viewed simply in Excel etc.
It requires the non-standard pandas module.
"""

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"

jrjhealey

#!/usr/bin/python

# This script is designed to take a genbank file and 'slice out'/'subset'
# regions (genes/operons etc.) and produce a separate file. This can be
# done explicitly by telling the script which base sites to use, or can
# 'decide' for itself by blasting a fasta of the sequence you're inter-
# ed in against the Genbank you want to slice a record out of.

# Note, the script (obviously) does not preseve the index number of the
# bases from the original 

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


#### 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

#!/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

#!/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

#!/bin/bash

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

# Capture inputs

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

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 colours:
df=$(tput sgr0)
tr=$(tput setaf 1)
tg=$(tput setaf 2)
ty=$(tput setaf 3)
tb=$(tput setaf 4)

usage(){