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
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 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

#!/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

#!/bin/bash

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

usage(){

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(){

jrjhealey

Finger Binary

What's Finger Binary?

Here is a description of Finger Binary in Wikipedia.

Finger binary is a system for counting and displaying binary numbers on the

jrjhealey

PVCpnf_1	PAU_03353	PAU_03392	5W5F	5W5F_F	99.4	1.7e-16	2.8e-21	108.8	>5W5F_F Tail tube protein gp19; T4 tail tube, dose limit;{Enterobacteria phage T4 sensu lato}
PVCpnf_2	PAU_03352	PAU_03391	3J9Q	3J9Q_B	100.0	3.6e-34	6e-39	243.2	>3J9Q_B sheath, tube; pyocin, bacteriocin, sheath, tube, STRUCTURAL; 3.5A {Pseudomonas aeruginosa}
PVCpnf_3	PAU_03351	PAU_03390	3J9Q	3J9Q_B	99.9	8.9e-32	1.5e-36	234.4	>3J9Q_B sheath, tube; pyocin, bacteriocin, sheath, tube, STRUCTURAL; 3.5A {Pseudomonas aeruginosa}
PVCpnf_4	PAU_03350	PAU_03389	3J9Q	3J9Q_B	99.9	9.3e-28	1.6e-32	207.6	>3J9Q_B sheath, tube; pyocin, bacteriocin, sheath, tube, STRUCTURAL; 3.5A {Pseudomonas aeruginosa}
PVCpnf_5	PAU_03349	PAU_03388	5IV5	5IV5_I	99.0	2.4e-13	4e-18	93.6	>5IV5_IB Baseplate wedge protein gp6, Baseplate; T4, baseplate-tail tube complex, pre-attachment; 4.11A {Enterobacteria phage T4}
PVCpnf_6	PAU_03348	PAU_03387	3SLS	3SLS_B	75.1	1.5	2.5e-05	26.7	>3SLS_B Dual specificity mitogen-activated protein kinase; Serine-threonine kinase, Signalling, TRANSFER

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

#!/bin/bash

# Script to align fastq reads to a given reference, and output the necessary files sorted etc.

# Script requires bwa and samtools in path - check for existence:

command -v bwa >/dev/null 2>&1 || { echo >&2 "BWA doesn't appear to be installed. Aborting."; exit 1; }
command -v samtools >/dev/null 2>&1 || { echo >&2 "samtools doesn't appear to be installed. Aborting."; exit 1; }
# Capture inputs