Peter Cock

biopython_workshop. A basic introduction to Biopython, intended for a classroom based workshop. Now on Codeberg.

flake8-black. flake8 plugin to run black for checking Python coding style

galaxy_blast. Galaxy wrappers for NCBI BLAST+ and related BLAST tools.

mediawiki_to_git_md. Convert a MediaWiki export XML file into MarkDown as a series of git commits. Now on Codeberg.

flake8-rst-docstrings. flake8 plugin to validate Python docstrings as reStructuredText (RST)

backports.lzma. Backport of Python 3.3's standard library module lzma for LZMA/XY compressed files

picobio. Miscellaneous Bioinformatics scripts etc mostly in Python

longsight. Python code for capturing images from a webcam etc. Migrated to Codeberg.

biopython. My fork of the official Biopython repository, used for experimental branches etc

pico_galaxy. Galaxy tools and wrappers for sequence analysis

maf2sam. Convert MIRA Assembly Format (MAF) to Sequence Alignment/Map (SAM) format. Also archieved on Codeberg.

thapbi-pict. Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool

flake8-sfs. Python flake8 plugin for String Formatting Style (SFS)

zmk-config. My personalised ZMK firmare configuration for my Tutte-Coxeter Graph based keyboard etc.

tarball2git. Simple Python script to take a set of versioned tar balls and import them into a git repository. Now on Codeberg

galaxy_mira. Galaxy wrappers for MIRA assembler

split-dist. Unofficial repository for Thomas Mailund's tool Split-Dist (sdist)

ccn. Coupled Cell Networks

forked-daapd. A re-write of the firefly media server (mt-daapd). It's released under GPLv2+. Please note that this git repository is a mirror of the official one at git://git.debian.org/~jblache/forked-daapd.git

bioruby. bioruby

samtools-old. This is *NOT* the official repository of samtools.

hts-specs. This is my clone of the new official SAM/BAM specification github repository, to be used for proposed patches etc.

qmk_userspace. Userspace for the open-source QMK keyboard firmware.

kana-chording-ke. Japanese Keyboard layouts on macOS using Karabiner Elements: Now on CodeBerg

zmk-keyboard-graph-theory. ZMK firmware for my Graph Theory based diode-free mechanical keyboard PCB designs.

screed. a short read database

bioinformatics. Tools for bioinformatics

samtools. This is my clone of the new official samtools github repository, to be used for proposed patches etc.

rich. Rich is a Python library for rich text and beautiful formatting in the terminal.

planemo. Command-line utilities to assist in developing tools for the Galaxy project.

blast_max_target_seqs. Reproducible test case for the "-max_taget_seqs issue" found by Sujai Kumar in Dec 2015. Also archived on Codeberg.

bioperl-live. Core BioPerl 1.x code

Teaching. Code and files used in teaching and training courses.

bcbb. Useful bioinformatics code, primarily in Python and R

vbench. vbench: A tool for benchmarking your code through time, for showing performance improvement or regressions

enrich. Enrich adds few missing features to the wonderful rich library.

Teaching-Intro-to-Bioinf. Introduction to Bioinformatics training course slides

MDT-INTR-EXP-MET. Economics behavioural experiments using oTree