Wayne's Bioinformatics Code Portal fomightez

Summary

The %run magic provided by IPython not only supports the execution of regular Python scripts, it also runs Jupyter Notebook files (.ipynb).

Example

The run_demo.ipynb notebook below uses %run to execute all of the cells in reusable_stuff.ipynb. Once it does, both globals defined in reusable_stuff are available in run_demo for use.

	import mmap


	def get_last_lines(path: str, count: int) -> list[str]:
	"""Get count last lines from a file."""
	with open(path, "r+b") as text_file:
	text_mmap = mmap.mmap(text_file.fileno(), 0, mmap.ACCESS_READ)
	position = len(text_mmap)
	while count and (position := text_mmap.rfind(b"\n", 0, position)) != -1:
	count -= 1

	#!/bin/bash

	# TODO: you will need to have conda installed

	# create a python environment
	conda create -n env_tmp python=3.8.13 -y

	# activate environment
	conda activate env_tmp

	import rich.progress
	import rich.spinner
	import time
	import random


	class RandomChars(rich.progress.ProgressColumn):
	"""Simulation of computer 'thinking' by displaying random characters
	Args:
	chars (str): characters from which to choose for display. Defaults to 0-9A-F.

	import time

	def executeSomething():
	#code here
	print ('.')
	time.sleep(480) #60 seconds times 8 minutes

	while True:
	executeSomething()

	library(magick)
	library(reshape2)
	library(dplyr)
	library(tidygraph)
	library(particles)
	library(animation)

	plot_fun <- function(sim) {
	df <- as_tibble(sim)
	plot(df$x, df$y, col = df$color, pch = '.', axes = FALSE, xlim = c(-100, 317), ylim = c(-268, 100), xlab = NA, ylab = NA)

	# These are meant to work in both Python 2 and 3, except where noted.

	# See my useful_pandas_snippets.py for those related to dataframes (such as pickling/`df.to_pickle(save_as)`)
	# https://gist.github.com/fomightez/ef57387b5d23106fabd4e02dab6819b4
	# also see https://gist.github.com/fomightez/324b7446dc08e56c83fa2d7af2b89a33 for examples of my
	# frequently used Python functions and slight variations for more expanded, modular structures.


	#argparse
	# good snippet collection at https://mkaz.tech/code/python-argparse-cookbook/