Wayne's Bioinformatics Code Portal fomightez

Pertinent Stackoverflow post with SageMath code that plots 3D surfaces using SageMath 10.7 kernel in Jupyter at present: https://stackoverflow.com/q/79733626/8508004
See my comments there on how to run the demonstration.

JupyterLab current on Binder with awscli and zstd

To work with LOGAN Search data, see slide 35 of Rayan Chikhi | Project Logan Assembling all public sequencing data | CGSI 2024 (around 20.32 minute mark), need awscli and zst installed

	#Useful snippets and examples for use of JupyterLite with commands typically related to the shell available in standard Jupyter
	# (Also see 'Useful snippets and examples for when converting command line commands from Jupyter/IPython back to Pure Python' at
	# https://gist.github.com/fomightez/ed79e33e97601d839dd550fd224d583c because a lot of these overlap, yet JupyterLite has some magics that obviously don't work with Pure Python
	# MAGIC COMMANDS THAT SHOULD WORK IN JUPYTERLITE
	%pwd
	%store s >test_store.txt # if `s` previously define.

	#`%ls` fails at present, but you can do
	import os
	os.listdir()

	def collect_time_info(input_text_filepath):
	'''
	Take the entire row of columns and return that row of columns plus extra
	columns with the details gleaned from timestamps in the the corresponding
	`logs/???????_<accession>.out`
	'''
	with open(input_text_filepath, 'r') as thelog_stdout_file:
	std_out_string=thelog_stdout_file.read()
	# with std_out log read in, parse it for the informaiton in the three timestamps
	start_ts = std_out_string.split('Current timestamp at start: ')[1].split('\n')[0].strip()