fomightez

# meant to be run with `uv run https://gist.githubusercontent.com/fomightez/eee9a448be7287a024d260ec80751120/raw/6fcaeed31d62b0f138e265684ceebfcc49c0f6e5/streamlined_timestamp_start_end_miner_checker.py out.txt`, or similar
# This handles evaluating date timestamp info in start and end timestamps of a pipeline.
#####*****------------------------------------------------------------*****#####
# This is meant to use with `uv` to run. 
# First install `uv` with `pip install uv` then run `!uv run {script_url} {input_text_filepath}` where defined those variables prior
#-------------------------------------------------------------#
# Times printed for now. (Make a dataframe?)
#-------------------------------------------------------------#
# /// script
# requires-python = ">=3.12"

fomightez

#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()

fomightez

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.

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fomightez

fomightez

# meant to be run with `uv run https://gist.githubusercontent.com/fomightez/f036794b91d10761466341644b3c1cac/raw/15da0209f7b09c1ba0130cf66646635c80a58bae/evaluate_date_timestamps_in_pipeline_stdout.py out.txt`, or similar
# This handles evaluating date timestamp info in typical long and short read pipeline.
#####*****------------------------------------------------------------*****#####
# This is meant to use with `uv` to run. 
# First install `uv` with `pip install uv` then run `!uv run {script_url} {input_text_filepath}` where defined those variables prior
#-------------------------------------------------------------#
# Times printed for now. (Make a dataframe?)
#-------------------------------------------------------------#
# /// script
# requires-python = ">=3.12"

fomightez

fomightez

fomightez

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

fomightez