Wayne's Bioinformatics Code Portal 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

	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()

	import pandas as pd
	import numpy as np
	import matplotlib as mpl
	import re

	df = pd.DataFrame({
	"Gene_name": ["sdsR", "arrS","gadF"],
	"Genes_in_same_transcription_unit": ['pphA, sdsR', 'arrS','mdtF, mdtE, gadF, gadE'],
	})
	# Convert Gene_name column to a set for quick lookup