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.

---

---

---

fomightez

fomightez

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()

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

fomightez

fomightez

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