How to visualize complex sets intersections with Python?

Examples about when using Venn diagrams or Upset plots

How to visualize if there are any common elements between lists? Most people will reply with something between “potatoes” and Venn diagrams. Venn works well with two lists, but what if you have three or… six? Read more

May 27, 2015

Run jobs in parallel with python

How do you manage efficiently multiples jobs with modern computer cores ? This is a real problem that had me stuck for a while. I am working on a framework to analyze next generation sequencing data, consequently I have numerous files to manages, differents types of data that have to undergo a specific analysis. On the other hand, I have a few cores (24), some RAM (32Go) and decent hard drives. Read more

June 3, 2012

Logging shell commands outputs with python

The analysis of sequencing data (at least in the first steps) is often a matter of starting multiple scripts one after an other. I found out that to log the stdout and the stderr with python was not that much obivous for me. I struggled quite a bit with the logging module but finally I came with the following. import os import subprocess import logging import logging.handlers import datetime as dt class ShellLaunchAndLog: ''' logging of shell commands output ''' def __init__(self): self. Read more

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