Follow me
-
Recent Posts
calendar
December 2024 M T W T F S S 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Recent Comments
- Stan on python argparse issues with the help argument (TypeError: %o format: a number is required, not dict)
- Cormac on Pandas : how to compare dataframe with None
- LP on AWK: the substr command to select a substring
- jrab on python argparse issues with the help argument (TypeError: %o format: a number is required, not dict)
- How to disable SSL verification for urlretrieve? – Peter's blog on python: certificate verified failed
Archives
Categories
Meta
Author Archives: Thomas Cokelaer
GIT tutorial
I finally decided to use GIT for one of my new project. I know this sounds odd given that everybody nowadays seems to use it… Having used SVN for a while the transition should be smooth though. There are a … Continue reading
Entropy and information
In everyday parlance, entropy refers to the inevitable deterioration of a system (including a society). As you may remember from a physics course, there is a far more formal definition that originates from thermodynamics. I’ll spare you the equation but … Continue reading
latex: same footnote but different reference places (with hyperlink)
I had the following issue with LaTeX: I first created a footnote. Later on in the text I wanted to refer to the same footnote. The issue is that the footnote contains a hyperlink. After reading the few pages from … Continue reading
Python: ValueError: unknown locale: UTF-8
When installing bioservices (a python package) using pip or easy_install, I got this error Mac OS X 10.7 – Lion: ValueError: unknown locale: UTF-8ValueError: unknown locale: UTF-8 Although the installation is successful, the error will appear as soon as we … Continue reading
Posted in Uncategorized
Leave a comment
Using valgrind to debug R programs
If you want to debug your R program because of a segmentation fault or memory leak, you can use valgrind as follows in a shell: R -d "valgrind –leak-check=full –show-reachable=yes" -f your_script.RR -d "valgrind –leak-check=full –show-reachable=yes" -f your_script.R
ipython error
If you get this kind of error when starting ipython: /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/kernmagic/__init__.py in activate(ip, *args) 14 continue 15 magic_name = name[len(’magic_’):] —> 16 ip.shell.define_magic(magic_name, getattr(mymagics, name)) 17 18 def activate_aliases(ip, *args): AttributeError: ‘TerminalInteractiveShell’ object has no attribute ‘shell’/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/kernmagic/__init__.py in activate(ip, … Continue reading
Accessing Life Science Web Services from Python
In a previous post, I started to discuss about Web Services in Life Science and what a maze it is to navigate between them. Some Web Services provides Python code to access to their databases but not all of them. … Continue reading
Posted in biology, Life Science
Tagged bioservices, kegg, python, uniprot, web services
Leave a comment
LSF cluster commands
From Wikipedia, Load Sharing Facility (or simply LSF) is a commercial computer software, job scheduler sold by Platform Computing. It can be used to execute batch jobs on networked Unix. Here is a summary of some commands I’ve been using. … Continue reading
Python: pip installation
References: http://www.pip-installer.org/en/latest/installing.html The installation of pip depends on your system. For instance under ubuntu it is as easy as sudo apt-get install python-pipsudo apt-get install python-pip Another way to install it if you are familiar with virtualenv tool consists in … Continue reading
R warnings when starting rpy2 and installation
On Fedora 15 When I start rpy2 using this command import rpy2 from rpy2 import robjectsimport rpy2 from rpy2 import robjects I was getting these annoying warnings, which do not appear when starting a pure R session: During startup – … Continue reading
