Python and Bioinformatics and Perl: Chomp in python

Update: As many readers have commented, I have just missed the obvious – there are functions in python to do this. See comments section for details.
So I do a lot of file processing in my bioinformatics work and I’ve always really liked the perl function chomp.
I wanted to implement something in python to do this [...]

Python for Perl Programmers (and Bioinformatics people)

Mark Bieda python getting started quick tips hints tutorial
I wanted to write a short post about getting started in python.
What you will like about Python as a perl person:
(1) A great thing is the interpreter. This will allow really rapid learning of python. For a perl person, python should come really fast. I was very, [...]

I wish I had… started with python earlier…

So far, my bioinformatics work has used a melange of perl, R, and bash scripting. While this has worked pretty well, it does have limits. For one, it is very not portable (bash scripting). I’ve already had problems with distributing software.
I wanted something that I could distribute in an easier way, yet had the advantages [...]

TAMALPAIS and promoter arrays

TAMALPAIS NimbleGen Promoter Arrays Array Analysis Problems Mark Bieda
I’ve been receiving some questions on TAMALPAIS usage for promoter arrays via email.
On the TAMALPAIS website, I say “Do not use this for promoter arrays.“
This is actually not quite true; there are a limited number of cases in which TAMALPAIS will perform well for promoter arrays. In [...]

TAMALg and TAMALPAIS: NimbleGen data analysis

Ok, I wanted to write about the relationship between TAMALPAIS and TAMALg.
keywords: Mark Bieda, TAMALPAIS, TAMALg, NimbleGen, ChIP-chip
Background
A major part of my research is developing algorithms and statistical models for analysis of ChIP-chip experiments – specifically those done with NimbleGen arrays.
TAMALPAIS (available here) predicts binding sites from NimbleGen array data and also does some basic [...]

NCBI GEO submission: howto hints

Ok, NCBI GEO submission of data can be a pain. I mean a big pain.
But there are a few simple things that can make it less painful.
here are my hints and a few steps:
1. Don’t assume that you will get the submission right the first time; it’s easy to have errors.
2. DO assume that NCBI [...]

TAMALPAIS: howto open files

key words: TAMALPAIS, NimbleGen, Mark Bieda, ChIP, server
Background:
TAMALPAIS is the webserver that I created to analyze NimbleGen ChIP-chip data (note that it is not for promoter data). You can find it at:
http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi
I’ve received queries from a number of people on opening files from my TAMALPAIS server.
Some people have trouble opening the files from the TAMALPAIS [...]