Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis?

From: Jason Swails <>
Date: Fri, 25 Mar 2011 08:23:50 -0700

On Fri, Mar 25, 2011 at 1:31 AM, <> wrote:

> Hi Catherine,
> I would suggest using Perl for this. There are plenty of web resources on
> how to manipulate text files. Also, O'Reilly's 'Learning Perl' by
> Schwartz&Phoenix is a must have for anyone writing scripts. It's actually
> the only manual I ever saw that is good and fun to read.
> Why not use Python? Because I'm trying to start a flamewar here!

haha -- then you should cross-post this on the python mailing list. I'd
cast my vote for Python since I know it much better. I won't draw any
comparisons with Perl because I don't use it or know it very well. I found
Python incredibly easy to learn, and it's a very natural language.

There are also many 3rd party packages that are ideally suited for common
applications. There are also intuitive Python bindings to basically every
toolkit/API out there (MPI, NetCDF, CUDA, GTK, OpenGL, etc.). Of course you
have to learn about these bindings/APIs in order to use them, but that's
always true.

If you decide to go the Python route, check out scipy and numpy (as already
suggested). These have linear algebra routines among many others.

Hope this helps,

> Ok, admittedly Perl and Python will both do a good job...
> Thomas
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Mar 25 2011 - 08:30:08 PDT
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