On Thu, 2012-09-13 at 13:21 -0500, Jacob Keller wrote:
Java anyone?!
Your subject line asks about scripting languages. I would think that
even the most inveterate Java advocate would hesitate before
recommending Java for the kind of informal scripting that you were
asking about :-)
I've
On 09/14/2012 12:30 AM, Eric Bennett wrote:
Actually it's a bit of a hindrance. In Perl I can call the int function on
anything and get a sensible answer. In python if you call int on a string that
contains a floating point number the default behavior is that it will crash:
The sensible
I'd just use a decent shell scripting language (like zsh) in conjunction with a
unix tool like awk. But the gnuplot option sounds ideal.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
] Off-topic: Best Scripting Language
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Hi James,
I don't read blaming in George's words, just reasoning for a
personal decision.
Maybe I suffer from similar prejudice: I have the impression that
python programmers spend a lot of effort in trying
On Sep 13, 2012, at 3:24 AM, Tim Gruene wrote:
I have the impression that
python programmers spend a lot of effort in trying to convince others
that python is a good choice. Why bother rather than let people make
their own decision?
Someone asked.
Plus, python programmers put no more
Like most computer users and many scientists I don't write scripts to
organize or analyse my data unless I get desperate. I've used both Python
and Perl a few years ago, but it would take quite a lot of time and effort
and staring at on-line tutorials to get back into either of them right now.
In my opinion, the Python equivalent of your pseudo-code is fairly close to
how you would write the instructions logically. But then maybe not everyone
thinks in the same way that I do :-)
for x in range(1, 10):
if age_of_person(x) 50:
print name_of_person(x), is an old man (or woman)
Of
On Sep 13, 2012, at 11:02 AM, Patrick Shaw Stewart wrote:
Like most computer users and many scientists I don't write scripts to
organize or analyse my data unless I get desperate. I've used both Python
and Perl a few years ago, but it would take quite a lot of time and effort
and staring
It turns out that the syntax and semantics of all reasonable programming
languages are very similar, or fall into only a few classes (e.g. C-like,
S-expressions, etc.), so once you are fluent in one from a class, it's
easy to pick up the others. This can't be said of natural languages, which
Another option that could be cheap or free (if your university offers
license deals, as mine does) is SPSS. It has a lot of the quick and dirty
spreadsheet functionality of Excel, is much faster than Excel with large
tables, has lots of good analysis tools, has its own scripting language,
and is
On Sep 12, 2012, at 2:28 PM, Ethan Merritt wrote:
Why are you dis-ing python? Seems everybody loves it...
I'm sure you can google for many reasons I hate Python lists.
Mine would start
1) sensitive to white space == fail
2) dynamic typing makes it nearly impossible to verify program
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of tab-delimited data on
which I would like to do some math (averaging, sigmas, simple
Try R. :)
http://www.r-project.org/
Eric
On Wed, Sep 12, 2012 at 10:32 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
I always use FORTRAN for such tasks, especially if speed is important.
George
On 09/12/2012 04:32 PM, Jacob Keller wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection
files and so on, I was curious what people thought would be the best
language for the
Le Mercredi 12 Septembre 2012 16:40 CEST, George M. Sheldrick
gshe...@shelx.uni-ac.gwdg.de a écrit:
May I add a little personal joke to the serious remark by George.
This remembers me a discussion I had with Jorge Navaza, let's say 15 years ago,
about the programming language of the future.
One thing to keep in mind is that there's usually a trade-off between
setup (writing and testing) and execution time. For one-off data
processing, I'd focus on implementation speed rather than execution
speed (in other words, FORTRAN might not be ideal unless you're already
fluent with it).
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of
A similar remark was made to me by David Blow, while he was on sabbatical at
UNC in the 1980s, working with the UNC Computer Science Department and in a
moment of intense frustration with the overpowering ignorance of fortran and
the enthusiasm for Unix exhibited by that department.
Charlie
On Wednesday, September 12, 2012 07:32:54 am Jacob Keller wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of tab-delimited
For the specific purpose you list -
input from tab-delimited data
output to simple statisitical summaries and (I assume) plots
- it sounds like gnuplot could do the job nicely.
I wasn't aware that gnuplot can do calculations--can it? I was probably
going to use it somewhere as a plotting
All you need is scipy library to get those pesky statistic functions :)
On 09/12/2012 11:11 AM, Pete Meyer wrote:
Python's relatively easy to learn, and more flexible than octave/R;
but it doesn't have the built-in statistic functions that octave and R
do.
Why are you dis-ing python? Seems everybody loves it...
Depends on if you like the object model, some don't. In the end it
really boils down to what you're used to and what you've learned to
use.
-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter,
Charlie
Sent: Wednesday, September 12, 2012 11:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: Best Scripting Language
A similar remark was made to me by David Blow, while he was on sabbatical at
UNC
On Sep 12, 2012, at 9:11 AM, Pete Meyer wrote:
That said, I'd take a look at python, octave or R. Python's relatively easy
to learn, and more flexible than octave/R; but it doesn't have the built-in
statistic functions that octave and R do.
import scipy
Now it does!
It is the lack of compatibility between different versions mentioned by
Ethan that really put me off learning PYTHON. In contrast, the
FORTRAN-66 program SHELX76 still compiles and runs correctly with any
modern FORTRAN compiler. The only significant 'new' features that I now
use are dynamic
Python sorting 1 records of 1 floats for each record, finding the max,
min, and mean of entire 100,000,000 32 bit float array (400 MB) on a 6 year old
white imac.
*11.6 seconds.
*This doesn't include the time to generate the 400 MB of random (normal) data.
Try it on your own
Hi,
Python, of course (if you know some basic math). Otherwise, Python and a
good math text book -:)
Pavel
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I
On Sep 12, 2012, at 1:00 PM, George Sheldrick wrote:
It is the lack of compatibility between different versions mentioned by Ethan
that really put me off learning PYTHON.
Python is backwards compatible. I have reams of code I wrote in python 2.3 that
still works in 2.7 without
Ethan,
I think majority of your complaints about python result from its very
purpose - to be readable/portable for the sake of facilitating rapid
implementation. There are many other languages that provide tools to
accomplish what Jacob wants to do (well, I would stay away from P''),
but
On Wed, Sep 12, 2012 at 12:49 PM, James Stroud xtald...@gmail.com wrote:
Also, python (aka python 2) and python 3000 (aka python 3) are considered
two different languages. It's not reasonable to consider them one language
and then complain that they are incompatible. Python 3 was created as a
Colleagues: Another country is heard from:
Since no one has mentioned MATLAB, let me mention it.
--Can easily do any math from 2+2 to matrix SVD etc.
--Statistics toolbox does most of what anyone would want.
--Lots of easy quick graphics that can be prettied up if needed.
--If you know FORTRAN,
I encourage trainees to learn a programming language that they
will help their careers beyond their short time in my lab. Many or
most of them will not continue in structural biology or even science.
For the moment, I am pushing python even though I am minimally
literate in it myself. They
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