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 ans
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 ac
On Sep 13, 2012, at 10:30 PM, Eric Bennett wrote:
> [woz:~] bennette%
> /Library/Frameworks/Python.framework/Versions/2.6/bin/python pytest.py
> Traceback (most recent call last):
> File "pytest.py", line 2, in
>number = int(example_string)
> ValueError: invalid literal for int() with base
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 pr
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 co
>
> 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,
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 starin
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)"
O
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.
So
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
] 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
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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 to convince others
that python is a "good
Another vote for R.
huge (100s MB) tables of tab-delimited data on which I would like to do
> some math (averaging, sigmas, simple arithmetic, etc) as well as some
> sorting and rejecting
This is precisely what R is meant for. It was mentioned that it isn't so
good at really large datasets, but
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An astronomer, a physicist and a mathematician are on a train in
Scotland. The astronomer looks out of the window, sees a black sheep
standing in a field, and remarks, "How odd. Scottish sheep are black."
"No, no, no!" says the physicist. "Only some Sc
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
Universi
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 sho
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, yo
On Wed, Sep 12, 2012 at 12:49 PM, James Stroud 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 new
> language (a
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 pyt
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 modificatio
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
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 comp
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 ar
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!
al Message-
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
> 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.
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.
>
> 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 plotti
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-delim
Hi Jacob,
As the preceding discussion has illustrated, there are obviously a
number of options, nearly all of which will work well for what you
describe. As Pete Meyer suggested above, the best language may be the
one you already know (I also echo his suggestion to test your code on
a small subset
I agree with Pete. Moreover, Python doesn't have built-in statistic
functions but adding package (numpy and scipy in this case) is very simple.
Quentin
Le 12/09/2012 17:11, Pete Meyer a écrit :
One thing to keep in mind is that there's usually a trade-off between
setup (writing and testing) an
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
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
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 tab-delimited data on
> which I woul
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).
Le Mercredi 12 Septembre 2012 16:40 CEST, "George M. Sheldrick"
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.
(To a good approximation, 15
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 th
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
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
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