Re: [Tutor] green brackets?
Hi f.write(n\) should be f.write(\n) Paulo elis aeris wrote: def mousemove(x,y): f.write(n\) f.write(command + = + mousemove\n) f.write(parameter_1 = + str(x) + \n) f.write(parameter_2 = + str(y) + \n) f.write(n\) for some reason that last bracket of the 2nd and last line line in IDLE are green.\ why is that? ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Finding all locations of a sequence
Hi Lauren
I use the find string method to search DNA motifs. Here is an example
while sp len(fasta[j].sequence):
pos = string.find(fasta[j].sequence,
motif[i], sp)
if pos != -1 and pos 0:
plist.append(int(size) - pos)
mlist.append(toprint)
sp = pos
else:
sp = len(fasta[j].sequence)-1
sp+=1
pos = 0
sp = 0
You might even be able to trim a bit this code, but it is a start.
HTH
Paulo
Lauren wrote:
Ok, what I have is a RNA sequence (about 5 million nucleotides
[characters] long) and have (4100) subsequences (from another
sequence) and the sub-sequences are 6 characters long, that I want to
find in it.
The problem is the exceptional bond of U:G, which results in U bonding
to A (as per normal) and G (the abnormal bond) and G to bond with C
(as per normal) and U. Normally I'd go to search software already
available, however what I need done isn't covered b y anything out
there so far. That and I believe that they do not deal with the
exceptional bond. In any event, I want to know where the subsequences
can bind in the larger RNA sequence (ie, the location of binding in
the larger sequence) so I'm not (just) for where they would bind
normally, but also where the abnormal bonds would figure in.
Unfortunately my first attempt at this was unbearably slow, so I'm
hoping there is a faster way.
So an example with this would be:
Subseq AU can bind to UA (which is normal) and UG (not so
normal) and I want to know where UA, and UG are in the large
RNA sequence, and the locations to show up as one...thing.
I don't know if that is more helpful or not than the chicken example...
Thanks again for the help
On 14/06/07, Teresa Stanton [EMAIL PROTECTED] wrote:
OK, I'm going to take a shot at this. If what I'm understanding is correct,
a dictionary might help. But that would depend on the format of the
original sequence. If you have a list:
Lst1 = ['cow', 'pig', 'chicken', 'poultry', 'beef', 'pork']
Then you could:
Lst1.index('chicken')
And get 2, because the list starts with 0, not 1, as the first index.
Or this:
for i in Lst1:
if i == 'chicken':
print Lst1.index(i)
if i == 'poultry':
print Lst1.index(i)
2
3
Now, Kent or Alan and perhaps others will have a much more sophisticated way
of doing this same problem. I'm still not exactly sure what it is you are
looking for, because there isn't enough information for me to really get a
grasp on your problem. My response is a simple list structure that has
simple operations.
Hope it helps :)
T
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf
Of Lauren
Sent: Thursday, June 14, 2007 11:35 AM
To: tutor@python.org
Subject: [Tutor] Finding all locations of a sequence
Ok, please bear with me, I'm very new to programming and python. And
my question is rather...convoluted.
I have a bunch of sequences (about 4100 or so), and want to know where
they are in a very, very large string of letters. But wait, there's
more. Some of these sequences match to more than 'word' (for
example...to be consistent with later, chicken could match to poultry
or chicken).
example of what I want to do (on a much smaller scale):
Say I have chicken and I want to know where it occurs in a string of
words, but I want it to match to both chicken and poultry and have the
output of:
chicken (locations of chicken and poultry in the string)
or something like that.
The string I'm dealing with is really large, so whatever will get
through it the fastest is ideal for me.
I hope this all makes sense...
If it's possible to have pseudocode that would be helpful.
___
Tutor maillist - Tutor@python.org
http://mail.python.org/mailman/listinfo/tutor
___
Tutor maillist - Tutor@python.org
http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Multi-line comments?
Hi Brad Use something like this '''your comments here''' Three single quotes will do it. HTH Paulo Brad Tompkins wrote: Hello everyone, This may seem like a pretty basic question but it's driving me crazy. Is there a way to make use of multi-line comments when programming using python? Having to stick a # in front of every line gets pretty tedious when I want to make a comment more detailed than I normally would. If there isn't a way, can someone recommend a text editor (I know emacs and probably vi can do this, but they seem difficult to use) that will comment out blocks of text automatically for me? Thanks, Brad ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] i++
Hi You can use i += 1 or i -=1 HTH Paulo scott wrote: Hi, is there any way in Python to simply add or subtract one from a variable like i++ or i--? I don't mind doing a i = i + 1, but would prefer something more simple and faster. ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] (no subject)
Hi Richard Have you try running it with Python in front of the script name? Such as: python my_script.py Usually on Windows command prompt, if Python is not on your path you have to enter the whole path to it, something like C:\Python25\python. HTH Paulo Richard Henderson wrote: Hello, I am a rank beginner, as I'm sure my question will show. After I enter and save a script using Notepad, it is not recognized by DOS and will not run. What might I be doing wrong. I am using PythonWin and Windows XP. Thanks, Richard Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://us.rd.yahoo.com/evt=48224/*http://sims.yahoo.com/ ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Queueing
Hi Thanks a lot Alan and Kent for the replies. Cheers Paulo Kent Johnson wrote: Paulo Nuin wrote: Hi Everyone I need to a write a script that would do a queuing job on a cluster running openMosix Linux. I have checked the Queue module and that part I can say it is covered. My problem regards on thecode to check if the process has ended. As some most of the jobs would be run in different nodes I am having difficulties getting some example code to accomplish that. I don't think the Queue module will help you with multi-processing, it is useful for inter-thread communication within a single process. There are several Python packages that help with multi-processing; one is here: http://www.parallelpython.com/ and others are referenced in the Links section of the above site. Also http://www.python.org/pypi?%3Aaction=searchterm=parallelsubmit=search HTH Kent ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
[Tutor] Queueing
Hi Everyone I need to a write a script that would do a queuing job on a cluster running openMosix Linux. I have checked the Queue module and that part I can say it is covered. My problem regards on thecode to check if the process has ended. As some most of the jobs would be run in different nodes I am having difficulties getting some example code to accomplish that. Thanks a lot for any helpful advice. Cheers Paulo ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
