Lauren wrote:
> Firstly, I'd like to thank everyone for their help. I ended up
> throwing something together using dictionaries (because I understood
> those best out of what I had), that was a lot faster than my initial
> attempt, but have run into a different problem, that I was hoping for
>
l.python.org/pipermail/tutor/attachments/20070618/1cf0ac67/attachment-0001.html
--
Message: 2
Date: Mon, 18 Jun 2007 21:12:02 +0100
From: "Alan Gauld" <[EMAIL PROTECTED]>
Subject: Re: [Tutor] Help converting base32 to base16
To: tutor@python.org
Message
> From: Lauren <[EMAIL PROTECTED]>
> To: Danny Yoo <[EMAIL PROTECTED]>
> Subject: Re: [Tutor] Finding all locations of a sequence
>
> after I download the one you wrote (which I think I understand
> better than
> the one listed previous...famous last words
auren <[EMAIL PROTECTED]>
To: Danny Yoo <[EMAIL PROTECTED]>
Subject: Re: [Tutor] Finding all locations of a sequence
Ok, these may be useful. I do have a potentially embarrassing problem,
however I will preface this with I'm practically computer illiterate. Ok
after I download the
> 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.
Hi Lauren,
I am positive that this problem has been tackled before. Have you ta
"Lauren" <[EMAIL PROTECTED]> wrote
Caveat: I am not into the realms of DNA sequencing so this may
not be viable but...
> 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 (loca
On Thu, 14 Jun 2007, Lauren wrote:
> 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.
How about something like this?
=
oultry':
>> 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
>> lo
> 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 s
Hi Lauren
You can use two approaches:
1- String method find
This returns a int value with the lowest position of your search on the
string (sequence) you are searching. From the documentation:
*find*( sub[, start[, end]])
Return the lowest index in the string where substring sub is found, suc
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
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
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