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 help with. So, what I have
is all the subsequences that I was looking for in separate entries in the
dictionary, and where each of them is found as the value. If a subsequence
binds to more than one other item, I want to have the locations of the items
all together.
The closest I've been able to manage to get to what I want is this:
dict_of_bond_location = {}
dict1 = {'AAA':['UUU'], 'AAU':['UUG', 'UUA'], 'AAC':['UUG'], 'AAG':['UUC',
'UUU'], 'CCC':['GGG']}
dict2 = {'AAA':[1], 'AAU':[2], 'AAC':[3], 'AAG':[0, 4], 'GGG':[10]}
dict3 = {'UUU':[3, 5], 'UUG':[0], 'UUA':[1], 'UUC':[2], 'GGG':[14]}
for key in dict2:
if key in dict1:
matching_subseq = dict1.get(key)
for item in matching_subseq:
if item in dict3:
location = dict3.get(item)
dict_of_bond_location.setdefault(key, []).append(location)
print dict_of_bond_location
which gives this:
{'AAU': [[0], [1]], 'AAG': [[2], [3, 5]], 'AAA': [[3, 5]], 'AAC': [[0]]}
but what I want is
'AAU':[0, 1], 'AAG':[2, 3, 5], 'AAA':[3. 5], 'AAC':[0]
the setdefault(key, []).append(location) thing sort of does what I want, but
I don't want the result to be a list of lists...just one big list. The
production of a new dictionary is not necessary, but it made sense to me a
few hours ago. Anyway, is there a fast and dirty way to add lists together,
if the lists are not named (I think that's essentially what I want?)
Thanks again,
Lauren
On 19/06/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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Today's Topics:
1. Re: iterating over a sequence question.. (Luke Paireepinart)
2. Re: Help converting base32 to base16 (Alan Gauld)
3. Re: Finding all locations of a sequence (fwd) (Danny Yoo)
4. Re: sockets ( Linus Nordstr?m )
5. Re: sockets (Alan Gauld)
6. Re: Finding all locations of a sequence (fwd) (Alan Gauld)
7. Re: cannot pickle instancemethod objects (hok kakada)
8. Re: Python and XSI (Vishal Jain)
----------------------------------------------------------------------
Message: 1
Date: Mon, 18 Jun 2007 13:37:21 -0500
From: "Luke Paireepinart" <[EMAIL PROTECTED]>
Subject: Re: [Tutor] iterating over a sequence question..
To: "Simon Hooper" <[EMAIL PROTECTED]>, tutor@python.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
On 6/18/07, Simon Hooper <[EMAIL PROTECTED]> wrote:
>
> Hi Luke,
>
> * On 17/06/07, Luke Paireepinart wrote:
> > a more expanded version that accounts for either list being the longer
> > one, or both being the same length, would be:
> >
> > >>> if len(t) > len(l): x = len(t)
> > else: x = len(l)
> > >>> print [(l[i%len(l)],t[i%len(t)]) for i in range(x)]
> > [(1, 'r'), (2, 'g'), (3, 'b'), (4, 'r'), (5, 'g')]
>
> Being the duffer that I am, I'm very pleased with myself that I came up
> with a similar solution (albeit as a function rather than a list
> comprehension) :)
>
> You do not need the if statement either,
Yeah, I never knew about the max() function!
I noticed someone else used it in one of their solutions.
I'm pretty sure I've seen it a lot before, just didn't remember it.
-Luke
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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-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=original
"Jason Massey" <[EMAIL PROTECTED]> wrote
> Nice entry at wikipedia:
>
> http://en.wikipedia.org/wiki/Base_32
>
Thanks for the link, I should have thought of oooking there!
I've heardof Base64 for encoding email but never come
across Base32 - any of the versions!
Alan G.
------------------------------
Message: 3
Date: Mon, 18 Jun 2007 16:54:53 -0400 (EDT)
From: Danny Yoo <[EMAIL PROTECTED]>
Subject: Re: [Tutor] Finding all locations of a sequence (fwd)
To: tutor@python.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi everyone,
Can someone help Lauren? I apologize for this, but I am very time
constrained at this moment, and won't be able to reply back for at least a
few hours. His question is below. Thanks!
---------- Forwarded message ----------
Date: Mon, 18 Jun 2007 16:41:39 -0400
From: Lauren <[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 one you wrote (which I think I understand better than
the one listed previous...famous last words, I'm sure), but when I ask to
import the ahocorasick module, it says it can't find it :( Is it possible
to
get step by step instructions on how to open the module? Do I need
something
other than the latest download for it?
Again, I'm not good at this programming thing, so I'm sure I'm missing
something obvious
Thank you for your help,
Lauren
On 18/06/07, Danny Yoo <[EMAIL PROTECTED]> 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.
>
> Hi Lauren,
>
> I am positive that this problem has been tackled before. Have you
talked
> to any of your fellow bioinformaticists? It might not be effective to
ask
> on Python-tutor because, for typical problems, regexes are sufficient.
> For your particular scenario, regexes may not be, so you may want to ask
> specialists like those on the Biopython mailing lists:
>
> http://biopython.org/wiki/Mailing_lists
>
> It may seem like a simple extension of regular expression search, but as
> you may have noticed, feeding 4100 regex searches across that RNA
sequence
> is going to take some time. And trying to feed all of those
subsequences
> as a single regular expression (using ORs) is probably not going to work
> too well either: the engine has limitations on how large the pattern can
> be before it starts behaving very badly.
>
>
> To scale to this problem, we need to do something different. What
you're
> probably looking for is more typically known as the keyword matching
> problem, and there are algorithms specifically used for keyword
matching.
> For example, take a look at Nicholas Lehuen's Pytst package, which
> implements ternary search trees:
>
> http://nicolas.lehuen.com/index.php/category/Pytst
>
> I've also written a different package that uses the "Aho-Corasick"
> automata matcher, but to tell the truth I've let the code stale a bit,
and
> can't support it (too busy with other work). But if you're interested
in
> tinkering with it, it's here:
> http://hkn.eecs.berkeley.edu/~dyoo/python/ahocorasick/<
http://hkn.eecs.berkeley.edu/%7Edyoo/python/ahocorasick/>
> .
>
>
> If you're going to do more string-matching stuff, I'd recommend a look
> into "Algorithms on Strings, Trees, and Sequences".
>
> http://www.cambridge.org/uk/catalogue/catalogue.asp?isbn=0521585198
>
> It's one of the better books on bioinformatics string algorithms, and it
> specifically covers this class of sequence-searching problems.
>
--
Lauren
[EMAIL PROTECTED]
------------------------------
Message: 4
Date: Tue, 19 Jun 2007 01:19:45 +0200
From: " Linus Nordstr?m " <[EMAIL PROTECTED]>
Subject: Re: [Tutor] sockets
To: Tutor@python.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
gusse i use this thread as my own little help thread.. :)
im having problem whit recv. It will not break the loop if ther are
nothing more to recive. It dose recv all tit should, but then it go
another round in the loop and get stuck on recv, as far as print
debugging has showed, Dont realy know waht ells information i could
write sown to make my problem anny clrearer, so ask if anythin is
unclear :)
And on another note, is there a way to use the self. less, it might be
just me but it looks rather ugly :)
def recive(self):
all_data = []
while 1:
self.buf = self.s.recv(4096)
if not self.buf: break
all_data.append(self.buf)
return all_data
On 6/18/07, Linus Nordstr?m <[EMAIL PROTECTED]> wrote:
> Hello
> I'm trying to rewrite a chat-program i did in school this spring in
> python, the school program was in java. All this to leran python.
>
> Anyway. I m trying to send a message using udp to a server that
> conntains the message 3 0 0 0, it has to be in network byte order and
> unsigned. I have tried to send it like a string "3000" but get an
> error message from the server saying that it did recive 4 bytes, but
> that it was an unknown message
>
> So what i am wondering is if there are anny special byte arrays, or
> some thing i should use. or if there are anny other way than to send
> the message than a string.
>
------------------------------
Message: 5
Date: Tue, 19 Jun 2007 00:34:28 +0100
From: "Alan Gauld" <[EMAIL PROTECTED]>
Subject: Re: [Tutor] sockets
To: tutor@python.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=original
"Linus Nordstr?m" <[EMAIL PROTECTED]> wrote
> im having problem whit recv. It will not break the loop if ther are
> nothing more to recive.
Take a look at the client side of the address book
example in my network profgramming topic. It shows
an example of breaking out of a recv loop.
Another option is to use the select module services
> And on another note, is there a way to use the self. less,
> it might be just me but it looks rather ugly :)
No, it's good practice, it distinguishes between class level
variables and local variables. The use of self/this etc is usually
required in industrial coding standards for C++ and Java
(eg Dept of defense/Government etc) for the same reason,
even though those languages don't require it. As in many
things python is simply enforcing what is already considered
good practice elsewhere.
HTH,
--
Alan Gauld
Author of the Learn to Program web site
http://www.freenetpages.co.uk/hp/alan.gauld
------------------------------
Message: 6
Date: Tue, 19 Jun 2007 00:37:46 +0100
From: "Alan Gauld" <[EMAIL PROTECTED]>
Subject: Re: [Tutor] Finding all locations of a sequence (fwd)
To: tutor@python.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=original
> 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, I'm sure), but when I
> ask to
> import the ahocorasick module, it says it can't find it :(
You will need to ocate and download the module too.
Either store it along with your program or in the site-packages
folder in your python installation.
> get step by step instructions on how to open the module?
You just import it.
You can read more about that in my modules and functions topic
if that helps.
--
Alan Gauld
Author of the Learn to Program web site
http://www.freenetpages.co.uk/hp/alan.gauld
------------------------------
Message: 7
Date: Tue, 19 Jun 2007 12:19:31 +0700
From: hok kakada <[EMAIL PROTECTED]>
Subject: Re: [Tutor] cannot pickle instancemethod objects
To: tutor-python <tutor@python.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="utf-8"
?????? ??? 13 ?????? 2007 19:09, Kent Johnson ??????????????
> hok kakada wrote:
> >> What kind of object is matcher? Does it have any attributes that are
> >> functions? (Not methods you defined for the class, but functions or
> >> methods that you assign to attributes of self.)
> >
> > Actually, I use the translate-toolkit from
> > http://translate.sourceforge.net/snapshots/translate-toolkit-1.0.1rc1/
> > in translate/search/match.py:
> > if comparer is None:
> > comparer = lshtein.LevenshteinComparer(max_length)
> >
> > self.comparer = comparer
> >
> > I just found the problem that it is because of the
LevenshteinComparer.
> > Once I assign self.comparer = None, the I can dump the matcher
> > successfully. However, I still don't understand what could be wrong
with
> > LevenshteinComparer.
>
> I think the problem is this code in LevenshteinComparer.__init__():
>
> if Levenshtein:
> self.distance = self.native_distance
> else:
> self.distance = self.python_distance
>
> which assigns an instance method to an instance attribute; this is the
> instancemethod that can't be pickled.
Ok...but how can we deal with it?
Kind Regards,
da
------------------------------
Message: 8
Date: Tue, 19 Jun 2007 12:08:36 +0400
From: "Vishal Jain" <[EMAIL PROTECTED]>
Subject: Re: [Tutor] Python and XSI
To: tutor@python.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Yes XSI is a 3D package from Avid. Also knows as Softimage|XSI
By everything failed I mean that XSI isnt registering Python resulting in
I
cant select scripitng langauge as Python inside XSI. After running the
said
script the command prompt says "Python:Registered" but no error messages.
Yes XSI supports only ActiveX Scripts.
If everything goes good I expect to select scripting langauge as Python
inside XSI and start scripting. But apparently eveything went good as per
the manuals and docs except my luck :(
I did search google but will search more as per your guidlines. And I am a
beginner too in Python. I never coded before.
Thanks a lot for ur suggestions and concern.
By the way are you the same Alan Gauld who posts in XSI Base and CG Talk??
Vishal
Message: 6
Date: Mon, 18 Jun 2007 16:09:35 +0100
From: "Alan Gauld" <[EMAIL PROTECTED]>
Subject: Re: [Tutor] Python and XSI
To: tutor@python.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed; charset="iso-8859-1";
reply-type=original
"Vishal Jain" <[EMAIL PROTECTED]> wrote
> I am trying to get Python registered with XSI but
> everything described in docs failed.
OK, I'm assuming that XSI is the 3D Graphics software from Avid?
Can you tell us which docs and what exactly 'failed' means?
What did you do and what actually happened?
Any error messages?
> C:\Python25\Lib\site-packages\win32comext\axscript\client\pyscript.py
ISTR that as being the script for registering Python as an
Active Scripting language for WSH and the IE ActiveX engine.
I assume from that, that XSI uses active scripting?
What did you expect to happen after running it?
And what did happen?
> still no luck. Is anybody else also facing the same situation? I am
> not very
> sure how many people here uses Python for XSI but still hoping to
> get some
I had to do a Google search...
You might have more luck on the main comp.lang.python list or
maybe even in the pyGame list. This group is for beginners to Python
and XSI looks a tad advanced for most beginners, going by the couple
of pages I browsed. OTOH there is usually somebody here with an
interest in most things...
--
Alan Gauld
Author of the Learn to Program web site
http://www.freenetpages.co.uk/hp/alan.gauld
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*************************************
--
Lauren
[EMAIL PROTECTED]
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