[Tutor] order loop from methos on class
Dear All, What is the best way to loop on methos on a class? class Rna(): def trim(): ... def align(): ... ena = Rna() ena.trim() ena.aling() Thanks for any suggestion!!! ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] order loop from methos on class
On Mon, Jan 26, 2015 at 11:48:52AM +0100, jarod...@libero.it wrote: > > > Dear All, > What is the best way to loop on methos on a class? I do not understand the question. Can you explain in more detail? > class Rna(): > def trim(): > ... > def align(): > ... Both methods need a "self" parameter: def trim(self): ... def align(self): ... > ena = Rna() > ena.trim() > ena.aling() ena.align() -- Steve ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Tutor Digest, Vol 131, Issue 59 Order loop from methos on class (jarod...@libero.it)
> Message: 1
> Date: Mon, 26 Jan 2015 11:48:52 +0100 (CET)
> From: "jarod...@libero.it"
> To: tutor@python.org
> Subject: [Tutor] order loop from methos on class
> Message-ID:
> <2044122047.125321422269332108.JavaMail.defaultUser@defaultHost>
> Content-Type: text/plain; charset=UTF-8
>
>
>
> Dear All,
> What is the best way to loop on methos on a class?
>
> class Rna():
> def trim():
> ...
> def align():
> ...
>
> ena = Rna()
>
> ena.trim()
> ena.aling()
>
>
>
> Thanks for any suggestion!!!
Not quite sure where you're going with this, but to loop through the
methods of a class can be done and is dependent on the python
version...
For py3:
class Rna():
def trim():
print(1)
def align():
print(2)
ena = Rna()
for method in dir(Rna):
if method[:2] != "__":
ena.__getattribute__(method)()
the other way to do it is to:
for method in dir(Rna):
if method[:2] != "__":
getattr(ena, method)()
DO NOTICE HOW "WONKY" THIS IS. If you have a method that expects
input, or if you defined private methods (with __) this will either
skip them, or in worse case, if you cut out the if question, try to
call all the builtin methods (such as getattribute) and it will fail
because no proper input has been sent. This will only work for C style
"void" kind of methods.
Probably the best way to get them, though, do it is to:
import inspect
inspect.getmembers(Rna(), predicate=inspect.ismethod)
[('__init__', >), ('align', >), ('trim', >)]
This gets you tuples of (name, reference) kind of deal you can run
through. This does help to weed out some of the builtin methods, but
__init__ (or possibly __new__ ?) will still show up. If you need the
builtins as well you can ask for inspect.isbuiltin.
In python2 the first way is not going to work for sure, I don't think
there exist a __getattribute__, but the 2nd way (getattr) and the
inpect module will.
I do wonder why do you need this though. I've only once run into a
situation where I did something similar and that was _ONLY_ because I
was too lazy to write up proper classes and decompose the problem, for
what at the time seemed like a simple test run, so I ended up reading
a lot of properties from a file and did not want to name all of them
myself in the code. I ended up paying the price and wrote all the
necessary classes because it was hard to debug
Hopefully you'll think it through, don't be lazy it never pays off!
Best of luck,
Dino
___
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
[Tutor] R: Re: Tutor Digest, Vol 131, Issue 59 Order loop from methos on class (jarod...@libero.it)
Thanks so much!! Now I understood it is a stupid thing! So, could you elpme to decompose the problem? I initiazlizate the class with the file to use so all the function have all the parameters that I need. At the moment I have in mind only to do this: ena = Rna() job1 = ena.trim() job2 = ena.align() It is no so elegant.. Any suggestion? ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Tutor Digest, Vol 131, Issue 59 Order loop from methos on class (jarod...@libero.it)
2015-01-26 14:54 GMT+01:00 jarod...@libero.it :
> Thanks so much!! Now I understood it is a stupid thing!
> So, could you elpme to decompose the problem?
> I initiazlizate the class with the file to use so all the function have all
> the parameters that I need.
>
> At the moment I have in mind only to do this:
> ena = Rna()
> job1 = ena.trim()
> job2 = ena.align()
> It is no so elegant..
>
>
>
> Any suggestion?
>
Without seeing what exactly are you trying to do (I'm not a
chemist/biologist) I'm not sure. Any detail about what you're trying
to do would be helpful.
If you're bothered by having to call 2 methods except of 1 you could
always make another method that uses the two. It really depends on the
decision if you want to do the operations in place or not, that is
transform the original object through it's methods, or do you want to
return a new object of the same class.
In your example you write "job" as if you're dealing with threads. I
can't tell if you want job1 and job2 to be another different objects
(maybe of Rna class maybe not) or is it just that you don't understand
that you can also call a method on an object without having a variable
to hold a return value.
If you want to return another Rna object that is the same as the
original one, maybe something like this is what you need?
i.e.
import copy
class Rna():
def __init__(self):
self.trimmed = False
self.aligned = False
#NOT a part of the class
def trim(rna):
temp = copy.copy(rna)
temp.trimmed = True
return temp
#in interpreter
ena = Rna()
ena.trimmed
False
tena = trim(ena)
ena.trimmed
False
tena.trimmed
True
and both of ena and tena will be of class Rna. So you now have 2
different Rna objects.
You could also have it done in place, which saves memory and is more
natural and I'd recommend it:
class Rna():
def __init__(self):
self.trimmed=False
self.aligned=False
def trim(self):
self.trimmed=True
def align(self):
self.aligned=True
def DoBoth(self):
self.trim()
self.align()
print("Done!")
#in the interpreter
ena = Rna()
ena.trimmed
False
ena.aligned
False
ena.DoBoth()
Done!
ena.trimmed
True
ena.aligned
True
This way you can do both without having to constantly write them
yourself... you issue 1 call which then calls various other methods
you have on the instance itself
Even that print isn't necessary, that's just there to show it
finished. You don't always have to have a variable to catch potential
output of a method. But maybe if you need/want to catch the output
maybe that output is an object of a different class(?) maybe it's a
tuple, or an array?
class Rna():
def __init__(self):
self.trimmed=False
self.aligned=False
def trim(self):
self.trimmed=True
def align(self):
self.aligned=True
def DoBoth(self):
self.trim()
self.align()
print("Done! We return an list of solutions:")
return [1,2,3,4,5,6,7,8,9]
#in the interpreter
ena = Rna()
solutions = ena.DoBoth()
Done! We return an list of solutions:
solutions
[1,2,3,4,5,6,7,8,9]
You could also add the solutions as an attribute to the object you
just did the calculation on:
def DoBoth(self):
self.trim()
self.align()
print("Done! We return an list of solutions:")
self.solutions = [1,2,3,4,5,6,7,8,9]
#in the interpreter
ena = Rna()
ena.DoBoth()
Done! We return an list of solutions:
ena.solutions
[1,2,3,4,5,6,7,8,9]
The better you describe WHAT you want and HOW you want it the better
people here will be able to help you
Best of luck,
Dino
___
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] R: Re: Tutor Digest, Vol 131, Issue 59 Order loop from methos on class (jarod...@libero.it)
On 26/01/15 13:54, jarod...@libero.it wrote: I initiazlizate the class with the file to use so all the function have all the parameters that I need. At the moment I have in mind only to do this: ena = Rna() job1 = ena.trim() job2 = ena.align() It is no so elegant.. You originally posted a solution where you had a list of methods in an attribute called steps. That's a better solution than trying to iterate over all the methods in the class. for method in self.steps: method() But you don't really tell us what you are trying to do. So its hard to determine what an elegant solution is when we don't know the problem we are trying to solve. It looks as if you are trying to create a workflow of some sort? Does the flow always follow the same sequence - use a list of methods Does the workflow vary depending on results - use a table where the return value of each method indicates which column to call next. Is each method called only once or can it repeat steps? How are errors to be handled? Is timing critical? Do you need to fully process one record at a time or can it be batch oriented? There are lots of questions to consider, all of which affect the "best" solution. hth -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ http://www.amazon.com/author/alan_gauld Follow my photo-blog on Flickr at: http://www.flickr.com/photos/alangauldphotos ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] Inquiry regarding GSoC 2015
Hello, I want to take part in GSoC 2015 under PSF. I am a beginner in python and have started contributing and i am also registerd at github. Please suggest as from which projects i should start for contributing as i am beginner in python. thanks. ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] SQLAlchemy
Hey folks, I'm working my way through Thinkful with python and I'm trying to get a setup working. Part of this setup is using SQLAlchemy. While I understand this is a python tutor list, would it be OK to ask questions like 'how do I change my SQLAlchemy URL to include a user name' here? -- ~MEN ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] SQLAlchemy
Greetings Mike, : I'm working my way through Thinkful with python and I'm trying to : get a setup working. Part of this setup is using SQLAlchemy. : While I understand this is a python tutor list, would it be OK to : ask questions like 'how do I change my SQLAlchemy URL to include : a user name' here? You could ask here about this (excellent) third-party library, but you will doubtless find a much richer pool of knowledge to draw from if you were to ask this question directly of the SQLAlchemy crowd [0]. There's a mailing list [1] or IRC [2]. I expect that you are calling sqlalchemy.engine.create_engine() at some point. When you are doing that, you can/should pass your desired user credentials into this function. http://docs.sqlalchemy.org/en/rel_0_9/core/engines.html Good luck, -Martin [0] http://www.sqlalchemy.org/support.html [1] https://groups.google.com/forum/#!forum/sqlalchemy [2] 'The IRC channel is on the Freenode network as #sqlalchemy.' -- Martin A. Brown http://linux-ip.net/ ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Inquiry regarding GSoC 2015
We (the Tutor list) are not a mentor for GSoC. You'll want to talk to the right organization for this, because I don't think any of us here have any direct experience with that program. GSoC has a Frequently Asked Questions that you should read: http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2015/help_page#whatis There are mailing lists specific to GSoC. See: https://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2015/about_page for details. On Mon, Jan 26, 2015 at 7:56 AM, Arpit Agarwal wrote: > Hello, > > I want to take part in GSoC 2015 under PSF. I am a beginner in python > and have started contributing and i am also registerd at github. > Please suggest as from which projects i should start for contributing > as i am beginner in python. > > thanks. > ___ > Tutor maillist - Tutor@python.org > To unsubscribe or change subscription options: > https://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Tutor Digest, Vol 131, Issue 59 Order loop from methos on class (jarod...@libero.it)
On 26/01/2015 14:41, Dino Bektešević wrote:
2015-01-26 14:54 GMT+01:00 jarod...@libero.it :
Thanks so much!! Now I understood it is a stupid thing!
So, could you elpme to decompose the problem?
I initiazlizate the class with the file to use so all the function have all
the parameters that I need.
At the moment I have in mind only to do this:
ena = Rna()
job1 = ena.trim()
job2 = ena.align()
It is no so elegant..
Any suggestion?
Without seeing what exactly are you trying to do (I'm not a
chemist/biologist) I'm not sure. Any detail about what you're trying
to do would be helpful.
If you're bothered by having to call 2 methods except of 1 you could
always make another method that uses the two. It really depends on the
decision if you want to do the operations in place or not, that is
transform the original object through it's methods, or do you want to
return a new object of the same class.
In your example you write "job" as if you're dealing with threads. I
can't tell if you want job1 and job2 to be another different objects
(maybe of Rna class maybe not) or is it just that you don't understand
that you can also call a method on an object without having a variable
to hold a return value.
If you want to return another Rna object that is the same as the
original one, maybe something like this is what you need?
i.e.
import copy
class Rna():
def __init__(self):
self.trimmed = False
self.aligned = False
#NOT a part of the class
def trim(rna):
temp = copy.copy(rna)
temp.trimmed = True
return temp
#in interpreter
ena = Rna()
ena.trimmed
False
tena = trim(ena)
ena.trimmed
False
tena.trimmed
True
and both of ena and tena will be of class Rna. So you now have 2
different Rna objects.
You could also have it done in place, which saves memory and is more
natural and I'd recommend it:
class Rna():
def __init__(self):
self.trimmed=False
self.aligned=False
def trim(self):
self.trimmed=True
def align(self):
self.aligned=True
def DoBoth(self):
self.trim()
self.align()
print("Done!")
#in the interpreter
ena = Rna()
ena.trimmed
False
ena.aligned
False
ena.DoBoth()
Done!
ena.trimmed
True
ena.aligned
True
This way you can do both without having to constantly write them
yourself... you issue 1 call which then calls various other methods
you have on the instance itself
Even that print isn't necessary, that's just there to show it
finished. You don't always have to have a variable to catch potential
output of a method. But maybe if you need/want to catch the output
maybe that output is an object of a different class(?) maybe it's a
tuple, or an array?
class Rna():
def __init__(self):
self.trimmed=False
self.aligned=False
def trim(self):
self.trimmed=True
def align(self):
self.aligned=True
def DoBoth(self):
self.trim()
self.align()
print("Done! We return an list of solutions:")
return [1,2,3,4,5,6,7,8,9]
#in the interpreter
ena = Rna()
solutions = ena.DoBoth()
Done! We return an list of solutions:
solutions
[1,2,3,4,5,6,7,8,9]
You could also add the solutions as an attribute to the object you
just did the calculation on:
def DoBoth(self):
self.trim()
self.align()
print("Done! We return an list of solutions:")
self.solutions = [1,2,3,4,5,6,7,8,9]
#in the interpreter
ena = Rna()
ena.DoBoth()
Done! We return an list of solutions:
ena.solutions
[1,2,3,4,5,6,7,8,9]
The better you describe WHAT you want and HOW you want it the better
people here will be able to help you
Best of luck,
Dino
___
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
I do not know exactly what the OP wants to do, but it sounds like he is
aligning RNA sequences.
At this stage I would suggest that he studies the possibilities of the
BioPython package and the programs available at the NLM, USA or the
Sanger Lab in Cambridge, England.
But I am only a beginner myself, so I might be way off track.
--
Sydney
___
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
[Tutor] R: Tutor Digest, Vol 131, Issue 60 order loop from methos on class
dear all, thanks so much!! I explain better my problem :http://pastebin.com/iiPZMi2U this is my workflow. Take my data from readset an create a command list ena = Rnaseq() The order of the self.step are the order I wan to to execute my analisys. So this is the order: In [160]: ena.show() 1- trimmomatic 2- merge_trimmomatic_stats 3- star 4- picard_sort_sam 5- rnaseqc 6- wiggle 7- cufflinks 8- cuffquant 9- gq_seq_utils_exploratory_analysis_rnaseq First aim is to write a code to write all the pipeline . up to now I use this: job1 = ena.trimming() ena.prepare_run(job1) ena.prepare_run(job2) .. the other aim is to selcet a range number to execute i.e. 2-9 or 1-4... ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] R: Tutor Digest, Vol 131, Issue 60 order loop from methos on class
Hello, > The order of the self.step are the order I wan to to execute my analisys. > So this is the order: > In [160]: ena.show() > 1- trimmomatic > 2- merge_trimmomatic_stats > 3- star > 4- picard_sort_sam > 5- rnaseqc > 6- wiggle > 7- cufflinks > 8- cuffquant > 9- gq_seq_utils_exploratory_analysis_rnaseq > > First aim is to write a code to write all the pipeline . > up to now I use this: > job1 = ena.trimming() > ena.prepare_run(job1) > ena.prepare_run(job2) > .. > the other aim is to selcet a range number to execute i.e. 2-9 or 1-4... In this case, yes, you probably want to explicitly represent the sequence of steps as an explicit list of operators. I think you may have wanted somehow to get this ordered sequence "for free" by iterating over the class's methods, perhaps through a dir(). However, trying to get this ordering from the class via method iteration is unreliable because, underneath the service, the iteration is walking through a dictionary, and dictionaries do not give us a deterministic ordering: the ordering is allowed to change on us between program runs. And in fact, in certain environments, dictionary iteration is _guaranteed_ to give us a different ordering on every program run. See: https://docs.python.org/2/using/cmdline.html#envvar-PYTHONHASHSEED Ultimately, this means that if we want an ordered sequence, we can't depend on dictionary iteration. Lists are what we want. ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] Overlay Quiver Plot on Contours
Hello,
I have the following script:
import netCDF4
import numpy as np
import matplotlib.pyplot as plt
import pylab
ncfile = netCDF4.Dataset('30JUNE2012_0300UTC.cdf', 'r')
dbZ = ncfile.variables['MAXDBZF']
data = dbZ[0,0]
data.shape
x = np.array([0,10,11])
y = np.array([0,15,16])
X,Y = np.meshgrid(x,y)
u = 5*X
v = 5*Y
plt.figure()
plt.rcParams['figure.figsize'] = (12.0,8.0)
c = plt.contourf(data, 20, cmap='jet')
plt.hold(True)
q = plt.quiver(X,Y,u,v,angles='xy',scale=1000,color='r')
p = plt.quiverkey(q,1,16.5,50,"50 m/s",coordinates='data',color='r')
plt.colorbar()
plt.show()
and I am getting this error:
TypeError: You must first set_array for mappable
Can anyone provide guidance on how you overlay quiver plots on top of
contours?
Please and thanks
Felisha Lawrence
--
Felisha Lawrence
Howard University Program for Atmospheric Sciences(HUPAS), Graduate Student
NASA URC/BCCSO Graduate Fellow
NOAA NCAS Graduate Fellow
Graduate Student Association for Atmospheric Sciences(GSAAS), Treasurer
(240)-535-6665 (cell)
felisha.lawre...@gmail.com (email)
___
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Overlay Quiver Plot on Contours
On 26/01/15 23:24, Felisha Lawrence wrote: Hello, I have the following script: import netCDF4 import numpy as np import matplotlib.pyplot as plt import pylab ... and I am getting this error: TypeError: You must first set_array for mappable Can anyone provide guidance on how you overlay quiver plots on top of contours? This list is for newcomers to Python and its standard library. This looks like a fairly specific SciPy/Numpy, and especially matplotlib type question. You would probably be better off asking on the SciPy forums/lists. HTH -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ http://www.amazon.com/author/alan_gauld Follow my photo-blog on Flickr at: http://www.flickr.com/photos/alangauldphotos ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Overlay Quiver Plot on Contours
>> and I am getting this error:
>>
>> TypeError: You must first set_array for mappable
>>
>> Can anyone provide guidance on how you overlay quiver plots on top of
>> contours?
>
>
> This list is for newcomers to Python and its standard
> library. This looks like a fairly specific SciPy/Numpy,
> and especially matplotlib type question.
>
> You would probably be better off asking on the SciPy
> forums/lists.
Agree with Alan. You'll get better help from people who know the
library. Very few of us here do things with SciPy.
Just to add: please add more context to your error message reports,
regardless of who you're asking help from.
To include the single line:
###
TypeError: You must first set_array for mappable
###
is somewhat helpful: it does have some information.
But unless you've suppressed error reporting, you should be getting
significantly more information from the error message.
I did a quick web search for your error message, and came up with:
http://stackoverflow.com/questions/6600579/colorbar-for-matplotlib-plot-surface-command
which might look reasonably close to what you're seeing. And note
how, in that message, they include a full stack trace of the problem,
which looks like:
#
Traceback (most recent call last):
File "", line 1, in
File
"C:\Python26\lib\site-packages\spyderlib\widgets\externalshell\startup.py",
line 122, in runfile
execfile(filename, glbs)
File "C:\Documents and Settings\mramacha\My
Documents\Python\Candela\test.py", line 22, in
fig.colorbar(surf, shrink=0.5, aspect=5)
File "C:\Python26\lib\site-packages\matplotlib\figure.py", line
1104, in colorbar
cb = cbar.Colorbar(cax, mappable, **kw)
File "C:\Python26\lib\site-packages\matplotlib\colorbar.py", line
706, in __init__
mappable.autoscale_None() # Ensure mappable.norm.vmin, vmax
File "C:\Python26\lib\site-packages\matplotlib\cm.py", line 261, in
autoscale_None
raise TypeError('You must first set_array for mappable')
TypeError: You must first set_array for mappable
#
This is the sort of thing that is a *joy* to see when debugging. If I
don't have a good stack trace when trying to diagnose a problem, I am
not as happy, because I don't have my hand on any useful context to
work with. It's like working in the dark.
In your case, I can't tell for sure if your scenario matches the
above, because the error message information content is low enough to
raise doubts.
___
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
[Tutor] functions first?
Please correct me if I am wrong, but I've assumed that it is proper to define all functions before embarking on the main body of a program. I find myself breaking this rule because I want to set the default values of some named function parameters based on a configuration file which I have to first read, hence the need to break the rule. ..so my question is "is this acceptable" or "is there a better way?" thks Alex ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] functions first?
Alex Kleider writes: > Please correct me if I am wrong, but I've assumed that it is proper to > define all functions before embarking on the main body of a program. I would say rather that as much code as possible should be in small well-defined functions, with the “main body” a tiny and trivial call to a function. That way, all the code is easily tested by unit testing tools. > I find myself breaking this rule because I want to set the default > values of some named function parameters based on a configuration file > which I have to first read, hence the need to break the rule. Module-level constants are fine, and they obviously need to be bound before the definition of the function which uses them for parameter defaults. But if they're not constants – as implied by your statement you read them from a configuration file – then they should not be in the function definition, because reading the configuration file should itself be encapsulated in a well-tested function. -- \ “It is the integrity of each individual human that is in final | `\examination. On personal integrity hangs humanity's fate.” | _o__) —Richard Buckminster Fuller, _Critical Path_, 1981 | Ben Finney ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
