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Search found 13 results on 1 pages for 'morlock'.

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• Python progression path - From apprentice to guru

  - by Morlock

  Hi all, I've been learning, working, and playing with Python for a year and a half now. As a biologist slowly making the turn to bio-informatics, this language has been a the very core of all the major contributions I have made in the lab. (bash and R scripts have helped some too. My C++ capabilities are very not functional yet). I more or less fell in love with the way Python permits me to express beautiful solutions and also with the semantics of the language that allows such a natural flow from thoughts to workable code. What I would like to know from you is your answer to a kind of question I have seldom seen in this or other forums. Let me sum up what I do NOT want to ask first ;) I don't want to know how to QUICKLY learn Python Nor do I want to find out the best way to get acquainted with the language Finally, I don't want to know a 'one trick that does it all' approach. What I do want to know your opinion about, is: What are the steps YOU would recommend to a Python journeyman, from apprenticeship to guru status (feel free to stop wherever your expertise dictates it), in order that one IMPROVES CONSTANTLY, becoming a better and better Python coder, one step at a time. The kind of answers I would enjoy (but feel free to surprise the readership :P ), is formatted more or less like this: Read this (eg: python tutorial), pay attention to that kind of details Code for so manytime/problems/lines of code Then, read this (eg: this or that book), but this time, pay attention to this Tackle a few real-life problems Then, proceed to reading Y. Be sure to grasp these concepts Code for X time Come back to such and such basics or move further to... (you get the point :) This process depicts an iterative Learn/Code cycle, and I really care about knowing your opinion on what exactly one should pay attention to, at various stages, in order to progress CONSTANTLY (with due efforts, of course). If you come from a specific field of expertise, discuss the path you see as appropriate in this field. Thanks a lot for sharing your opinions and good Python coding!

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• Classes, methods, and polymorphism in Python

  - by Morlock

  I made a module prototype for building complex timer schedules in python. The classe prototypes permit to have Timer objects, each with their waiting times, Repeat objects that group Timer and other Repeat objects, and a Schedule class, just for holding a whole construction or Timers and Repeat instances. The construction can be as complex as needed and needs to be flexible. Each of these three classes has a .run() method, permitting to go through the whole schedule. Whatever the Class, the .run() method either runs a timer, a repeat group for a certain number of iterations, or a schedule. Is this polymorphism-oriented approach sound or silly? What are other appropriate approaches I should consider to build such a versatile utility that permits to put all building blocks together in as complex a way as desired with simplicity? Thanks! Here is the module code: ##################### ## Importing modules from time import time, sleep ##################### ## Class definitions class Timer: """ Timer object with duration. """ def __init__(self, duration): self.duration = duration def run(self): print "Waiting for %i seconds" % self.duration wait(self.duration) chime() class Repeat: """ Repeat grouped objects for a certain number of repetitions. """ def __init__(self, objects=[], rep=1): self.rep = rep self.objects = objects def run(self): print "Repeating group for %i times" % self.rep for i in xrange(self.rep): for group in self.objects: group.run() class Schedule: """ Groups of timers and repetitions. Maybe redundant with class Repeat. """ def __init__(self, schedule=[]): self.schedule = schedule def run(self): for group in self.schedule: group.run() ######################## ## Function definitions def wait(duration): """ Wait a certain number of seconds. """ time_end = time() + float(duration) #uncoment for minutes# * 60 time_diff = time_end - time() while time_diff > 0: sleep(1) time_diff = time_end - time() def chime(): print "Ding!"

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• How to play sound in Python WITHOUT interrupting music/other sounds from playing

  - by Morlock

  I'm working on a timer in python which sounds a chime when the waiting time is over. I use the following code: from wave import open as wave_open from ossaudiodev import open as oss_open def _play_chime(): """ Play a sound file once. """ sound_file = wave_open('chime.wav','rb') (nc,sw,fr,nf,comptype, compname) = sound_file.getparams( ) dsp = oss_open('/dev/dsp','w') try: from ossaudiodev import AFMT_S16_NE except ImportError: if byteorder == "little": AFMT_S16_NE = ossaudiodev.AFMT_S16_LE else: AFMT_S16_NE = ossaudiodev.AFMT_S16_BE dsp.setparameters(AFMT_S16_NE, nc, fr) data = sound_file.readframes(nf) sound_file.close() dsp.write(data) dsp.close() It works pretty good, unless any other device is already outputing sound. How could I do basically the same (under linux) without having the prerequisite that no sound is being played? If you think the process would require an API to ensure software mixing, please suggest a method :) Thx for the support

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• How to define and use Python generators appropriately

  - by Morlock

  I want to define a generator from a list that will output the elements one at a time, then use this generator object in an appropriate manner. a = ["Hello", "world", "!"] b = (x for x in a) c = next(b, None) while c != None: print c, c = next(b, None) Is there anything wrong or improvable with the while approach here? Is there a way to avoid having to assign 'c' before the loop? Thanks!

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• Statistics: combinations in Python

  - by Morlock

  I need to compute combinatorials (nCr) in Python but cannot find the function to do that in 'math', 'numyp' or 'stat' libraries. Something like a function of the type: comb = calculate_combinations(n, r) I need the number of possible combinations, not the actual combinations, so itertools.combinations does not interest me. Finally, I want to avoid using factorials, as the numbers I'll be calculating the combinations for can get to big and the factorials are going to be monstruous. This seems like a REALLY easy to answer question, however I am being drowned in questions about generating all the actual combinations, which is not what I want. :) Many thanks

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• Importing Python module from the Bash

  - by Morlock

  I am launching a Python script from the command line (Bash) under Linux. I need to open Python, import a module, and then have lines of code interpreted. The console must then remain in Python (not quit it). How do I do that? I have tried an alias like this one: alias program="cd /home/myname/programs/; python; import module; line_of_code" But this only starts python and the commands are not executed (no module import, no line of code treated). What is the proper way of doing this, provided I need to keep Python open (not quit it) after the script is executed? Many thanks.

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• Easy to use time-stamps in Python

  - by Morlock

  I'm working on a journal-type application in Python. The application basically permits the user write entries in the journal and adds a time-stamp for later querying the journal. As of now, I use the time.ctime() function to generate time-stamps that are visually friendly. The journal entries thus look like: Thu Jan 21 19:59:47 2010 Did something Thu Jan 21 20:01:07 2010 Did something else Now, I would like to be able to use these time-stamps to do some searching/querying. I need to be able to search, for example, for "2010", or "feb 2010", or "23 feb 2010". My questions are: 1) What time module(s) should I use: time vs datetime? 2) What would be an appropriate way of creating and using the time-stamp objects? Many thanks!

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• Binomial test in Python

  - by Morlock

  I need to do a binomial test in Python that allows calculation for 'n' numbers of the order of 10000. I have implemented a quick binomial_test function using scipy.misc.comb, however, it is pretty much limited around n = 1000, I guess because it reaches the biggest representable number while computing factorials or the combinatorial itself. Here is my function: from scipy.misc import comb def binomial_test(n, k): """Calculate binomial probability """ p = comb(n, k) * 0.5**k * 0.5**(n-k) return p How could I use a native python (or numpy, scipy...) function in order to calculate that binomial probability? If possible, I need scipy 0.7.2 compatible code. Many thanks!

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• Multiple levels of 'collection.defaultdict' in Python

  - by Morlock

  Thanks to some great folks on SO, I discovered the possibilities offered by collections.defaultdict, notably in readability and speed. I have put them to use with success. Now I would like to implement three levels of dictionaries, the two top ones being defaultdict and the lowest one being int. I don't find the appropriate way to do this. Here is my attempt: from collections import defaultdict d = defaultdict(defaultdict) a = [("key1", {"a1":22, "a2":33}), ("key2", {"a1":32, "a2":55}), ("key3", {"a1":43, "a2":44})] for i in a: d[i[0]] = i[1] Now this works, but the following, which is the desired behavior, doesn't: d["key4"]["a1"] + 1 I suspect that I should have declared somewhere that the second level defaultdict is of type int, but I didn't find where or how to do so. The reason I am using defaultdict in the first place is to avoid having to initialize the dictionary for each new key. Any more elegant suggestion? Thanks pythoneers!

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• Proper way to assert type of variable in Python

  - by Morlock

  In using a function, I wish to ensure that the type of the variables are as expected. How to do it right? Here is an example fake function trying to do just this before going on with its role: def my_print(text, begin, end): """Print text in UPPER between 'begin' and 'end' in lower """ for i in (text, begin, end): assert type(i) == type("") out = begin.lower() + text.upper() + end.lower() print out Is this approach valid? Should I use something else than type(i) == type("") ? Should I use try/except instead? Thanks pythoneers

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• Working with multiple input and output files in Python

  - by Morlock

  I need to open multiple files (2 input and 2 output files), do complex manipulations on the lines from input files and then append results at the end of 2 output files. I am currently using the following approach: in_1 = open(input_1) in_2 = open(input_2) out_1 = open(output_1, "w") out_2 = open(output_2, "w") # Read one line from each 'in_' file # Do many operations on the DNA sequences included in the input files # Append one line to each 'out_' file in_1.close() in_2.close() out_1.close() out_2.close() The files are huge (each potentially approaching 1Go, that is why I am reading through these input files one at a time. I am guessing that this is not a very Pythonic way to do things. :) Would using the following form good? with open("file1") as f1: with open("file2") as f2: # etc. If yes, could I do it while avoiding the highly indented code that would result? Thanks for the insights!

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• Binomial test in Python for very large numbers

  - by Morlock

  I need to do a binomial test in Python that allows calculation for 'n' numbers of the order of 10000. I have implemented a quick binomial_test function using scipy.misc.comb, however, it is pretty much limited around n = 1000, I guess because it reaches the biggest representable number while computing factorials or the combinatorial itself. Here is my function: from scipy.misc import comb def binomial_test(n, k): """Calculate binomial probability """ p = comb(n, k) * 0.5**k * 0.5**(n-k) return p How could I use a native python (or numpy, scipy...) function in order to calculate that binomial probability? If possible, I need scipy 0.7.2 compatible code. Many thanks!

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• Multiple levels of 'collection.defaultdict' in Python

  - by Morlock

  Thanks to some great folks on SO, I discovered the possibilities offered by collections.defaultdict, notably in readability and speed. I have put them to use with success. Now I would like to implement three levels of dictionaries, the two top ones being defaultdict and the lowest one being int. I don't find the appropriate way to do this. Here is my attempt: from collections import defaultdict d = defaultdict(defaultdict) a = [("key1", {"a1":22, "a2":33}), ("key2", {"a1":32, "a2":55}), ("key3", {"a1":43, "a2":44})] for i in a: d[i[0]] = i[1] Now this works, but the following, which is the desired behavior, doesn't: d["key4"]["a1"] + 1 I suspect that I should have declared somewhere that the second level defaultdict is of type int, but I didn't find where or how to do so. The reason I am using defaultdict in the first place is to avoid having to initialize the dictionary for each new key. Any more elegant suggestion? Thanks pythoneers!

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