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  • Python structure mistake

    - by jaddy123
    I'm writing a program in which I can Reverse the sequence and Replace all As with Ts, all Cs with Gs, all Gs with Cs, and all Ts with As. the program is to read a sequence of bases and output the reverse complement sequence. I am having trouble to do it so can anyone please help me with this by having a look on my code: word = raw_input("Enter sequence: ") a = word.replace('A', 'T') b = word.replace('C', 'G') c = word.replace('G', 'C') d = word.replace('T', 'A') if a == word and b == word and c == word and d == word: print "Reverse complement sequence: ", word And I want this sort of output: Enter sequence: CGGTGATGCAAGG Reverse complement sequence: CCTTGCATCACCG Regards

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  • From Dictionary To File Python

    - by user3600560
    I am basically trying to write this information from my dictionary to this file. I have this dictionary named files = {} and it is for a filing system I am making. Anyhow it is always being update with new items, and I want those items to be uploaded to the file. Then if you exit the program the files are loaded back to the dictionary files = {}. Here is the code I have so far: file = {} for i in files: g = open(i, 'r') g.read(i) g.close() EDIT I want the contents of the dictionary to be written to a file. The items inside the dictionary are all stored like this: files[filename] = {filedate:filetext} where filename is the file's name, filedate is the date that the file was made on, and the filetext is the files contents.

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  • Python performance profiling (file close)

    - by user1853986
    First of all thanks for your attention. My question is how to reduce the execution time of my code. Here is the relevant code. The below code is called in iteration from the main. def call_prism(prism_input_file,random_length): prism_output_file = "path.txt" cmd = "prism %s -simpath %d %s" % (prism_input_file,random_length,prism_output_file) p = os.popen(cmd) p.close() return prism_output_file def main(prism_input_file, number_of_strings): ... for n in range(number_of_strings): prism_output_file = call_prism(prism_input_file,z[n]) ... return I used statistics from the "profile statistics browser" when I profiled my code. The "file close" system command took the maximum time (14.546 seconds). The call_prism routine is called 10 times. But the number_of_strings is usually in thousands, so, my program takes lot of time to complete. Let me know if you need more information. By the way I tried with subprocess, too. Thanks.

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  • Iterating through a range of dates in Python

    - by ShawnMilo
    This is working fine, but I'm looking for any feedback on how to do it better. Right now I think it's better than nested loops, but it starts to get Perl-one-linerish when you have a generator in a list comprehension. Any suggestions are welcome. day_count = (end_date - start_date).days + 1 for single_date in [d for d in (start_date + timedelta(n) for n in range(day_count)) if d <= end_date]: print strftime("%Y-%m-%d", single_date.timetuple()) Notes: I'm not actually using this to print; that's just for demo purposes. The variables start_date and end_date are datetime.date objects, because I don't need the timestamps (they're going to be used to generate a report). I checked the StackOverflow questions which were similar before posting this, but none were exactly the same. Sample Output (for a start date of 2009-05-30 and an end date of 2009-06-09): 2009-05-30 2009-05-31 2009-06-01 2009-06-02 2009-06-03 2009-06-04 2009-06-05 2009-06-06 2009-06-07 2009-06-08 2009-06-09

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  • Manipulating Directory Paths in Python

    - by G Ullman
    Basically I've got this current url and this other key that I want to merge into a new url, but there are three different cases. Suppose the current url is localhost:32401/A/B/foo if key is bar then I want to return localhost:32401/A/B/bar if key starts with a slash and is /A/bar then I want to return localhost:32401/A/bar finally if key is its own independent url then I just want to return that key = htt p://foo.com/bar - http://foo.com/bar I assume there is a way to do at least the first two cases without manipulating the strings manually, but nothing jumped out at me immediately in the os.path module.

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  • most widely used python web app deployment style

    - by mete
    I wonder which option is more stable (leaving performance aside) and is more widely used (I assume the widely used one is the most stable): apache - mod_wsgi apache - mod_fcgid apache - mod_proxy_ajp apache - mod_proxy_http for a project that will serve REST services with small json formatted input and output messages and web pages, up to 100 req/s. Please comment on apache if you think nginx etc. is more suitable. Thanks.

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  • Simple check authentication decorator in Python + Pylons

    - by ensnare
    I'd like to write a simple decorator that I can put above functions in my controller to check authentication and re-direct to the login page if the current user is not authenticated. What is the best way to do this? Where should the decorator go? How should I pass cookie info to the decorator? Sample code is greatly appreciated. Thank you!

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  • Appending item to lists - python

    - by ariel
    I have a list lets say a=[[1,2],[3,4],[5,6]]. I want to add to each item in a the char 'a'. when I use a=[x.append('a') for x in a] it return [None,None,None]. But if I use a1=[x.append('a') for x in a] then it do someting odd. a and not a1 is [[1,2,a],[3,4,a],[5,6,a]]. I don't understand why the first return [None, None, None] nor why the second works on a.

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  • Testing variable types in Python

    - by Jasper
    Hello, I'm creating an initialising function for the class 'Room', and found that the program wouldn't accept the tests I was doing on the input variables. Why is this? def __init__(self, code, name, type, size, description, objects, exits): self.code = code self.name = name self.type = type self.size = size self.description = description self.objects = objects self.exits = exits #Check for input errors: if type(self.code) != type(str()): print 'Error found in module rooms.py!' print 'Error number: 110' elif type(self.name) != type(str()): print 'Error found in module rooms.py!' print 'Error number: 111' elif type(self.type) != type(str()): print 'Error found in module rooms.py!' print 'Error number: 112' elif type(self.size) != type(int()): print 'Error found in module rooms.py!' print 'Error number: 113' elif type(self.description) != type(str()): print 'Error found in module rooms.py!' print 'Error number: 114' elif type(self.objects) != type(list()): print 'Error found in module rooms.py!' print 'Error number: 115' elif type(self.exits) != type(tuple()): print 'Error found in module rooms.py!' print 'Error number: 116' When I run this I get this error: Traceback (most recent call last): File "/Users/Jasper/Development/Programming/MyProjects/Game Making Challenge/Europa I/rooms.py", line 148, in <module> myRoom = Room(101, 'myRoom', 'Basic Room', 5, '<insert description>', myObjects, myExits) File "/Users/Jasper/Development/Programming/MyProjects/Game Making Challenge/Europa I/rooms.py", line 29, in __init__ if type(self.code) != type(str()): TypeError: 'str' object is not callable

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  • python equivalent of filter() getting two output lists

    - by FX
    Let's say I have a list, and a filtering function. Using something like >>> filter(lambda x: x > 10, [1,4,12,7,42]) [12, 42] I can get the elements matching the criterion. Is there a function I could use that would output two lists, one of elements matching, one of the remaining elements? I could call the filter() function twice, but that's kinda ugly :) Edit: the order of elements should be conserved, and I may have identical elements multiple times.

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  • Need help in writting re in python

    - by laspal
    Hi, My string is mystring = "<tr><td><span class='para'><b>Total Amount : </b>INR (Indian Rupees) 100.00</span></td></tr>" My problem here is I have to search and get the total amount test = re.search("(Indian Rupees)(\d{2})(?:\D|$)", mystring) but my test give me None. How can I get the values and values can be 10.00, 100.00, 1000.00 Thanks

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  • handling matrix data in python

    - by Ovisek
    I was trying to progressively subtract values of a 3D matrix. The matrix looks like: ATOM 1223 ZX SOD A 11 2.11 -1.33 12.33 ATOM 1224 ZY SOD A 11 -2.99 -2.92 20.22 ATOM 1225 XH HEL A 12 -3.67 9.55 21.54 ATOM 1226 SS ARG A 13 -6.55 -3.09 42.11 ... here the last three columns are representing values for axes x,y,z respectively. now I what I wanted to do is, take the values of x,y,z for 1st line and subtract with 2nd,3rd,4th line in a iterative way and print the values for each axes. I was using: for line in map(str.split,inp): x = line[-3] y = line[-2] z = line[-1] for separating the values, but how to do in iterative way. should I do it by using Counter.

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  • Serialize the @property methods in a Python class.

    - by ashchristopher
    Is there a way to have any @property definitions passed through to a json serializer when serializing a Django model class? example: class FooBar(object.Model) name = models.CharField(...) @property def foo(self): return "My name is %s" %self.name Want to serialize to: [{ 'name' : 'Test User', 'foo' : 'My name is Test User', },]

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  • Overriding Built-in Classes (Python)

    - by Yipeng
    How can I view and override the full definition for built in classes? I have seen the library docs but am looking for something more. For e.g. is it possible to override the Array Class such that the base index starts from 1 instead of 0, or to override .sort() of list to a sorting algorithm of my own liking?

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  • python dict.fromkeys() returns empty

    - by slooow
    I wrote the following function. It returns an empty dictionary when it should not. The code works on the command line without function. However I cannot see what is wrong with the function, so I have to appeal to your collective intelligence. def enter_users_into_dict(userlist): newusr = {} newusr.fromkeys(userlist, 0) return newusr ul = ['john', 'mabel'] nd = enter_users_into_dict(ul) print nd It returns an empty dict {} where I would expect {'john': 0, 'mabel': 0}. It is probably very simply but I don't see the solution.

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  • python: importing modules with incorrect import statements => unexhaustive info from resulting Impor

    - by bbb
    Hi there, I have a funny problem I'd like to ask you guys ('n gals) about. I'm importing some module A that is importing some non-existent module B. Of course this will result in an ImportError. This is what A.py looks like import B Now let's import A >>> import A Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/tmp/importtest/A.py", line 1, in <module> import B ImportError: No module named B Alright, on to the problem. How can I know if this ImportError results from importing A or from some corrupt import inside A without looking at the error's string representation. The difference is that either A is not there or does have incorrect import statements. Hope you can help me out... Cheers bb

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