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  • Can anyone tell me why these lines are not working?

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO_init_.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • differences between "d.clear()" and "d={}"

    - by Tshepang
    On my machine, the execution speed between "d.clear()" and "d={}" is over 100ns so am curious why one would use one over the other. import timeit def timing(): d = dict() if __name__=='__main__': t = timeit.Timer('timing()', 'from __main__ import timing') print t.repeat()

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  • Sending message from one server to another in Twisted

    - by Casey Patton
    I've implemented my servers in the following way: def makeServer(application, port): factory = protocol.ServerFactory() factory.protocol = MyChat factory.clients = [] internet.TCPServer(port, factory).setServiceParent(application) application = service.Application("chatserver") server1 = makeServer(application, port=1025) server2 = makeServer(application, port=1026) server3 = makeServer(application, port=1027) Note that MyChat is an event handling class that has a "receiveMessage" action: def lineReceived(self, line): print "received", repr(line) for c in self.factory.clients: c.transport.write(message + '\n') I want server1 to be able to pass messages to server2. Rather, I want server1 to be treated as a client of server2. If server1 receives the message "hi" then I want it to send that same exact message to server2. How can I accomplish this?

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  • How to override inner class methods if the inner class is defined as a property of the top class

    - by Maddy
    I have a code snippet like this class A(object): class b: def print_hello(self): print "Hello world" b = property(b) And I want to override the inner class b (please dont worry about the lowercase name) behaviour. Say, I want to add a new method or I want to change an existing method, like: class C(A): class b(A.b): def print_hello(self): print "Inner Class: Hello world" b = property(b) Now if I create C's object as c = C(), and call c.b I get TypeError: 'property' object is not callable error. How would I get pass this and call print_hello of the extended inner class? Disclaimer: I dont want to change the code for A class.

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  • why is this dictionary line number count not working?

    - by jad
    i have this piece of code the last bit of the code starting from d = {} im trying to print the words with its line number located in the text but it is not working its only printing the words anyone know why ??? need help ASAP import sys import string text = [] infile = open(sys.argv[1], 'r').read() for punct in string.punctuation: infile = infile.replace(punct, "") text = infile.split() dict = open(sys.argv[2], 'r').read() dictset = [] dictset = dict.split() words = [] words = list(set(text) - set(dictset)) words = [text.lower() for text in words] words.sort() d = {} counter = 0 for lines in text: counter += 1 if word not in d: d[words] = [counter] else: d[words.append[counter] print(word, d)

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  • Simplifying for-if messes with better structure?

    - by HH
    # Description: you are given a bitwise pattern and a string # you need to find the number of times the pattern matches in the string # any one liner or simple pythonic solution? import random def matchIt(yourString, yourPattern): """find the number of times yourPattern occurs in yourString""" count = 0 matchTimes = 0 # How can you simplify the for-if structures? for coin in yourString: #return to base if count == len(pattern): matchTimes = matchTimes + 1 count = 0 #special case to return to 2, there could be more this type of conditions #so this type of if-conditionals are screaming for a havoc if count == 2 and pattern[count] == 1: count = count - 1 #the work horse #it could be simpler by breaking the intial string of lenght 'l' #to blocks of pattern-length, the number of them is 'l - len(pattern)-1' if coin == pattern[count]: count=count+1 average = len(yourString)/matchTimes return [average, matchTimes] # Generates the list myString =[] for x in range(10000): myString= myString + [int(random.random()*2)] pattern = [1,0,0] result = matchIt(myString, pattern) print("The sample had "+str(result[1])+" matches and its size was "+str(len(myString))+".\n" + "So it took "+str(result[0])+" steps in average.\n" + "RESULT: "+str([a for a in "FAILURE" if result[0] != 8])) # Sample Output # # The sample had 1656 matches and its size was 10000. # So it took 6 steps in average. # RESULT: ['F', 'A', 'I', 'L', 'U', 'R', 'E']

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  • pyPDF - Retrieve page numbers from document

    - by SquidneyPoitier
    At the moment I'm looking into doing some PDF merging with pyPdf, but sometimes the inputs are not in the right order, so I'm looking into scraping each page for its page number to determine the order it should go in (e.g. if someone split up a book into 20 10-page PDFs and I want to put them back together). I have two questions - 1.) I know that sometimes the page number is stored in the document data somewhere, as I've seen PDFs that render on Adobe as something like [1243] (10 of 150), but I've read documents of this sort into pyPDF and I can't find any information indicating the page number - where is this stored? 2.) If avenue #1 isn't available, I think I could iterate through the objects on a given page to try to find a page number - likely it would be its own object that has a single number in it. However, I can't seem to find any clear way to determine the contents of objects. If I run: pdf.getPage(0).getContents() This usually either returns: {'/Filter': '/FlateDecode'} or it returns a list of IndirectObject(num, num) objects. I don't really know what to do with either of these and there's no real documentation on it as far as I can tell. Is anyone familiar with this kind of thing that could point me in the right direction?

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  • Problem with sys.argv[1] when unittest module is in a script

    - by chrissygormley
    Hello, I have a script that does various things and access paramenters using sys.argv but when the script gets to the unittest part of the code it says there is no module for this. The script that I have is: class MyScript(): def __init__(self): self.value = sys.argv[1] def hello(self): print self.value def suite(self): modules_to_test = ('external_sanity_onvif', 'starttest') alltests = unittest.TestSuite() for module in map(__import__, modules_to_test): alltests.addTest(unittest.findTestCases(module)) return alltests if __name__ == '__main__': Run = MyScript() Run.hello() log_file = 'log_file.txt' test_file = open(log_file, "w") runner = unittest.TextTestRunner(test_file) unittest.main(defaultTest='Run.suite', testRunner=runner) Say I enter ./script.py Hello in the command line. The error I get is: AttributeError: 'module' object has no attribute 'Hello' If I remove the unittest module it works. Also if I remove the testrunner log and leave it at: unittest.main(defaultTest='Run.suite') This still doesn't work. Can anyone help. Thanks

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  • Return 0 where django quersyet is none

    - by gramware
    I have a django queryset in my views whose values I pack before passing to my template. There is a problem when the queryset returns none since associated values are not unpacked. the quersyet is called comments. Here is my views.py def forums(request ): post_list = list(forum.objects.filter(child='0')&forum.objects.filter(deleted='0').order_by('postDate')) user = UserProfile.objects.get(pk=request.session['_auth_user_id']) newpostform = PostForm(request.POST) deletepostform = PostDeleteForm(request.POST) DelPostFormSet = modelformset_factory(forum, exclude=('child','postSubject','postBody','postPoster','postDate','childParentId')) readform = ReadForumForm(request.POST) comments =list( forum.objects.filter(deleted='0').filter(child='1').order_by('childParentId').values('childParentId').annotate(y=Count('childParentId'))) if request.user.is_staff== True : staff = 1 else: staff = 0 staffis = 1 if newpostform.is_valid(): topic = request.POST['postSubject'] poster = request.POST['postPoster'] newpostform.save() return HttpResponseRedirect('/forums') else: newpostform = PostForm(initial = {'postPoster':user.id}) if request.GET: form = SearchForm(request.GET) if form.is_valid(): query = form.cleaned_data['query'] post_list = list((forum.objects.filter(child='0')&forum.objects.filter(deleted='0')&forum.objects.filter(Q(postSubject__icontains=query)|Q(postBody__icontains=query)|Q(postDate__icontains=query)))or(forum.objects.filter(deleted='0')&forum.objects.filter(Q(postSubject__icontains=query)|Q(postBody__icontains=query)|Q(postDate__icontains=query)).values('childParentId'))) if request.method == 'POST': delpostformset = DelPostFormSet(request.POST) if delpostformset.is_valid(): delpostformset.save() return HttpResponseRedirect('/forums') else: delpostformset = DelPostFormSet(queryset=forum.objects.filter(child='0', deleted='0')) """if readform.is_valid(): user=get_object_or_404(UserProfile.objects.all()) readform.save() else: readform = ReadForumForm()""" post= zip( post_list,comments, delpostformset.forms) paginator = Paginator(post, 10) # Show 10 contacts per page # Make sure page request is an int. If not, deliver first page. try: page = int(request.GET.get('page', '1')) except ValueError: page = 1 # If page request (9999) is out of range, deliver last page of results. try: post = paginator.page(page) except (EmptyPage, InvalidPage): post = paginator.page(paginator.num_pages) return render_to_response('forum.html', {'post':post, 'newpostform': newpostform,'delpost':delpostformset, 'username':user.username, 'comments':comments, 'user':user, },context_instance = RequestContext( request ))

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  • Capturing stdout from an imported module in wxpython and sending it to a textctrl, without blocking the GUI

    - by splafe
    There are alot of very similar questions to this but I can't find one that applies specifically to what I'm trying to do. I have a simulation (written in SimPy) that I'm writing a GUI for, the main output of the simulation is text - to the console from 'print' statements. Now, I thought the simplest way would be to create a seperate module GUI.py, and import my simulation program into it: import osi_model I want all the print statements to be captured by the GUI and appear inside a Textctrl, which there's countless examples of on here, along these lines: class MyFrame(wx.Frame): def __init__(self, *args, **kwds): <general frame initialisation stuff..> redir=RedirectText(self.txtCtrl_1) sys.stdout=redir class RedirectText: def __init__(self,aWxTextCtrl): self.out=aWxTextCtrl def write(self,string): self.out.WriteText(string) I am also starting my simulation from a 'Go' button: def go_btn_click(self, event): print 'GO' self.RT = threading.Thread(target=osi_model.RunThis()) self.RT.start() This all works fine, and the output from the simulation module is captured by the TextCtrl, except the GUI locks up and becomes unresponsive - I still need it to be accessible (at the very minimum to have a 'Stop' button). I'm not sure if this is a botched attempt at creating a new thread that I've done here, but I assume a new thread will be needed at some stage in this process. People suggest using wx.CallAfter, but I'm not sure how to go about this considering the imported module doesn't know about wx, and also I can't realistically go through the entire simulation architecture and change all the print statements to wx.CallAfter, and any attempt to capture the shell from inside the imported simulation program leads to the program crashing. Does anybody have any ideas about how I can best achieve this? So all I really need is for all console text to be captured by a TextCtrl while the GUI remains responsive, and all text is solely coming from an imported module. (Also, secondary question regarding a Stop button - is it bad form to just kill the simulation thread?). Thanks, Duncan

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  • Django adminsite customize search_fields query

    - by dArignac
    Howdy! In the django admin you can set the search_fields for the ModelAdmin to be able to search over the properties given there. My model class has a property that is not a real model property, means it is not within the database table. The property relates to another database table that is not tied to the current model through relations. But I want to be able to search over it, so I have to somehow customize the query the admin site creates to do the filtering when the search field was filled - is this possible and if, how? I can query the database table of my custom property and it then returns the ids of the model classes fitting the search. This then, as I said, has to flow into the admin site search query. Thanks!

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  • How to bind a double precision using psycopg2

    - by user337636
    I'm trying to bind a float to a postgresql double precision using psycopg2. ele = 1.0/3.0 dic = {'name': 'test', 'ele': ele} sql = '''insert into waypoints (name, elevation) values (%(name)s, %(ele)s)''' cur = db.cursor() cur.execute(sql, dic) db.commit() sql = """select elevation from waypoints where name = 'test'""" cur.execute(sql_out) ele_out = cur.fetchone()[0] ele_out 0.33333333333300003 ele 0.33333333333333331 Obviously I don't need the precision, but I would like to be able to simply compare the values. I could use the struct module and save it as a string, but thought there should be a better way. Thanks

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  • Optimization of Function with Dictionary and Zip()

    - by eWizardII
    Hello, I have the following function: def filetxt(): word_freq = {} lvl1 = [] lvl2 = [] total_t = 0 users = 0 text = [] for l in range(0,500): # Open File if os.path.exists("C:/Twitter/json/user_" + str(l) + ".json") == True: with open("C:/Twitter/json/user_" + str(l) + ".json", "r") as f: text_f = json.load(f) users = users + 1 for i in range(len(text_f)): text.append(text_f[str(i)]['text']) total_t = total_t + 1 else: pass # Filter occ = 0 import string for i in range(len(text)): s = text[i] # Sample string a = re.findall(r'(RT)',s) b = re.findall(r'(@)',s) occ = len(a) + len(b) + occ s = s.encode('utf-8') out = s.translate(string.maketrans("",""), string.punctuation) # Create Wordlist/Dictionary word_list = text[i].lower().split(None) for word in word_list: word_freq[word] = word_freq.get(word, 0) + 1 keys = word_freq.keys() numbo = range(1,len(keys)+1) WList = ', '.join(keys) NList = str(numbo).strip('[]') WList = WList.split(", ") NList = NList.split(", ") W2N = dict(zip(WList, NList)) for k in range (0,len(word_list)): word_list[k] = W2N[word_list[k]] for i in range (0,len(word_list)-1): lvl1.append(word_list[i]) lvl2.append(word_list[i+1]) I have used the profiler to find that it seems the greatest CPU time is spent on the zip() function and the join and split parts of the code, I'm looking to see if there is any way I have overlooked that I could potentially clean up the code to make it more optimized, since the greatest lag seems to be in how I am working with the dictionaries and the zip() function. Any help would be appreciated thanks!

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  • Mean of Sampleset and powered Sampleset

    - by Milla Well
    I am working on an ICA implementation wich is based on the assumption, that all source signals are independent. So I checked on the basic concepts of Dependence vs. Correlation and tried to show this example on sample data from numpy import * from numpy.random import * k = 1000 s = 10000 mn = 0 mnPow = 0 for i in arange(1,k): a = randn(s) a = a-mean(a) mn = mn + mean(a) mnPow = mnPow + mean(a**3) print "Mean X: ", mn/k print "Mean X^3: ", mnPow/k But I couldn't produce the last step of this example E(X^3) = 0: >> Mean X: -1.11174580826e-18 >> Mean X^3: -0.00125229267144 First value I would consider to be zero, but second value is too large, isn't it? Since I subtract the mean of a, I expected the mean of a^3 to be zero as well. Does the problem lie in the random number generator, the precision of the numerical values in my misunderstanding of the concepts of mean and expected value?

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  • Append to list of lists

    - by Joel
    Hello, I am trying to build a list of lists using the following code: list=3*[[]] Now I am trying to append a string to the list in position 0: list[0].append("hello") However, instead of receiving the list [ ["hello"] , [], [] ] I am receiving the list: [ ["hello"] ,["hello"] , ["hello"] ] Am I missing something? Thanks, Joel

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  • How do I upload a files to google app engine app when field name is not known

    - by Michael Neale
    I have tried a few options, none of which seem to work (if I have a simple multipart form with a named field, it works well, but when I don't know the name I can't just grab all files in the request...). I have looked at http://stackoverflow.com/questions/81451/upload-files-in-google-app-engine and it doesn't seem suitable (or to actually work, as someone mentioned the code snipped it untested).

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  • How to clear wxpython frame content when dragging a panel?

    - by aF
    Hello, I have 3 panels and I want to make drags on them. The problem is that when I do a drag on one this happens: How can I refresh the frame to happear its color when the panel is no longer there? This is the code that I have to make the drag: def onMouseMove(self, event): (self.pointWidth, self.pointHeight) = event.GetPosition() (self.width, self.height) = self.GetSizeTuple() if (self.pointWidth>100 and self.pointWidth<(self.width-100) and self.pointHeight < 15) or self.parent.dragging: self.SetCursor(wx.StockCursor(wx.CURSOR_SIZING)) """implement dragging""" if not event.Dragging(): self.w = 0 self.h = 0 return self.CaptureMouse() if self.w == 0 and self.h == 0: (self.w, self.h) = event.GetPosition() else: (posw, posh) = event.GetPosition() displacement = self.h - posh self.SetPosition( self.GetPosition() - (0, displacement)) else: self.SetCursor(wx.StockCursor(wx.CURSOR_ARROW)) def onDraggingDown(self, event): if self.pointWidth>100 and self.pointWidth<(self.width-100) and self.pointHeight < 15: self.parent.dragging = 1 self.SetCursor(wx.StockCursor(wx.CURSOR_ARROW)) self.SetBackgroundColour('BLUE') self.parent.SetTransparent(220) self.Refresh() def onDraggingUp(self, event): self.parent.dragging = 0 self.parent.SetTransparent(255) self.SetCursor(wx.StockCursor(wx.CURSOR_ARROW)) and this are the binds for this events: self.Bind(wx.EVT_MOTION, self.onMouseMove) self.Bind(wx.EVT_LEFT_DOWN, self.onDraggingDown) self.Bind(wx.EVT_LEFT_UP, self.onDraggingUp) With this, if I click on the top of the panel, and move down or up, the panel position changes (I drag the panel) to the position of the mouse.

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  • passing self data into a recursive function

    - by user272689
    I'm trying to set a function to do something like this def __binaryTreeInsert(self, toInsert, currentNode=getRoot(), parentNode=None): where current node starts as root, and then we change it to a different node in the method and recursivly call it again. However, i cannot get the 'currentNode=getRoot()' to work. If i try calling the funcion getRoot() (as above) it says im not giving it all the required variables, but if i try to call self.getRoot() it complains that self is an undefined variable. Is there a way i can do this without having to specify the root while calling this method?

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  • What does "str indices must be integers" mean?

    - by digitala
    I'm working with dicts in jython which are created from importing/parsing JSON. Working with certain sections I see the following message: TypeError: str indices must be integers This occurs when I do something like: if jsondata['foo']['bar'].lower() = 'baz': ... Where jsondata looks like: {'foo': {'bar':'baz'} } What does this mean, and how do I fix it?

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  • add a decorate function to a class

    - by wiso
    I have a decorated function (simplified version): class Memoize: def __init__(self, function): self.function = function self.memoized = {} def __call__(self, *args, **kwds): hash = args try: return self.memoized[hash] except KeyError: self.memoized[hash] = self.function(*args) return self.memoized[hash] @Memoize def _DrawPlot(self, options): do something... now I want to add this method to a pre-esisting class. ROOT.TChain.DrawPlot = _DrawPlot when I call this method: chain = TChain() chain.DrawPlot(opts) I got: self.memoized[hash] = self.function(*args) TypeError: _DrawPlot() takes exactly 2 arguments (1 given) why doesn't it propagate self?

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