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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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  • The truth value of an array with more than one element is ambigous when trying to index an array

    - by user1440194
    I am trying to put all elements of rbs into a new array if the elements in var(another numpy array) is =0 and <=.1 . However when I try the following code I get this error: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() rbs = [ish[4] for ish in realbooks] for book in realbooks: var -= float(str(book[0]).replace(":", "")) bidsred = rbs[(var <= .1) and (var >=0)] any ideas on what I'm doing wrong?

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  • Efficient way to store tuples in the datastore

    - by Drew Sears
    If I have a pair of floats, is it any more efficient (computationally or storage-wise) to store them as a GeoPtProperty than it would be pickle the tuple and store it as a BlobProperty? If GeoPt is doing something more clever to keep multiple values in a single property, can it be leveraged for arbitrary data? Can I store the tuple ("Johnny", 5) in a single entity property in a similarly efficient manner?

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  • Clean Method for a ModelForm in a ModelFormSet made by modelformset_factory

    - by Salyangoz
    I was wondering if my approach is right or not. Assuming the Restaurant model has only a name. forms.py class BaseRestaurantOpinionForm(forms.ModelForm): opinion = forms.ChoiceField(choices=(('yes', 'yes'), ('no', 'no'), ('meh', 'meh')), required=False, )) class Meta: model = Restaurant fields = ['opinion'] views.py class RestaurantVoteListView(ListView): queryset = Restaurant.objects.all() template_name = "restaurants/list.html" def dispatch(self, request, *args, **kwargs): if request.POST: queryset = self.request.POST.dict() #clean here return HttpResponse(json.dumps(queryset), content_type="application/json") def get_context_data(self, **kwargs): context = super(EligibleRestaurantsListView, self).get_context_data(**kwargs) RestaurantFormSet = modelformset_factory( Restaurant,form=BaseRestaurantOpinionForm ) extra_context = { 'eligible_restaurants' : self.get_eligible_restaurants(), 'forms' : RestaurantFormSet(), } context.update(extra_context) return context Basically I'll be getting 3 voting buttons for each restaurant and then I want to read the votes. I was wondering from where/which clean function do I need to call to get something like: { ('3' : 'yes'), ('2' : 'no') } #{ 'restaurant_id' : 'vote' } This is my second/third question so tell me if I'm being unclear. Thanks.

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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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  • Google App Engine django model form does not pick up BlobProperty

    - by Wes
    I have the following model: class Image(db.Model): auction = db.ReferenceProperty(Auction) image = db.BlobProperty() thumb = db.BlobProperty() caption = db.StringProperty() item_to_tag = db.StringProperty() And the following form: class ImageForm(djangoforms.ModelForm): class Meta: model = Image When I call ImageForm(), only the non-Blob fields are created, like this: <tr><th><label for="id_auction">Auction:</label></th><td><select name="auction" id="id_auction"> <option value="" selected="selected">---------</option> <option value="ahRoYXJ0bWFuYXVjdGlvbmVlcmluZ3INCxIHQXVjdGlvbhgKDA">2010-06-19 11:00:00</option> </select></td></tr> <tr><th><label for="id_caption">Caption:</label></th><td><input type="text" name="caption" id="id_caption" /></td></tr> <tr><th><label for="id_item_to_tag">Item to tag:</label></th><td><input type="text" name="item_to_tag" id="id_item_to_tag" /></td></tr> I want the Blob fields to be included in the form as well (as file inputs). What am I doing wrong?

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  • Not work variables in django templates

    - by ??????? ???????
    My context dictionary not sending to my templates. I have function from django.shortcuts import render_to_response def home(request): return render_to_response('home.html',{'test':'test'}) and i have simple template such as: <html> <body> my test == {{test}} </body> </html> When i open my site in browser, i have "my test == ". settings.py is default. I dont use something custom. What the problem? Server is apache with wsgi module.

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  • Counting amount of items in Pythons 'for'

    - by Markum
    Kind of hard to explain, but when I run something like this: fruits = ['apple', 'orange', 'banana', 'strawberry', 'kiwi'] for fruit in fruits: print fruit.capitalize() It gives me this, as expected: Apple Orange Banana Strawberry Kiwi How would I edit that code so that it would "count" the amount of times it's performing the for, and print this? 1 Apple 2 Orange 3 Banana 4 Strawberry 5 Kiwi

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  • Installing twisted.mail.smtp

    - by user3506985
    I am using Ubuntu 14.04 and trying to install twisted.mail.smtp using the following commnands -sudo add-apt-repository ppa:jesstess/twisted-12.1-testing -sudo apt-get update There are no errors in the installation,but when I specify the command that is from twisted.mail.smtp import ESMTPSenderFactory I am getting the following error Error: ImportError: No module named mail.smtp Please help me out

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  • Is there a value in using map() vs for?

    - by roder
    Does map() iterate through the list like "for" would? Is there a value in using map vs for? If so, right now my code looks like this: for item in items: item.my_func() If it makes sense, I would like to make it map(). Is that possible? What is an example like?

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  • Using Range Function

    - by Michael Alexander Riechmann
    My goal is to make a program that takes an input (Battery_Capacity) and ultimately spits out a list of the (New_Battery_Capacity) and the Number of (Cycle) it takes for it ultimately to reach maximum capacity of 80. Cycle = range (160) Charger_Rate = 0.5 * Cycle Battery_Capacity = float(raw_input("Enter Current Capacity:")) New_Battery_Capacity = Battery_Capacity + Charger_Rate if Battery_Capacity < 0: print 'Battery Reading Malfunction (Negative Reading)' elif Battery_Capacity > 80: print 'Battery Reading Malfunction (Overcharged)' elif float(Battery_Capacity) % 0.5 !=0: print 'Battery Malfunction (Charges Only 0.5 Interval)' while Battery_Capacity >= 0 and Battery_Capacity < 80: print New_Battery_Capacity I was wondering why my Cycle = range(160) isn't working in my program?

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  • OpenCV performance in different languages

    - by h0b0
    I'm doing some prototyping with OpenCV for a hobby project involving processing of real time camera data. I wonder if it is worth the effort to reimplement this in C or C++ when I have it all figured out or if no significant performance boost can be expected. The program basically chains OpenCV functions, so the main part of the work should be done in native code anyway.

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  • Tying PyQt4 QAction triggered() to local class callable doesn't seem to work. How to debug this?

    - by Jon Watte
    I create this object when I want to create a QAction. I then add this QAction to a menu: class ActionObject(object): def __init__(self, owner, command): action = QtGui.QAction(command.name, owner) self.action = action self.command = command action.setShortcut(command.shortcut) action.setStatusTip(command.name) QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'), self.triggered) def triggered(self): print("got triggered " + self.command.id + " " + repr(checked)) Unfortunately, when the menu item is selected, the 'triggered' function is not called. QtCore.QObject.connect() returns True. Nothing is printed on the console to indicate that anything is wrong, and no exception is thrown. How can I debug this? (or, what am I doing wrong?)

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  • JQuery cookie access has stopped working for GAE app

    - by Greg
    I have a google app engine app that has been running for some time, and some javascript code that checks for a login cookie has suddenly stopped working. As far as I can tell, NO code has changed. The relevant code uses the jquery cookies plugin (jquery.cookies.2.2.0.min.js)... // control the default screen depending // if someone is logged in if( $.cookies.get('dev_appserver_login') != null || $.cookies.get('ACSID') != null ) { alert("valid cookie!") $("#inventory-container").show(); } else { alert("INvalid cookie!") $("#welcome-container").show(); } The reason for the two checks is that in the GAE SDK, the cookies are named differently. The production system uses 'ACSID'. This if statement works in the SDK and now fails 100% of the time in production. I have verified that the cookie is, in fact, present when I inspect the page. Thoughts?

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  • PyParsing: Is this correct use of setParseAction()?

    - by Rosarch
    I have strings like this: "MSE 2110, 3030, 4102" I would like to output: [("MSE", 2110), ("MSE", 3030), ("MSE", 4102)] This is my way of going about it, although I haven't quite gotten it yet: def makeCourseList(str, location, tokens): print "before: %s" % tokens for index, course_number in enumerate(tokens[1:]): tokens[index + 1] = (tokens[0][0], course_number) print "after: %s" % tokens course = Group(DEPT_CODE + COURSE_NUMBER) # .setResultsName("Course") course_data = (course + ZeroOrMore(Suppress(',') + COURSE_NUMBER)).setParseAction(makeCourseList) This outputs: >>> course.parseString("CS 2110") ([(['CS', 2110], {})], {}) >>> course_data.parseString("CS 2110, 4301, 2123, 1110") before: [['CS', 2110], 4301, 2123, 1110] after: [['CS', 2110], ('CS', 4301), ('CS', 2123), ('CS', 1110)] ([(['CS', 2110], {}), ('CS', 4301), ('CS', 2123), ('CS', 1110)], {}) Is this the right way to do it, or am I totally off? Also, the output of isn't quite correct - I want course_data to emit a list of course symbols that are in the same format as each other. Right now, the first course is different from the others. (It has a {}, whereas the others don't.)

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  • Improving the join of two wave file?

    - by kaki
    I have written a code for joining two wave files.It works fine when i am joining larger segments but as i need to join very small segments the clarity is not good. I have learned that the signal processing technique such a windowed join can be used to improve the joining of file. y[n] = w[n]s[n] Multiply value of signal at sample number n by the value of a windowing function hamming window w[n]= .54 - .46*cos(2*Pi*n)/L 0 I am not understanding how to get the value to signal at sample n and how to implement this?? the code i am using for joining is import wave m=['C:/begpython/S0001_0002.wav', 'C:/begpython/S0001_0001.wav'] i=1 a=m[i] infiles = [a, "C:/begpython/S0001_0002.wav", a] outfile = "C:/begpython/S0001_00367.wav" data= [] data1=[] for infile in infiles: w = wave.open(infile, 'rb') data1=[w.getnframes] data.append( [w.getparams(), w.readframes(w.getnframes())] ) #data1 = [ord(character) for character in data1] #print data1 #data1 = ''.join(chr(character) for character in data1) w.close() output = wave.open(outfile, 'wb') output.setparams(data[0][0]) output.writeframes(data[0][1]) output.writeframes(data[1][1]) output.writeframes(data[2][1]) output.close()

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  • Sending file over socket

    - by johannix
    I'm have a problem sending data as a file from one end of a socket to the other. What's happening is that both the server and client are trying to read the file so the file never gets sent. I was wondering how to have the client block until the server's completed reading the file sent from the client. I have this working with raw packets using send and recv, but figured this was a cleaner solution... Client: connects to server creating socket connection creates a file on socket and sends data waits for file from server Server: waits for file from client Complete interraction: client sends data to server server sends data to client

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  • Looping through a directory on the web and displaying its contents (files and other directories) via

    - by al jaffe
    In the same vein as http://stackoverflow.com/questions/2593399/process-a-set-of-files-from-a-source-directory-to-a-destination-directory-in-pyth I'm wondering if it is possible to create a function that when given a web directory it will list out the files in said directory. Something like... files[] for file in urllib.listdir(dir): if file.isdir: # handle this as directory else: # handle as file I assume I would need to use the urllib library, but there doesn't seem to be an easy way of doing this, that I've seen at least.

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  • PyQt QAbstractListModel seems to ignore tristate flags

    - by mcieslak
    I've been trying for a couple days to figure out why my QAbstractLisModel won't allow a user to toggle a checkable item in three states. The model returns the Qt.IsTristate and Qt.ItemIsUserCheckable in the flags() method, but when the program runs only Qt.Checked and Qt.Unchecked are toggled on edit. class cboxModel(QtCore.QAbstractListModel): def __init__(self, parent=None): super(cboxModel, self).__init__(parent) self.cboxes = [ ['a',0], ['b',1], ['c',2], ['d',0] ] def rowCount(self,index=QtCore.QModelIndex()): return len(self.cboxes) def data(self,index,role): if not index.isValid: return QtCore.QVariant() myname,mystate = self.cboxes[index.row()] if role == QtCore.Qt.DisplayRole: return QtCore.QVariant(myname) if role == QtCore.Qt.CheckStateRole: if mystate == 0: return QtCore.QVariant(QtCore.Qt.Unchecked) elif mystate == 1: return QtCore.QVariant(QtCore.Qt.PartiallyChecked) elif mystate == 2: return QtCore.QVariant(QtCore.Qt.Checked) return QtCore.QVariant() def setData(self,index,value,role=QtCore.Qt.EditRole): if index.isValid(): self.cboxes[index.row()][1] = value.toInt()[0] self.emit(QtCore.SIGNAL("dataChanged(QModelIndex,QModelIndex)"), index, index) print self.cboxes return True return False def flags(self,index): if not index.isValid(): return QtCore.Qt.ItemIsEditable return QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsTristate You can test it with this, class MainForm(QtGui.QMainWindow): def __init__(self, parent=None): super(MainForm, self).__init__(parent) model = cboxModel(self) self.view = QtGui.QListView() self.view.setModel(model) self.setCentralWidget(self.view) app = QtGui.QApplication(sys.argv) form = MainForm() form.show() app.exec_() and see that only 2 states are available. I'm assuming there's something simple I'm missing. Any ideas? Thanks!

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