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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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  • BeautifulSoup: just get inside of a tag, no matter how many enclosing tags there are

    - by AP257
    I'm trying to scrape all the inner html from the <p> elements in a web page using BeautifulSoup. There are internal tags, but I don't care, I just want to get the internal text. For example, for: <p>Red</p> <p><i>Blue</i></p> <p>Yellow</p> <p>Light <b>green</b></p> How can I extract: Red Blue Yellow Light green Neither .string nor .contents[0] does what I need. Nor does .extract(), because I don't want to have to specify the internal tags in advance - I want to deal with any that may occur. Is there a 'just get the visible HTML' type of method in BeautifulSoup? ----UPDATE------ On advice, trying: p_tags = page.findAll('p',text=True) for i, p_tag in enumerate(p_tags): print str(p_tag) But that doesn't help - it just prints out: Red <i>Blue</i> Yellow Light <b>green</b>

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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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • threading.local equivalent for twisted.web?

    - by defnull
    In asynchronous environments, threading.local is not guaranteed to be context-local anymore, because several contexts may coexist within a single thread. Most asynchronous frameworks (gevent, eventlet) provide a get_current_context() functionality to identify the current context. Some offer a way to monkey-patch threading.local so it is local to 'greenthreads' or other framework-specific contexts. I cannot find such a functionality in the twisted documentation. How do I do this?

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