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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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  • pyInotify performance

    - by tranimatronic
    I have a very large directory tree I am wanting pyInotify to watch. Is it better to have pyInotify watch the entire tree or is it better to have a number of watches reporting changes to specific files ? Thanks

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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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  • Django - Passing arguments to models through ForeignKey attributes

    - by marshall
    I've got a class like this: class Image (models.Model): ... sizes = ((90,90), (300,250)) def resize_image(self): for size in sizes: ... and another class like this: class SomeClassWithAnImage (models.Model): ... an_image = models.ForeignKey(Image) what i'd like to do with that class is this: class SomeClassWithAnImage (models.Model): ... an_image = models.ForeignKey(Image, sizes=((90,90), (150, 120))) where i'm can specify the sizes that i want the Image class to use to resize itself as a argument rather than being hard coded on the class. I realise I could pass these in when calling resize_image if that was called directly but the idea is that the resize_image method is called automatically when the object is persisted to the db. if I try to pass arguments through the foreign key declaration like this i get an error straight away. is there an easy / better way to do this before I begin hacking down into django?

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  • Django paging object has issues with Postgresql QuerySets

    - by pivotal
    I have some django code that runs fine on a SQLite database or on a MySQL database, but it runs into problems with Postgres, and it's making me crazy that no one has has this issue before. I think it may also be related to the way querysets are evaluated by the pager. In a view I have: def index(request, page=1): latest_posts = Post.objects.all().order_by('-pub_date') paginator = Paginator(latest_posts, 5) try: posts = paginator.page(page) except (EmptyPage, InvalidPage): posts = paginator.page(paginator.num_pages) return render_to_response('blog/index.html', {'posts' : posts}) And inside the template: {% for post in posts.object_list %} {# some rendering jazz #} {% endfor %} This works fine with SQLite, but Postgres gives me: Caught TypeError while rendering: 'NoneType' object is not callable To further complicate things, when I switch the Queryset call to: latest_posts = Post.objects.all() Everything works great. I've tried re-reading the documentation, but found nothing, although I admit I'm a bit clouded by frustration at this point. What am I missing? Thanks in advance.

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  • App Engine Bulkloader

    - by gurkan
    Hi all, I am trying to use Bulkloader of google app engine but unfortunately could not understand what to do from documentation. It says add this part to app.yaml builtins: - remote_api: on ok i have added. Then says that i have to execute this command appcfg.py update but i don't have any appcfg.py file. And also what is the command which executes this line? Please somebody tell me what i am missing I use AppEngineLauncher to upload my project to server.. I have naver used a command to update or upload it. Thanks in advance..

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  • django test client trouble

    - by Anton Koval'
    I've got a problem... we're writing project using django, and i'm trying to use django.test.client with nose test-framework for tests. Our code is like this: from simplejson import loads from urlparse import urljoin from django.test.client import Client TEST_URL = "http://smakly.localhost:9090/" def test_register(): cln = Client() ref_data = {"email": "[email protected]", "name": "???????", "website": "http://hot.bear.com", "xhr": "true"} print urljoin(TEST_URL, "/accounts/register/") response = loads(cln.post(urljoin(TEST_URL, "/accounts/register/"), ref_data)) print response["message"] and in nose output I catch: Traceback (most recent call last): File "/home/psih/work/svn/smakly/eggs/nose-0.11.1-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/psih/work/svn/smakly/src/smakly.tests/smakly/tests/frontend/test_profile.py", line 25, in test_register response = loads(cln.post(urljoin(TEST_URL, "/accounts/register/"), ref_data)) File "/home/psih/work/svn/smakly/parts/django/django/test/client.py", line 313, in post response = self.request(**r) File "/home/psih/work/svn/smakly/parts/django/django/test/client.py", line 225, in request response = self.handler(environ) File "/home/psih/work/svn/smakly/parts/django/django/test/client.py", line 69, in __call__ response = self.get_response(request) File "/home/psih/work/svn/smakly/parts/django/django/core/handlers/base.py", line 78, in get_response urlconf = getattr(request, "urlconf", settings.ROOT_URLCONF) File "/home/psih/work/svn/smakly/parts/django/django/utils/functional.py", line 273, in __getattr__ return getattr(self._wrapped, name) AttributeError: 'Settings' object has no attribute 'ROOT_URLCONF' My settings.py file does have this attribute. If I get the data from the server with standard urllib2.urllopen().read() it works in the proper way. Any ideas how I can solve this case?

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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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  • Django - urls.py - Filenames with a hash/pound (#) sign?

    - by miya
    I'm using django and realized that when the filename that the user wants to access (let's say a photo) has the pound sign, the entry in the url.py does not match. Any ideas? url(r'^static/(?P<path>.*)$', 'django.views.static.serve', {'document_root': MEDIA_ROOT}, it just says: "/home/user/project/static/upload/images/hello" does not exist when actually the name of the file is: hello#world.jpg Thanks, Nico

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  • Testing for the existence of a field in a class

    - by Brett
    Hi, i have a quick question. I have a 2D array that stores an instance of a class. The elements of the array are assigned a particular class based on a text file that is read earlier in the program. Since i do not know without looking in the file what class is stored at a particular element i could refer to a field that doesn't exist at that index (referring to appearance when an instance of temp is stored in that index). i have come up with a method of testing this, but it is long winded and requires a second matrix. Is there a function to test for the existence of a field in a class? class temp(): name = "default" class temp1(): appearance = "@"

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  • How to update Geo-Location in fireeagle

    - by Ganesh
    Hi Every One, I am developing an application on fireeagle, there i need to update the users exact location, with out asking any information from the user (i.e) lat, long e.t.c., If it is not possible using yahoo fireeagle, please let me know if there exists any other api's other than yahoo fireeagle. If they can get the exact location of web user in 'Lat' and 'Long', either from 'Pc' or from 'Mobile' browser. Thanks in advance.

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  • Can pydoc/help hide the documentation for inherited class methods and attributes?

    - by EOL
    When declaring a class that inherits from a specific class: class C(dict): added_attribute = 0 the documentation for C lists all the methods of dict (either through help(C) or pydoc). Is there a way to hide the inherited methods from the automatically generated documentation (the documentation string can refer to the base class, for non-overwritten methods)? This would be useful: pydoc lists the functions defined in a module after its classes. Thus, when the classes have a very long documentation, a lot of less than useful information is printed before the new functions provided by the module are presented, which makes the documentation harder to exploit (you have to skip all the documentation for the inherited methods until you reach something specific to the module being documented).

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  • Validation on ManyToManyField before Save in Models.py

    - by Heyl1
    I have the following models: class Application(models.Model): users = models.ManyToManyField(User, through='Permission') folder = models.ForeignKey(Folder) class Folder(models.Model): company = models.ManyToManyField(Compnay) class UserProfile(models.Model): user = models.OneToOneField(User, related_name='profile') company = models.ManyToManyField(Company) What I would like to do is to check whether one of the users of the Application has the same company as the Application (via Folder). If this is the case the Application instance should not be saved. The problem is that the ManyToManyFields aren't updated until after the 'post-save' signal. The only option seems to be the new m2m_changed signal. But I'm not sure how I then roll back the save that has already happened. Another option would be to rewrite the save function (in models.py, because I'm talking about the admin here), but I'm not sure how I could access the manytomanyfield content. Finally I've read something about rewriting the save function in the admin of the model in admin.py, however I still wouldn't know how you would access the manytomanyfield content. I have been searching for this everywhere but nothing I come across seems to work for me. If anything is unclear, please tell me. Thanks for your help! Heleen

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  • Writing csv header removes data from numpy array written below

    - by user338095
    I'm trying to export data to a csv file. It should contain a header (from datastack) and restacked arrays with my data (from datastack). One line in datastack has the same length as dataset. The code below works but it removes parts of the first line from datastack. Any ideas why that could be? s = ','.join(itertools.chain(dataset)) + '\n' newfile = 'export.csv' f = open(newfile,'w') f.write(s) numpy.savetxt(newfile, (numpy.transpose(datastack)), delimiter=', ') f.close()

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  • how to detect escape characters in a string

    - by mix
    Given a string named line whose raw version has this value: \rRAWSTRING how can I detect if it has the escape character \r? What I've tried is: if repr(line).startswith('\r'): blah... but it doesn't catch it. I also tried find, such as: if repr(line).find('\r') != -1: blah doesn't work either. What am I missing? thx!

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  • How to improve efficiency in loops?

    - by Jacob Worldly
    I have the following code, which translates the input string into morse code. My code runs through every letter in the string and then through every character in the alphabet. This is very inefficient, because what if I was reading from a very large file, instead of a small alphabet string. Is there any way that I could improve my code, Maybe using the module re, to match my string with the morse code characters? morse_alphabet = ".- -... -.-. -.. . ..-. --. .... .. .--- -.- .-.. -- -. --- .--. --.- .-. ... - ..- ...- .-- -..- -.-- --.." ALPHABET = "abcdefghijklmnopqrstuvwxyz" morse_letters = morse_alphabet.split(" ") result = [] count_character = 0 def t(code): for character in code: count_letter = 0 for letter in ALPHABET: lower_character = code[count_character].lower() lower_letter = letter.lower() if lower_character == lower_letter: result.append(morse_letters[count_letter]) count_letter += 1 count_character += 1 return result

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  • Pickling a class definition

    - by Giorgio
    Is there a way to pickle a class definition? What I'd like to do is pickle the definition (which may created dynamically), and then send it over a TCP connection so that an instance can be created on the other end. I understand that there may be dependencies, like modules and global variables that the class relies on. I'd like to bundle these in the pickling process as well, but I'm not concerned about automatically detecting the dependencies because it's okay if the onus is on the user to specify them.

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  • Extend argparse to write set names in the help text for optional argument choices and define those sets once at the end

    - by Kent
    Example of the problem If I have a list of valid option strings which is shared between several arguments, the list is written in multiple places in the help string. Making it harder to read: def main(): elements = ['a', 'b', 'c', 'd', 'e', 'f'] parser = argparse.ArgumentParser() parser.add_argument( '-i', nargs='*', choices=elements, default=elements, help='Space separated list of case sensitive element names.') parser.add_argument( '-e', nargs='*', choices=elements, default=[], help='Space separated list of case sensitive element names to ' 'exclude from processing') parser.parse_args() When running the above function with the command line argument --help it shows: usage: arguments.py [-h] [-i [{a,b,c,d,e,f} [{a,b,c,d,e,f} ...]]] [-e [{a,b,c,d,e,f} [{a,b,c,d,e,f} ...]]] optional arguments: -h, --help show this help message and exit -i [{a,b,c,d,e,f} [{a,b,c,d,e,f} ...]] Space separated list of case sensitive element names. -e [{a,b,c,d,e,f} [{a,b,c,d,e,f} ...]] Space separated list of case sensitive element names to exclude from processing What would be nice It would be nice if one could define an option list name, and in the help output write the option list name in multiple places and define it last of all. In theory it would work like this: def main_optionlist(): elements = ['a', 'b', 'c', 'd', 'e', 'f'] # Two instances of OptionList are equal if and only if they # have the same name (ALFA in this case) ol = OptionList('ALFA', elements) parser = argparse.ArgumentParser() parser.add_argument( '-i', nargs='*', choices=ol, default=ol, help='Space separated list of case sensitive element names.') parser.add_argument( '-e', nargs='*', choices=ol, default=[], help='Space separated list of case sensitive element names to ' 'exclude from processing') parser.parse_args() And when running the above function with the command line argument --help it would show something similar to: usage: arguments.py [-h] [-i [ALFA [ALFA ...]]] [-e [ALFA [ALFA ...]]] optional arguments: -h, --help show this help message and exit -i [ALFA [ALFA ...]] Space separated list of case sensitive element names. -e [ALFA [ALFA ...]] Space separated list of case sensitive element names to exclude from processing sets in optional arguments: ALFA {a,b,c,d,e,f} Question I need to: Replace the {'l', 'i', 's', 't', 's'} shown with the option name, in the optional arguments. At the end of the help text show a section explaining which elements each option name consists of. So I ask: Is this possible using argparse? Which classes would I have to inherit from and which methods would I need to override? I have tried looking at the source for argparse, but as this modification feels pretty advanced I don´t know how to get going.

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  • Django: Serving a Download in a Generic View

    - by TheLizardKing
    So I want to serve a couple of mp3s from a folder in /home/username/music. I didn't think this would be such a big deal but I am a bit confused on how to do it using generic views and my own url. urls.py url(r'^song/(?P<song_id>\d+)/download/$', song_download, name='song_download'), The example I am following is found in the generic view section of the Django documentations: http://docs.djangoproject.com/en/dev/topics/generic-views/ (It's all the way at the bottom) I am not 100% sure on how to tailor this to my needs. Here is my views.py def song_download(request, song_id): song = Song.objects.get(id=song_id) response = object_detail( request, object_id = song_id, mimetype = "audio/mpeg", ) response['Content-Disposition'= "attachment; filename=%s - %s.mp3" % (song.artist, song.title) return response I am actually at a loss of how to convey that I want it to spit out my mp3 instead of what it does now which is to output a .mp3 with all of the current pages html contained. Should my template be my mp3? Do I need to setup apache to serve the files or is Django able to retrieve the mp3 from the filesystem(proper permissions of course) and serve that? If it do need to configure Apache how do I tell Django that? Thanks in advanced. These files are all on the HD so I don't need to "generate" anything on the spot and I'd like to prevent revealing the location of these files if at all possible. A simple /song/1234/download would be fantastic.

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  • Djangoo Foreign key queries

    - by Hulk
    In the following model: class header(models.Model): title = models.CharField(max_length = 255) created_by = models.CharField(max_length = 255) def __unicode__(self): return self.id() class criteria(models.Model): details = models.CharField(max_length = 255) headerid = models.ForeignKey(header) def __unicode__(self): return self.id() class options(models.Model): opt_details = models.CharField(max_length = 255) headerid = models.ForeignKey(header) def __unicode__(self): return self.id() If there is a row in the database for table header as Id=1, title=value-mart , createdby=CEO How do i query criteria and options tables to get all the values related to header table id=1 Also can some one please suggest a good link for queries examples, Thanks..

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