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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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  • Reading path in templates

    - by DJPython
    Hello, is it any way to read path to current page? For example, I am at www.example.com/foo/bar/ - and I want to read '/foo/bar/'. But, all have to be done in template file without modyficating views. I have to many view files to edit each one. Sorry for my english, hope everyone understand. Cheers.

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  • Encoding with url and api

    - by user2950824
    So I have this web app set up and running and it works fine for any username that you request, but when i try http://mrcastelo.pythonanywhere.com/lol/euw/Nazaré, it simply doesnt work - the error that I get on the server is the following: iddata= getJSON(urllolbase+region+urlid+username) #SummonerID UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 5: ordinal not in range(128) It is annoying me greatly, I've tried some other threads but none of them came to a fix. The api that I am using (www.legendaryapi.com) does accept this because this works. Any idea on how to fix this?

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  • Connecting slots and events in PyQt4 in a loop

    - by LukaD
    Im trying to build a calculator with PyQt4 and connecting the 'clicked()' signals from the buttons doesn't as expected. Im creating my buttons for the numbers inside a for loop where i try to connect them afterwards. def __init__(self): for i in range(0,10): self._numberButtons += [QPushButton(str(i), self)] self.connect(self._numberButtons[i], SIGNAL('clicked()'), lambda : self._number(i)) def _number(self, x): print(x) When I click on the buttons all of them print out '9'. Why is that so and how can i fix this?

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  • Update Facebook Page's status using pyfacebook

    - by thornomad
    I am attempting to add functionality to my Django app: when a new post is approved, I want to update the corresponding Facebook Page's status with a message and a link to the post automatically. Basic status update. I have downloaded and installed pyfacebook - and I have read through the tutorial from Facebook. I have also seen this suggestion here on SO: import facebook fb = facebook.Facebook('YOUR_API_KEY', 'YOUR_SECRET_KEY') fb.auth.createToken() fb.login() # THIS IS AS FAR AS I CAN GET fb.auth.getSession() fb.set_status('Checking out StackOverFlow.com') When I get to the login() call, however, pyfacebook tries to open lynx so I can login to Facebook 'via the web' -- this is, obviously, not going to work for me because the system is supposed to be automated ... I've been looking, but can't find out how I can keep this all working with the script and not having to login via a web browser. Any ideas?

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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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  • 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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  • How do I create a Django ModelForm, so that it's fields are sometimes required, sometimes not?

    - by Graf
    Ok, here is the question. Imagine I have a ModelForm which have only two fields. like this one: class ColorForm(forms.Form): color_by_name = forms.CharField() color = forms.IntegerField(widget = forms.Select(choices=COLOR_CHOICES)) So a user can either input a color name, a choose it from a list. Color is required, but that doesn't mean, that user should enter it manually. There do I put validation, so that my code checks if user selected color in dropdownlist and if not then he should write it manually?

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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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  • Query for model by key

    - by Jason Hall
    What I'm trying to do is query the datastore for a model where the key is not the key of an object I already have. Here's some code: class User(db.Model): partner = db.SelfReferenceProperty() def text_message(self, msg): user = User.get_or_insert(msg.sender) if not user.partner: # user doesn't have a partner, find them one # BUG: this line returns 'user' himself... :( other = db.Query(User).filter('partner =', None).get() if other: # connect users else: # no one to connect to! The idea is to find another User who doesn't have a partner, that isn't the User we already know. I've tried filter('key !=, user.key()), filter('__key__ !=, user.key()) and a couple others, and nothing returns another User who doesn't have a partner. filter('foo !=, user.key()) also returns nothing, for the record.

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  • Character Sets explained for Dummies!

    - by Imran
    I don't think i fully understand character sets so i was wondering if anyone would be kind enough to explain it in layman's terms with examples ( for Dummies).I know there is utf8, latin1, ascii ect The more answers the better really. Thank you in advance;-)

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  • Simple numpy question

    - by dassouki
    I can't get this snippet to work: #base code A = array([ [ 1, 2, 10 ], [ 1, 3, 20 ], [ 1, 4, 30 ], [ 2, 1, 15 ], [ 2, 3, 25 ], [ 2, 4, 35 ], [ 3, 1, 17 ], [ 3, 2, 27 ], [ 3, 4, 37 ], [ 4, 1, 13 ], [ 4, 2, 23 ], [ 4, 3, 33 ] ]) # Number of zones zones = unique1d(A[:,0]) for origin in zones: for destination in zones: if origin != destination: A_ik = A[(A[:,0] == origin & A[:,1] == destination), 2]

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  • Does this introduce security vulnerabilities?

    - by mcmt
    I don't think I'm missing anything. Then again I'm kind of a newbie. def GET(self, filename): name = urllib.unquote(filename) full = path.abspath(path.join(STATIC_PATH, filename)) #Make sure request is not tricksy and tries to get out of #the directory, e.g. filename = "../.ssh/id_rsa". GET OUTTA HERE assert full[:len(STATIC_PATH)] == STATIC_PATH, "bad path" return open(full).read()

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  • Declare models elsewhere than in "models.py"

    - by sebpiq
    Hi ! I have an application that splits models into different files. Actually the folder looks like : >myapp __init__.py models.py >hooks ... ... myapp don't care about what's in the hooks, folder, except that there are models, and that they have to be declared somehow. So, I put this in myapp.__init__.py : from django.conf import settings for hook in settings.HOOKS : try : __import__(hook) except ImportError as e : print "Got import err !", e #where HOOKS = ("myapp.hooks.a_super_hook1", ...) The problem is that it doesn't work when I run syncdb(and throws some strange "Got import err !"... strange considering that it's related to another module of my program that I don't even import anywhere :/ ) ! So I tried successively : 1) for hook in settings.HOOKS : try : exec ("from %s import *" % hook) doesn't work either : syncdb doesn't install the models in hooks 2) from myapp.hooks.a_super_hook1 import * This works 3) exec("from myapp.hooks.a_super_hook1 import *") This works to So I checked that in the test 1), the statement executed is the same than in tests 2) and 3), and it is exactly the same ... Any idea ???

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  • Using sqlalchemy to query using multiple column where in clause

    - by crunkchitis
    I'm looking to execute this query using sqlalchemy. SELECT name, age, favorite_color, favorite_food FROM kindergarten_classroom WHERE (favorite_color, favorite_food) IN (('lavender','lentil soup'),('black','carrot juice')); I only want kids that like (lavender AND lentil soup) OR (black and carrot juice). This is similar, but doesn't get me all of the way there: Sqlalchemy in clause

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  • mount command pid

    - by lakshmipathi
    Trying to mount a device and get the pid of mount command. cmd="/bin/mount /dev/sda1 /mnt" os.system(cmd) Now how to obtain the pid of mount command? There plenty of mounted device available on my system ,something like ps | grep mount won't work.

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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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  • Wordpress & Django -- One domain, two servers. Possible?

    - by DomoDomo
    My question is about hosting Django and Wordpress under one domain, but two physical machines (actually, they are VMs but same diff). Let's say I have a Django webapp at example.com. I'd like to start a Wordpress blog about my webapp, so any blog page rank mojo flows back to my webapp, I'd like the blog address t be example.com/blog. My understanding is blog.example.com would not transfer said page rank mojo. Because I'm worried about Wordpress security flaws compromising my Django webapp, I want to host Django and Wordpress on two physically separate machines. Given all that, is it possible using re-write rules or a reverse proxy server to do this? I know the easy way is to make my Wordpress blog a subdomain, but I really don't want to do that. Has anyone done this in the past, is it stable? If I need a third server to be a dedicated reverse proxy, that's totally fine. Thanks!

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  • How do I modify gitstats to only utilize a specified file extension for it's statistics?

    - by Fake Code Monkey Rashid
    Hello good people! The website of the statistics generator in question is: http://gitstats.sourceforge.net/ It's git repo can be cloned from: git clone git://repo.or.cz/gitstats.git What I want to do is something like: ./gitstatus --ext=".py" /input/foo /output/bar Failing being able to easily pass the above option without heavy modification, I'd just hardcore the file extentsion I want to be included. However, I'm unsure of the relevant section of code to modify and even if I did no, I'm unsure of how to start such modifications. It's seems like it'd be rather simple but alas...

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  • Django complex queries

    - by Josh K
    I need to craft a filter for an object that checks date ranges. Right now I'm performing a very inefficient loop which checks all the objects. I would like to simplify this to a database call. The logic is you have a start and an end date objects. I need to check if the start OR the end is within the range of an appointment. if (start >= appointment.start && start < appointment.end) || (end > appointment.start && end <= appointment.end) I could do this in SQL, but I'm not as familiar with the Django model structure for more complex queries.

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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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  • How to get the related_name of a many-to-many-field?

    - by amann
    I am trying to get the related_name of a many-to-many-field. The m2m-field is located betweeen the models "Group" and "Lection" and is declared in the group-model as following: lections = models.ManyToManyField(Lection, blank=True) The field looks like this: <django.db.models.fields.related.ManyToManyField object at 0x012AD690> The print of field.__dict__ is: {'_choices': [], '_m2m_column_cache': 'group_id', '_m2m_name_cache': 'group', '_m2m_reverse_column_cache': 'lection_id', '_m2m_reverse_name_cache': 'lection', '_unique': False, 'attname': 'lections', 'auto_created': False, 'blank': True, 'column': 'lections', 'creation_counter': 71, 'db_column': None, 'db_index': False, 'db_table': None, 'db_tablespace': '', 'default': <class django.db.models.fields.NOT_PROVIDED at 0x00FC8780>, 'editable': True, 'error_messages': {'blank': <django.utils.functional.__proxy__ object at 0x00FC 7B50>, 'invalid_choice': <django.utils.functional.__proxy__ object at 0x00FC7A50>, 'null': <django.utils.functional.__proxy__ object at 0x00FC7 A70>}, 'help_text': <django.utils.functional.__proxy__ object at 0x012AD6F0>, 'm2m_column_name': <function _curried at 0x012A88F0>, 'm2m_db_table': <function _curried at 0x012A8AF0>, 'm2m_field_name': <function _curried at 0x012A8970>, 'm2m_reverse_field_name': <function _curried at 0x012A89B0>, 'm2m_reverse_name': <function _curried at 0x012A8930>, 'max_length': None, 'name': 'lections', 'null': False, 'primary_key': False, 'rel': <django.db.models.fields.related.ManyToManyRel object at 0x012AD6B0>, 'related': <RelatedObject: mymodel:group related to lections>, 'related_query_name': <function _curried at 0x012A8670>, 'serialize': True, 'unique_for_date': None, 'unique_for_month': None, 'unique_for_year': None, 'validators': [], 'verbose_name': 'lections'} Now the field should be accessed via a lection-instance. So this is done by lection.group_set But i need to access it dynamically, so there is the need to get the related_name attribute from somewhere. Here in the documentation, there is a note that it is possible to access ManyToManyField.related_name, but this doesn't work for my somehow.. Help would be a lot appreciated. Thanks in advance.

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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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