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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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  • 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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  • Shuttle control in wxPython

    - by Mridang Agarwalla
    Hi, I'm trying to implement a shuttle control in wxPython but there doesn't seem to be one. I've decided to use two listbox controls. The shuttle control looks like this: I've got two listboxes — one's populated, one's not. Could someone show me how to add a selected item to the second list box when it is double clicked? It should be removed from the first. When it is double clicked in the second, it should be added to the first and removed from the second. The shuttle control implements these by default but it's a pity it isn't there. Thank you.

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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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  • Why do all module run together?

    - by gunbuster363
    I just made a fresh copy of eclipse and installed pydev. In my first trial to use pydev with eclipse, I created 2 module under the src package(the default one) FirstModule.py: ''' Created on 18.06.2009 @author: Lars Vogel ''' def add(a,b): return a+b def addFixedValue(a): y = 5 return y +a print "123" run.py: ''' Created on Jun 20, 2011 @author: Raymond.Yeung ''' from FirstModule import add print add(1,2) print "Helloword" When I pull out the pull down menu of the run button, and click "ProjectName run.py", here is the result: 123 3 Helloword Apparantly both module ran, why? Is this the default setting?

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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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  • 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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  • How do I get PyLint to find namespace packages?

    - by tjd.rodgers
    I have a virtualenv where I've installed two packages, both using the company.project_name namespace. So the first package is importable from company.project_name.one and the second from company.project_name.two. The challenge is that I can't seem to be able to run PyLint on either one of them. If I issue: $ pylint company.project_name.one I get: ************* Module company.project_name.one F: 1, 0: No module named project_name.one(fatal) I suspect that I'm probably doing something wrong. Is there a proper way to do this? Edit: I should have made it clear that company.project_name and company are namespace packages and not regular packages.

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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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  • 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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  • How to use traceit to report function input variables in stack trace

    - by reckoner
    Hi, I've been using the following code to trace the execution of my programs: import sys import linecache import random def traceit(frame, event, arg): if event == "line": lineno = frame.f_lineno filename = frame.f_globals["__file__"] if filename == "<stdin>": filename = "traceit.py" if (filename.endswith(".pyc") or filename.endswith(".pyo")): filename = filename[:-1] name = frame.f_globals["__name__"] line = linecache.getline(filename, lineno) print "%s:%s:%s: %s" % (name, lineno,frame.f_code.co_name , line.rstrip()) return traceit def main(): print "In main" for i in range(5): print i, random.randrange(0, 10) print "Done." sys.settrace(traceit) main() Using this code, or something like it, is it possible to report the values of certain function arguments? In other words, the above code tells me "which" functions were called and I would like to know "what" the corresponding values of the input variables for those function calls. Thanks in advance.

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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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  • 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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  • How to print an Objectified Element?

    - by BeeBand
    I have xml of the format: <channel> <games> <game slot='1'> <id>Bric A Bloc</id> <title-text>BricABloc Hoorah</title-text> <link>Fruit Splat</link> </game> </games> </channel> I've parsed this xml using lxml.objectify, via: tree = objectify.parse(file) There will potentially be a number of <game>s underneath <games>. I understand that I can generate a list of <game> objects via: [ tree.games[0].game[0:4] ] My question is, what class are those objects and is there a function to print any object of whatever class these objects belong to?

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  • Check result of AX_PYTHON_MODULE in configure.ac

    - by tmatth
    In using the m4_ax_python_module.m4 macro in configure.ac (AX_PYTHON_MODULE), one can know at configure time if a given module is installed. It takes two arguments, the module name, and second argument which if not empty, will lead to an exit, useful when the module is a must-have. In the case where you don't want a fatal exit, how do you test in configure.ac which modules were found or not? They output "yes" or "no" when configure is run, but that's all I've found so far. Basically If I have these lines in configure.ac: AX_PYTHON_MODULE(json,[]) AX_PYTHON_MODULE(simplejson,[]) How do I test which of the two modules were found? See http://www.gnu.org/software/autoconf-archive/ax_python_module.html#ax_python_module for documentation about this macro.

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  • Can I move beaker.SessionMiddleware to handle method somehow?

    - by Alexander A.Sosnovskiy
    It's a bit ugly that many lines of code fall into "__main__". Can someone give me a tip of how to move SessionMiddleware into handle method? I should notice that I use session in CoreXmlParser. Thanks in advance ! def handle(environ, start_response): req = webob.Request(environ) c = CoreXmlParser(req) resp = webob.Response(body=c(), charset = 'utf-8', status='200 OK', \ request=req, content_type='text/xml') resp(environ, start_response) return resp.app_iter if __name__ == '__main__': #parse config file for session options app = SessionMiddleware(handle, some_session_opts_here) from flup.server.fcgi import WSGIServer WSGIServer(app).run()

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  • Import Error: No module named testrunner

    - by JiL
    I followed this to add zc.recipe.testrunner to my buildout. I can run buildout successfully but when I run bin/test, I get: ImportError: No module named testrunner I have zope.testrunner-4.0.4-py2.4.egg in /usr/local/lib/python2.4/site-packages I also pinned zope.testrunner = 4.0.4 zc.recipe.testruner = 1.4.0 zc.recipe.egg = 1.3.2 When I ran buildout, I used -vvv and I got: ... Installing 'zc.recipe.testrunner'. We have the distribution that satisfies 'zc.recipe.testrunner==1.4.0'. Egg from site-packages: z3c.recipe.scripts 1.0.1 Egg from site-packages: zope.testrunner 4.0.4 Egg from site-packages: zope.interface 3.8.0 Egg from site-packages: zope.exceptions 3.7.1 ... We have the distribution that satisfies 'zope.testrunner==4.0.4'. Egg from site-packages: zope.testrunner 4.0.4 Adding required 'zope.interface' required by zope.testrunner 4.0.4. We have a develop egg: zope.interface 0.0 Adding required 'zope.exceptions' required by zope.testrunner 4.0.4. We have a develop egg: zope.exceptions 0.0 ... Why is it I get an ImportError? Is zope.testrunner not installed correctly?

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  • Can I get the amount of time for which a key is pressed on a keyboard

    - by Adi
    Dear all, I am working on a project in which I have to develop bio-passwords based on user's keystroke style. Suppose a user types a password for 20 times, his keystrokes are recorded, like holdtime : time for which a particular key is pressed. digraph time : time it takes to press a different key. suppose a user types a password " COMPUTER". I need to know the time for which every key is pressed. something like : holdtime for the above password is C-- 200ms O-- 130ms M-- 150ms P-- 175ms U-- 320ms T-- 230ms E-- 120ms R-- 300ms The rational behind this is , every user will have a different holdtime. Say a old person is typing the password, he will take more time then a student. And it will be unique to a particular person. To do this project, I need to record the time for each key pressed. I would greatly appreciate if anyone can guide me in how to get these times. Editing from here.. Language is not important, but I would prefer it in C. I am more interested in getting the dataset.

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  • Django url tag multiple parameters

    - by Overdose
    I have two similar codes. The first one works as expected. urlpatterns = patterns('', (r'^(?P<n1>\d)/test/', test), (r'', test2), {% url testapp.views.test n1=5 %} But adding the second parameter makes the result return empty string. urlpatterns = patterns('', (r'^(?P<n1>\d)/test(?P<n2>\d)/', test), (r'', test2),) {% url testapp.views.test n1=5, n2=2 %} Views signature: def test(request, n1, n2=1):

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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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