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  • problem with hierarchical clustering in Python

    - by user248237
    I am doing a hierarchical clustering a 2 dimensional matrix by correlation distance metric (i.e. 1 - Pearson correlation). My code is the following (the data is in a variable called "data"): from hcluster import * Y = pdist(data, 'correlation') cluster_type = 'average' Z = linkage(Y, cluster_type) dendrogram(Z) The error I get is: ValueError: Linkage 'Z' contains negative distances. What causes this error? The matrix "data" that I use is simply: [[ 156.651968 2345.168618] [ 158.089968 2032.840106] [ 207.996413 2786.779081] [ 151.885804 2286.70533 ] [ 154.33665 1967.74431 ] [ 150.060182 1931.991169] [ 133.800787 1978.539644] [ 112.743217 1478.903191] [ 125.388905 1422.3247 ]] I don't see how pdist could ever produce negative numbers when taking 1 - pearson correlation. Any ideas on this? thank you.

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  • calling a function from another function in python

    - by user1040503
    I have written this function that takes to strings in order to see if they are anagrams: def anagram_check(str_x, str_y): x = string1.replace(" ","") y = string2.replace(" ","") lower1 = x.lower() lower2 = y.lower() sorted1 = sorted(lower1) sorted2 = sorted(lower2) if sorted1 == sorted2: return True else: return False this function works fine, the problem is that now I need to use this function in another function in order to find anagrams in a text file. I want to print a list of tuples with all the anagrams in it. this is what i have done so far def anagrams_finder(words_num): anagrams = [] f = open("words.txt") a = list(f) list1 = ([s.replace('\n', '') for s in a]) list2 = ([i.lower() for i in list1]) list3 = list2[0:words_num] #number of words from text that need to be checked. for i in list3: .... I tried using for loops, while loops, appand.... but nothing seems to work. how can I use the first function in order to help me with the second? Please help...

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  • Python: Problem Importing Function From Another Module

    - by Rafid K. Abdullah
    I have a module called nbemail.py and in this module I want to use the function package_post defined in the module main.py. I am using this statement: from api.main import package_post But I am getting this error: ImportError: cannot import name package_post I really don't know why I am getting this error! I do have _init_.py files in the api directory (which contains the files nbemail.py and main.py) and I do have the function package_post defined in main.py. Any idea to help fixing this problem?

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  • searching a list of tuples in python

    - by hdx
    So I have a list of tuple like: [(1,"juca"),(22,"james"),(53,"xuxa"),(44,"delicia")] I want this list for a tuple whose number value is equal to something. So that if I do search(53) it will return 2 Is is an easy way to do that?

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  • Calling a method with getattr in Python

    - by brain_damage
    How to call a method using getattr? I want to create a metaclass, which can call non-existing methods of some other class that start with the word 'oposite_'. The method should have the same number of arguments, but to return the opposite result. def oposite(func): return lambda s, *args, **kw: not oposite(s, *args, **kw) class Negate(type): def __getattr__(self, name): if name.startswith('oposite_'): return oposite(self.__getattr__(name[8:])) def __init__(self,*args,**kwargs): self.__getattr__ = Negate.__getattr__ class P(metaclass=Negate): def yep(self): return True But the problem is that self.__getattr__(sth) returns a NoneType object. >>> p = P() >>> p.oposite_yep() Traceback (most recent call last): File "<pyshell#115>", line 1, in <module> p.oposite_yep() TypeError: <lambda>() takes at least 1 positional argument (0 given) How to deal with this?

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  • Regex replace (in Python) - a more simple way?

    - by Evan Fosmark
    Any time I want to replace a piece of text that is part of a larger piece of text, I always have to do something like: "(?P<start>some_pattern)(?P<replace>foo)(?P<end>end)" And then concatenate the start group with the new data for replace and then the end group. Is there a better method for this?

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  • Dynamic dispatch and inheritance in python

    - by Bill Zimmerman
    Hi, I'm trying to modify Guido's multimethod (dynamic dispatch code): http://www.artima.com/weblogs/viewpost.jsp?thread=101605 to handle inheritance and possibly out of order arguments. e.g. (inheritance problem) class A(object): pass class B(A): pass @multimethod(A,A) def foo(arg1,arg2): print 'works' foo(A(),A()) #works foo(A(),B()) #fails Is there a better way than iteratively checking for the super() of each item until one is found? e.g. (argument ordering problem) I was thinking of this from a collision detection standpoint. e.g. foo(Car(),Truck()) and foo(Truck(), Car()) and should both trigger foo(Car,Truck) # Note: @multimethod(Truck,Car) will throw an exception if @multimethod(Car,Truck) was registered first? I'm looking specifically for an 'elegant' solution. I know that I could just brute force my way through all the possibilities, but I'm trying to avoid that. I just wanted to get some input/ideas before sitting down and pounding out a solution. Thanks

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  • Python: For loop problem

    - by James
    I have a PSP page with html embedded. I need to place another for loop so i can insert another %s next to background-color: which will instert a appropriate colour to colour in the html table. For example i need to insert for z in colours so it can loop over the colours list and insert the correct colour. Where ever i try to insert the for loop it doesnt seem to work it most commonly colours each cell in the table 60 times then moves onto the next cell and repeats itself and crashes my web browser. The colours are held in a table called colours. code below: <table> <% s = ''.join(aa[i] for i in table if i in aa) for i in range(0, len(s), 60): req.write('<tr><td><TT>%04d</td>' % (i+1)); for k in s[i:i+60]: req.write('<TT><td><TT><font style="background-color:">%s<font></td>' % (k)); req.write('</TT></tr>') #end %> </table>

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  • Python decorator question

    - by nsharish
    decorator 1: def dec(f): def wrap(obj, *args, **kwargs): f(obj, *args,**kwargs) return wrap decorator 2: class dec: def __init__(self, f): self.f = f def __call__(self, obj, *args, **kwargs): self.f(obj, *args, **kwargs) A sample class, class Test: @dec def disp(self, *args, **kwargs): print(*args,**kwargs) The follwing code works with decorator 1 but not with decorator 2. a = Test() a.disp("Message") I dont understand why decorator 2 is not working here. Can someone help me with this?

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  • python decorator to add function to list in current scope

    - by AlexH
    Goal: Make a decorator which can modify the scope that it is used in. If it worked: class Blah(): # or perhaps class Blah(ParentClassWhichMakesThisPossible) def one(self): pass @decorated def two(self): pass Blah.decorated ["two"] Why? I essentially want to write classes which can maintain specific dictionaries of methods, so that I can retrieve lists of available methods of different types on a per class basis. errr..... I want to do this: class RuleClass(ParentClass): @rule def blah(self): pass @rule def kapow(self): pass def shazam(self): class OtherRuleClass(ParentClass): @rule def foo(self): pass def bar(self): pass RuleClass.rules.keys() ["blah", "kapow"] OtherRuleClass.rules.keys() ["foo"]

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  • OpenVPN Configuration - Windows 7 client & debian server

    - by Guillaume
    I recently formatted my Windows 7 computer and lost my client's config files for OpenVPN. I recovered the certificates and default config that were left on the server but I haven't managed to make the whole thing work again. I assume the server's config and routing table are OK because it was working before (although quite some time ago). Would any of you experts be able to help? server.conf # Serveur TCP/666 mode server proto udp port 666 dev tun # Cles et certificats ca ca.crt cert server.crt key server.key dh dh1024.pem tls-auth ta.key 0 cipher AES-256-CBC # Reseau server 10.8.0.0 255.255.255.0 #push "redirect-gateway def1 bypass-dhcp" push "dhcp-option DNS 208.67.222.222" push "dhcp-option DNS 208.67.220.220" push "redirect-gateway def1" keepalive 10 120 # Securite user nobody group nogroup chroot /etc/openvpn/jail persist-key persist-tun comp-lzo # Log verb 3 mute 20 status openvpn-status.log log-append /var/log/openvpn.log client.conf # Client client dev tun proto udp remote *my server's ip address*:666 cipher AES-256-CBC # Cles ca ca.crt cert client1.crt key client1.key tls-auth ta.key 1 # Securite nobind persist-key persist-tun comp-lzo verb 3 Routing table on debian server when OpenVPN server is running: Destination Gateway Genmask Indic Metric Ref Use Iface 10.8.0.2 * 255.255.255.255 UH 0 0 0 tun0 10.8.0.0 10.8.0.2 255.255.255.0 UG 0 0 0 tun0 my server's ip * 255.255.255.0 U 0 0 0 eth0 default 72815.trg.dedic 0.0.0.0 UG 0 0 0 eth0 Routing table on Windows 7 client (OpenVPN not working) =========================================================================== Interface List 19...00 f0 8a 1b 6e 5c ......TAP-Win32 Adapter V9 12...90 2e 34 33 84 7b ......Atheros AR8151 PCI-E Gigabit Ethernet Controller ( NDIS 6.20) 1...........................Software Loopback Interface 1 12...00 00 00 00 00 00 00 e0 Microsoft ISATAP Adapter 13...00 00 00 00 00 00 00 e0 Teredo Tunneling Pseudo-Interface 16...00 00 00 00 00 00 00 e0 Microsoft ISATAP Adapter #2 =========================================================================== IPv4 Route Table =========================================================================== Active Routes: Network Destination Netmask Gateway Interface Metric 0.0.0.0 0.0.0.0 192.168.1.1 192.168.1.11 20 127.0.0.0 255.0.0.0 On-link 127.0.0.1 306 127.0.0.1 255.255.255.255 On-link 127.0.0.1 306 127.255.255.255 255.255.255.255 On-link 127.0.0.1 306 192.168.1.0 255.255.255.0 On-link 192.168.1.11 276 192.168.1.11 255.255.255.255 On-link 192.168.1.11 276 192.168.1.255 255.255.255.255 On-link 192.168.1.11 276 224.0.0.0 240.0.0.0 On-link 127.0.0.1 306 224.0.0.0 240.0.0.0 On-link 192.168.1.11 276 255.255.255.255 255.255.255.255 On-link 127.0.0.1 306 255.255.255.255 255.255.255.255 On-link 192.168.1.11 276 =========================================================================== Persistent Routes: None IPv6 Route Table =========================================================================== Active Routes: [...] =========================================================================== Persistent Routes: None And when the link is established between my client and the server: The server's routing table stays the same. The client's becomes: =========================================================================== Interface List 19...00 f0 8a 1b 6e 5c ......TAP-Win32 Adapter V9 12...90 2e 34 33 84 7b ......Atheros AR8151 PCI-E Gigabit Ethernet Controller ( NDIS 6.20) 1...........................Software Loopback Interface 1 12...00 00 00 00 00 00 00 e0 Microsoft ISATAP Adapter 13...00 00 00 00 00 00 00 e0 Teredo Tunneling Pseudo-Interface 16...00 00 00 00 00 00 00 e0 Microsoft ISATAP Adapter #2 =========================================================================== IPv4 Route Table =========================================================================== Active Routes: Network Destination Netmask Gateway Interface Metric 0.0.0.0 0.0.0.0 192.168.1.1 192.168.1.11 20 0.0.0.0 128.0.0.0 10.8.0.5 10.8.0.6 30 10.8.0.1 255.255.255.255 10.8.0.5 10.8.0.6 30 10.8.0.4 255.255.255.252 On-link 10.8.0.6 286 10.8.0.6 255.255.255.255 On-link 10.8.0.6 286 10.8.0.7 255.255.255.255 On-link 10.8.0.6 286 my server's ip 255.255.255.255 192.168.1.1 192.168.1.11 20 127.0.0.0 255.0.0.0 On-link 127.0.0.1 306 127.0.0.1 255.255.255.255 On-link 127.0.0.1 306 127.255.255.255 255.255.255.255 On-link 127.0.0.1 306 128.0.0.0 128.0.0.0 10.8.0.5 10.8.0.6 30 192.168.1.0 255.255.255.0 On-link 192.168.1.11 276 192.168.1.11 255.255.255.255 On-link 192.168.1.11 276 192.168.1.255 255.255.255.255 On-link 192.168.1.11 276 224.0.0.0 240.0.0.0 On-link 127.0.0.1 306 224.0.0.0 240.0.0.0 On-link 192.168.1.11 276 224.0.0.0 240.0.0.0 On-link 10.8.0.6 286 255.255.255.255 255.255.255.255 On-link 127.0.0.1 306 255.255.255.255 255.255.255.255 On-link 192.168.1.11 276 255.255.255.255 255.255.255.255 On-link 10.8.0.6 286 =========================================================================== Persistent Routes: None What's working: Server and client do connect to each other, SSL certificates are OK. The client gets an IP (10.8.0.6) from the server OpenVPN client is started as an administrator. But: I cannot ping the other one on either side. 'Gateway' value is empty on client's side (in the adapter's "status" window). Client has got no internet access when the link is up. Ideal configuration: I only want the client to be able to use the server's Internet access and access its resources (MySQL server in particular). I do not need or want the server to access the client's local network. The client needs to be able to access it's local network, although all Internet traffic should be redirected to the VPN link. I spent a considerable amount of time on this but it's still not working, any help would be much appreciated. Thanks :)

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  • python list directory , subdirectory and files

    - by thomytheyon
    Hi Alls, I'm trying to make a script to list all directory, subdirectory, and files in a given directory. I tried this : import sys,os root="/home/patate/directory/" path=os.path.join(root,"targetdirectory") for r,d,f in os.walk(path): for file in f: print os.path.join(root,file) Unfortunatly it doesn't work properly, i get all the files, but not them complete path. like : if the dir struct would be : /home/patate/directory/targetdirectory/123/456/789/file.txt It would print: /home/patate/directory/targetdirectory/file.txt What i need is the first result, any help would be greatly appreciated ! Thanks

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  • python global variable not working in apache

    - by Suhail
    I am facing issue with the global variable, when i run in the django development server it works fine, but in apache it doesn't work here is the code below: red= "/foodfolio3/test/" def showAddRecipe(request): #global objc if "userid" in request.session: objc["ErrorMsgURL"]= "" try: urlList= request.POST URL= str(urlList['url']) URL= URL.strip('http://') URL= "http://" + URL recipe= __addRecipeUrl__(URL) if (recipe == 'FailToOpenURL') or (recipe == 'Invalid-website-URL'): #request.session["ErrorMsgURL"]= "Kindly check URL, Please enter a valid URL" objc["ErrorMsgURL"]= "Kindly check URL, Please enter a valid URL" print "here global_context =", objc arurl= HttpResponseRedirect("/foodfolio3/add/import/") arurl['ErrorMsgURL']= objc["ErrorMsgURL"] #return HttpResponseRedirect("/foodfolio3/add/import/") #return render_to_response('addRecipeUrl.html', objc, context_instance = RequestContext(request)) return (arurl) else: objc["recipe"] = recipe return render_to_response('addRecipe.html', objc, context_instance = RequestContext(request)) except: objc["recipe"] = "" return render_to_response('addRecipe.html', objc, context_instance = RequestContext(request)) else: global red red= "/foodfolio3/add/" return HttpResponseRedirect("/foodfolio3/login") def showAddRecipeUrl(request): if "userid" in request.session: return render_to_response('addRecipeUrl.html', objc, context_instance = RequestContext(request)) else: global red red= "/foodfolio3/add/import/" return HttpResponseRedirect("/foodfolio3/login") def showLogin(request): obj = {} obj["error_message"] = "" obj["registered"] = "" if request.method == "POST": if (red == "/foodfolio3/test"): next= '/foodfolio3/recipes' else: next= red try: username = request.POST['username'] password = request.POST['password'] user = authenticate(username=username, password=password) except: user = authenticate(request=request) if user is not None: if user.is_active: login(request, user) request.session["userid"] = user.id # Redirect to a success page. return HttpResponseRedirect(next) this code works fine in django development server, but in apache, the url is getting redirected to '/foodfolio3/recipes'

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  • Logical python question - handeling directories and files in them

    - by Konstantin
    Hello! I'm using this function to extract files from .zip archive and store it on the server: def unzip_file_into_dir(file, dir): import sys, zipfile, os, os.path os.makedirs(dir, 0777) zfobj = zipfile.ZipFile(file) for name in zfobj.namelist(): if name.endswith('/'): os.mkdir(os.path.join(dir, name)) else: outfile = open(os.path.join(dir, name), 'wb') outfile.write(zfobj.read(name)) outfile.close() And the usage: unzip_file_into_dir('/var/zips/somearchive.zip', '/var/www/extracted_zip') somearchive.zip have this structure: somearchive.zip 1.jpeg 2.jpeg another.jpeg or, somethimes, this one: somearchive.zip somedir/ 1.jpeg 2.jpeg another.jpeg Question is: how do I modify my function, so that my extracted_zip catalog would always contain just images, not images in another subdirectory, even if images are stored in somedir inside an archive.

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  • Can't iterate over a list class in Python

    - by Vicky
    I'm trying to write a simple GUI front end for Plurk using pyplurk. I have successfully got it to create the API connection, log in, and retrieve and display a list of friends. Now I'm trying to retrieve and display a list of Plurks. pyplurk provides a GetNewPlurks function as follows: def GetNewPlurks(self, since): '''Get new plurks since the specified time. Args: since: [datetime.datetime] the timestamp criterion. Returns: A PlurkPostList object or None. ''' offset = jsonizer.conv_datetime(since) status_code, result = self._CallAPI('/Polling/getPlurks', offset=offset) return None if status_code != 200 else \ PlurkPostList(result['plurks'], result['plurk_users'].values()) As you can see this returns a PlurkPostList, which in turn is defined as follows: class PlurkPostList: '''A list of plurks and the set of users that posted them.''' def __init__(self, plurk_json_list, user_json_list=[]): self._plurks = [PlurkPost(p) for p in plurk_json_list] self._users = [PlurkUser(u) for u in user_json_list] def __iter__(self): return self._plurks def GetUsers(self): return self._users def __eq__(self, other): if other.__class__ != PlurkPostList: return False if self._plurks != other._plurks: return False if self._users != other._users: return False return True Now I expected to be able to do something like this: api = plurk_api_urllib2.PlurkAPI(open('api.key').read().strip(), debug_level=1) plurkproxy = PlurkProxy(api, json.loads) user = plurkproxy.Login('my_user', 'my_pass') ps = plurkproxy.GetNewPlurks(datetime.datetime(2009, 12, 12, 0, 0, 0)) print ps for p in ps: print str(p) When I run this, what I actually get is: <plurk.PlurkPostList instance at 0x01E8D738> from the "print ps", then: for p in ps: TypeError: __iter__ returned non-iterator of type 'list' I don't understand - surely a list is iterable? Where am I going wrong - how do I access the Plurks in the PlurkPostList?

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  • Find&Replace using Python - Binary file

    - by Aaron Hoffman
    Hello, I'm attempting to do a "find and replace" in a file on a Mac OS X computer. Although it appears to work correctly. It seems that the file is somehow altered. The text editor that I use (Text Wrangler) is unable to even open the file once this is completed. Here is the code as I have it: import fileinput for line in fileinput.FileInput("testfile.txt",inplace=1): line = line.replace("newhost",host) print line, When I view the file from the terminal, it does say "testfile" may be a binary file. See it anyway? Is there a chance that this replace is corrupting the file? Do I have another option for this to work? I really appreciate the help. Thank you, Aaron UPDATE: the actual file is NOT a .txt file it is a .plist file which is preference file in Mac OS X if that makes any difference

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  • Python Eggs on Google App Engine

    - by ott
    Usually I would use virtualenv and pip for deployment of web applications. With Google App Engine this doesn't work, because all import statement are relative to directory of the application. The most common approach I saw was to simply copy the packages from site-packages to the directory of the application. This involves manual work and is error-prone. Another approach was to changes install_lib and install_scripts in ~/.pydisutils.cfg, but this doesn't allow me to use pip in my home directory simultaneously. Do you have any suggestions for this?

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  • Global variables in Python

    - by rejinacm
    A global variable created in one function cannot be used in another function directly. Instead I need to store the global variable in a local variable of the function which needs its access. Am I correct? Why is it so?

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  • python logparse search specific text

    - by krisdigitx
    hi, I am using this function in my code to return the strings i want from reading the log file, I want to grep the "exim" process and return the results, but running the code gives no error, but the output is limited to three lines, how can i just get the output only related to exim process.. #output: {'date': '13', 'process': 'syslogd', 'time': '06:27:33', 'month': 'May'} {'date': '13', 'process': 'exim[23168]:', 'time': '06:27:33', 'month': 'May'} {'May': ['syslogd']} #function: def generate_log_report(logfile): report_dict = {} for line in logfile: line_dict = dictify_logline(line) print line_dict try: month = line_dict['month'] date = line_dict['date'] time = line_dict['time'] #process = line_dict['process'] if "exim" in line_dict['process']: process = line_dict['process'] break else: process = line_dict['process'] except ValueError: continue report_dict.setdefault(month, []).append(process) return report_dict

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  • use/run python's 2to3 as or like a unittest

    - by Vincent
    I have used the 2to3 utility to convert code from the command line. What I would like to do is run it basically as a unittest. Even if it tests the file rather than parts(funtions, methods...) as would be normal for a unittest. It does not need to be a unittest and I don't what to automatically convert the files I just want to monitor the py3 compliance of files in a unittest like manor. I can't seem to find any documentation or examples for this. An example and/or documentation would be great. Thanks

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