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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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  • Search for a pattern in a list of strings - Python

    - by Holtz
    I have a list of strings containing filenames such as, file_names = ['filei.txt','filej.txt','filek.txt','file2i.txt','file2j.txt','file2k.txt','file3i.txt','file3j.txt','file3k.txt'] I then remove the .txt extension using: extension = os.path.commonprefix([n[::-1] for n in file_names])[::-1] file_names_strip = [n[:-len(extension)] for n in file_names] And then return the last character of each string in the list file_names_strip: h = [n[-1:] for n in file_names_strip] Which gives h = ['i', 'j', 'k', 'i', 'j', 'k', 'i', 'j', 'k'] How can i test for a pattern of strings in h? So if i,j,k occur sequentially it would return True and False if not. I need to know this because not all file names are formatted like they are in file_names. So: test_ijk_pattern(h) = True no_pattern = ['1','2','3','1','2','3','1','2','3'] test_ijk_pattern(no_pattern) = False

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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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  • 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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  • Python and hebrew encoding/decoding error

    - by user340495
    Hey, I have sqlite database which I would like to insert values in Hebrew to I am keep getting the following error : UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 0: ordinal not in range(128) my code is as following : runsql(u'INSERT into personal values(%(ID)d,%(name)s)' % {'ID':1,'name':fabricate_hebrew_name()}) def fabricate_hebrew_name(): hebrew_names = [u'????',u'???',u'???',u'???',u'????',u'???',u'????',u'???',u'????',u'?????',u'????',u'???',u'????'] return random.sample(names,1)[0].encode('utf-8') note: runsql executing the query on the sqlite database fabricate_hebrew_name() should return a string which could be used in my SQL query. any help is much appreciated.

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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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  • 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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  • 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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  • 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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  • 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 2.6 + PIL + Google App Engine issue

    - by mswallace
    I am using OS X 1.6 snow leopard and I successfully got PIL installed. I am able to open terminal and type import Image without any errors. However, When using app engine I get Image error still saying that PIL is not installed. I am wondering if any of you have an thoughts as to how I can resolve this issue. -Matthew

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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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  • python / sets / dictionary / initialization

    - by Mario D
    Can someone explain help me understand how the this bit of code works? Particularly how the myHeap assignment works. I know the freq variable is assigned as a dictionary. But what about my myHeap? is it a Set? exe_Data = { 'e' : 0.124167, 't' : 0.0969225, 'a' : 0.0820011, 'i' : 0.0768052, } freq = exe_Data) myHeap = [[pct, [symbol, ""]] for symbol, pct in freq.items()]

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  • Sending http headers with python

    - by Niklas R
    I've set up a little script that should feed a client with html. import socket sock = socket.socket() sock.bind(('', 8080)) sock.listen(5) client, adress = sock.accept() print "Incoming:", adress print client.recv(1024) print client.send("Content-Type: text/html\n\n") client.send('<html><body></body></html>') print "Answering ..." print "Finished." import os os.system("pause") But it is shown as plain text in the browser. Can you please tell what I need to do ? I just can't find something in google that helps me.. Thanks.

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  • Python:Comparing Two Dictionaries

    - by saun jean
    The first Dict is fixed.This Dict will remain as it is List of Countries with there Short Names. firstDict={'ERITREA': 'ER', 'LAOS': 'LA', 'PORTUGAL': 'PT', "D'IVOIRE": 'CI', 'MONTENEGRO': 'ME', 'NEW CALEDONIA': 'NC', 'SVALBARD AND JAN MAYEN': 'SJ', 'BAHAMAS': 'BS', 'TOGO': 'TG', 'CROATIA': 'HR', 'LUXEMBOURG': 'LU', 'GHANA': 'GH'} However This Tuple result has multiple Dict inside it.This is the format in which MySQLdb returns result: result =({'count': 1L, 'country': 'Eritrea'}, {'count': 1L, 'country': 'Togo'}, {'count': 1L, 'country': 'Sierra Leone'}, {'count': 3L, 'country': 'Bahamas'}, {'count': 1L, 'country': 'Ghana'}) Now i want to compare these both results With COUNTRY Names and If 'Country' in Result is present in firstDict then put the value.else put the 0 The result desired is: mainRes={'ER':1,'TG':1,'BS':3,'GH':0,'LU':0}

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  • Problem with dictionary key in Python

    - by Hossein
    Hi all, For some project I have to make a dictionary in which the keys are urls,among which I have this url: http://www.microsoft.com/isapi/redir.dll prd=windows&sbp=mediaplayer&ar=Media&sba=Guide&pver=6.2 the url is too long to fit in here I guess in one single line. there is a space between .dll and prd. I can build a dictionary without any errors this url is also a key. but for some reason when I want to extract the values associated to this key(url). I cannot, I get and error "error key:...." Does someone know what is wrong with this url? Are dictionary keys sensitive to some stuff? thanks

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  • Python: Created nested dictionary from list of paths

    - by sberry2A
    I have a list of tuples the looks similar to this (simplified here, there are over 14,000 of these tuples with more complicated paths than Obj.part) [ (Obj1.part1, {<SPEC>}), (Obj1.partN, {<SPEC>}), (ObjK.partN, {<SPEC>}) ] Where Obj goes from 1 - 1000, part from 0 - 2000. These "keys" all have a dictionary of specs associated with them which act as a lookup reference for inspecting another binary file. The specs dict contains information such as the bit offset, bit size, and C type of the data pointed to by the path ObjK.partN. For example: Obj4.part500 might have this spec, {'size':32, 'offset':128, 'type':'int'} which would let me know that to access Obj4.part500 in the binary file I must unpack 32 bits from offset 128. So, now I want to take my list of strings and create a nested dictionary which in the simplified case will look like this data = { 'Obj1' : {'part1':{spec}, 'partN':{spec} }, 'ObjK' : {'part1':{spec}, 'partN':{spec} } } To do this I am currently doing two things, 1. I am using a dotdict class to be able to use dot notation for dictionary get / set. That class looks like this: class dotdict(dict): def __getattr__(self, attr): return self.get(attr, None) __setattr__ = dict.__setitem__ __delattr__ = dict.__delitem__ The method for creating the nested "dotdict"s looks like this: def addPath(self, spec, parts, base): if len(parts) > 1: item = base.setdefault(parts[0], dotdict()) self.addPath(spec, parts[1:], item) else: item = base.setdefault(parts[0], spec) return base Then I just do something like: for path, spec in paths: self.lookup = dotdict() self.addPath(spec, path.split("."), self.lookup) So, in the end self.lookup.Obj4.part500 points to the spec. Is there a better (more pythonic) way to do this?

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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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  • Python meta programming question

    - by orokusaki
    I have a meta class MyClass which adds an attribute to a class based on some of the properties of the class's methods. When I subclass MyClass I want it to still have that attribute, and append to the attribute's value based on the sub-class's methods (ie, sub-classing extends the same attribute that the base's meta creates.). Can this be done via the bases argument passed to __new__(cls, name, bases, dct)?

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