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  • Parse large XML file w/ script or use BioPython API ?

    - by jeremy04
    Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map the XML schema to the SAX parser? 2) BioPython - I already have BioSQL/Biopython installed, which literally created my SQL schema for me, and I was able to successfully insert one SwissProt/Uniprot txt file into the database. I'm running it right now (crosses fingers) on the entire 2.1gb. Here is the code I'm running: from Bio import SeqIO from BioSQL import BioSeqDatabase from Bio import SwissProt server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "root", passwd = "", host="localhost", db = "bioseqdb") db = server["uniprot"] iterator = SeqIO.parse(open("/path/to/uniprot_sprot.dat", "r"), "swiss") db.load(iterator) server.commit() Edit: it's now crashing because the transactions are getting locked (since the tables are Innodb) Error Number: 1205 Lock wait timeout exceeded; try restarting transaction. I'm using MySQL version: 5.1.43 Should I switch my database to Postgrelsql ?

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  • Mean of Sampleset and powered Sampleset

    - by Milla Well
    I am working on an ICA implementation wich is based on the assumption, that all source signals are independent. So I checked on the basic concepts of Dependence vs. Correlation and tried to show this example on sample data from numpy import * from numpy.random import * k = 1000 s = 10000 mn = 0 mnPow = 0 for i in arange(1,k): a = randn(s) a = a-mean(a) mn = mn + mean(a) mnPow = mnPow + mean(a**3) print "Mean X: ", mn/k print "Mean X^3: ", mnPow/k But I couldn't produce the last step of this example E(X^3) = 0: >> Mean X: -1.11174580826e-18 >> Mean X^3: -0.00125229267144 First value I would consider to be zero, but second value is too large, isn't it? Since I subtract the mean of a, I expected the mean of a^3 to be zero as well. Does the problem lie in the random number generator, the precision of the numerical values in my misunderstanding of the concepts of mean and expected value?

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  • better way of handling nested list

    - by laspal
    Hi, I have list my_list = [ [1,2,3,4,5,6], [1,3,4],[34,56,56,56]] for item in my_list: var1,var2,var3,var4,var5,var6 = None if len(item) ==1: var1 = item[0] if len(item) == 2: var1 = item[0] var2 = item[1] if len(item) == 3: var1 = item[0] var2 = item[1] var3 = item[2] if len(item) == 4: var1 = item[0] var2 = item[1] var3 = item[2] var4 = item[3] fun(var1,var2,var3,var4,var5,var6) I have a function def fun(var1, var2 = None, var3 = None, var4 = None, var5=None, var6= None) Depending upon the values in my inner list. I am passing it to function. I hope I made it clear. Thanks

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  • Numpy array, how to select indices satisfying multiple conditions?

    - by Bob
    Suppose I have a numpy array x = [5, 2, 3, 1, 4, 5], y = ['f', 'o', 'o', 'b', 'a', 'r']. I want to select the elements in y corresponding to elements in x that are greater than 1 and less than 5. I tried x = array([5, 2, 3, 1, 4, 5]) y = array(['f','o','o','b','a','r']) output = y[x > 1 & x < 5] # desired output is ['o','o','b','a'] but this doesn't work. How would I do this?

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  • How to disable translations during unit tests in django?

    - by Denilson Sá
    I'm using Django Internationalization tools to translate some strings from my application. The code looks like this: from django.utils.translation import ugettext as _ def my_view(request): output = _("Welcome to my site.") return HttpResponse(output) Then, I'm writing unit tests using the Django test client. These tests make a request to the view and compare the returned contents. How can I disable the translations while running the unit tests? I'm aiming to do this: class FoobarTestCase(unittest.TestCase): def setUp(self): # Do something here to disable the string translation. But what? # I've already tried this, but it didn't work: django.utils.translation.deactivate_all() def testFoobar(self): c = Client() response = c.get("/foobar") # I want to compare to the original string without translations. self.assertEquals(response.content.strip(), "Welcome to my site.")

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  • concatenate multi values in one record without duplication

    - by mikehjun
    I have a dbf table like below which is the result of one to many join from two tables. I want to have unique zone values from one Taxlot id field. table name: input table tid ----- zone 1 ------ A 1 ------ A 1 ------ B 1 ------ C 2 ------ D 2 ------ E 3 ------ C Desirable output table table name: input table tid ----- zone 1 ------ A, B, C 2 ------ D, E 3 ------ C I got some help but couldn't make it to work. inputTbl = r"C:\temp\input.dbf" taxIdZoningDict = {} searchRows = gp.searchcursor(inputTbl) searchRow = searchRows.next() while searchRow: if searchRow.TID in taxIdZoningDict: taxIdZoningDict[searchRow.TID].add(searchRow.ZONE) else: taxIdZoningDict[searchRow.TID] = set() #a set prevents dulpicates! taxIdZoningDict[searchRow.TID].add(searchRow.ZONE) searchRow = searchRows.next() outputTbl = r"C:\temp\output.dbf" gp.CreateTable_management(r"C:\temp", "output.dbf") gp.AddField_management(outputTbl, "TID", "LONG") gp.AddField_management(outputTbl, "ZONES", "TEXT", "", "", "20") tidList = taxIdZoningDict.keys() tidList.sort() #sorts in ascending order insertRows = gp.insertcursor(outputTbl) for tid in tidList: concatString = "" for zone in taxIdZoningDict[tid] concatString = concatString + zone + "," insertRow = insertRows.newrow() insertRow.TID = tid insertRow.ZONES = concatString[:-1] insertRows.insertrow(insertRow) del insertRow del insertRows

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  • Diminishing programmer wants to get back to programming

    - by Marcus TV
    I last programmed actively in 2002. It is almost 8 years now. I learned C and then moved to Visual Basic for our thesis project in the university. I would like to ask suggestions on what programming language should I learn and put to profitability use in areas such as desktop applications, web development, and database applications.

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  • Get the path to Django itself

    - by andybak
    I've got some code that runs on every (nearly) every admin request but doesn't have access to the 'request' object. I need to find the path to Django installation. I could do: import django django_path = django.__file__ but that seems rather wasteful in the middle of a request. Does putting the import at the start of the module waste memory? I'm fairly sure I'm missing an obvious trick here.

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  • how to create multiple selections in text edit box in qt4?

    - by Ronny
    Qt3.3 used to allow for multiple selections in the QTextEdit widget by calling the setSelection() function and specifying a different selection id (selNum) as the last argument in that function. In Qt4, to create a selection, I do it by creating a QTextCursor object and call the setPosition() or movePosition() methods. I have no problems being able to create a single selection of text. I am, however, unable to find a way to create multiple selections. The methods in Qt4 do not have an argument which allows you to set a selection id, nor can i find any other function in the QTextCursor or QTextEdit which looks like it might allow me to do so. Has this feature been completely removed from Qt4? or has is there a new and different way of doing it? Thanks. Ronny

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  • SQLAlchemy autocommiting?

    - by muckabout
    I have an issue with SQLAlchemy apparently committing. A rough sketch of my code: trans = self.conn.begin() try: assert not self.conn.execute(my_obj.__table__.select(my_obj.id == id)).first() self.conn.execute(my_obj.__table__.insert().values(id=id)) assert not self.conn.execute(my_obj.__table__.select(my_obj.id == id)).first() except: trans.rollback() raise I don't commit, and the second assert always fails! In other words, it seems the data is getting inserted into the database even though the code is within a transaction! Is this assessment accurate?

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  • Threaded Django task doesn't automatically handle transactions or db connections?

    - by Gabriel Hurley
    I've got Django set up to run some recurring tasks in their own threads, and I noticed that they were always leaving behind unfinished database connection processes (pgsql "Idle In Transaction"). I looked through the Postgres logs and found that the transactions weren't being completed (no ROLLBACK). I tried using the various transaction decorators on my functions, no luck. I switched to manual transaction management and did the rollback manually, that worked, but still left the processes as "Idle". So then I called connection.close(), and all is well. But I'm left wondering, why doesn't Django's typical transaction and connection management work for these threaded tasks that are being spawned from the main Django thread?

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  • find whether the string starts and ends with the same word

    - by Ajax
    I am trying to check whether the string starts and ends with the same word. egearth. s=raw_input(); m=re.search(r"^(earth).*(earth)$",s) if m is not None: print "found" my problem is when the string consists only of one word eg: earth At present I have hard coded this case by if m is not None or s=='earth': print "found" Is there any other way to do this? EDIT: words in a string are separated by spaces. looking for a regex solution some examples: "earth is earth" ,"earth", -- valid "earthearth", "eartheeearth", "earth earth mars" -- invalid

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  • How can I configure different worker pools using celery?

    - by Chris R
    I need to deploy a queued execution service with (generally) the following three classes of worker: A periodic, low-priority job class that takes a long time and can be processed serially; these jobs should only use 0..2 workers in the system at most. A periodic, deadline-sensitive job class that take a short to medium amount of time (say, topping out at 5 minutes) An ad-hoc job class, that is higher priority than #1, but can interleave with #2. Any workers from class #2 that are inactive when this type of job comes in should handle it, without ever starving the pool of workers for #2 All three job classes are the same task, the only difference between them is how they're requested; they'll take the same input and generate the same output, but each one has different performance guarantees. How can I implement this using celery?

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  • Dynamically create class attributes

    - by ahojnnes
    Hi, I need to dynamically create class attributes from a DEFAULTS dictionary. defaults = { 'default_value1':True, 'default_value2':True, 'default_value3':True, } class Settings(object): default_value1 = some_complex_init_function(defaults[default_value1], ...) default_value2 = some_complex_init_function(defaults[default_value2], ...) default_value3 = some_complex_init_function(defaults[default_value3], ...) I could also achive this by having sth. like __init__ for class creation, in order to dynamically create these attributes from dictionary and save a lot of code and stupid work. How would you do this? Thank you very much in advance!

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  • SQLAlchemy Mapping problem

    - by asdvalkn
    Dear Everyone, I am trying to sqlalchemy to correctly map my data. Note that a unified group is basically a group of groups. (One unifiedGroup maps to many groups but each group can only map to one ug). So basically this is the definition of my unifiedGroups: CREATE TABLE `unifiedGroups` ( `ugID` INT AUTO_INCREMENT, `gID` INT NOT NULL, PRIMARY KEY(`ugID`, `gID`), KEY( `gID`) ) ENGINE=MyISAM DEFAULT CHARSET=utf8 ; Note that each row is a ugID, gID tuple. ( I do not know before hand how many gID is per ugID so this is probably the most sensible and simplest method). Definition for my UnifiedGroup class class UnifiedGroup(object): """UnifiedProduct behaves very much like a group """ def __init__(self, ugID): self.ugID=ugID #Added by mapping self.groups=False def __str__(self): return '<%s:%s>' % (self.ugID, ','.join( [g for g in self.groups])) These are my mapping tables: tb_groupsInfo = Table( 'groupsInfo', metadata, Column('gID', Integer, primary_key=True), Column('gName', String(128)), ) tb_unifiedGroups = Table( 'unifiedGroups', metadata, Column('ugID', Integer, primary_key=True), Column('gID', Integer, ForeignKey('groupsInfo.gID')), ) My mapper maps in the following manner: mapper( UnifiedGroup, tb_unifiedGroups, properties={ 'groups': relation( Group, backref='unifiedGroup') }) However, when I tried to do groupInstance.unifiedGroup, I am getting an empty list [], while groupInstance.unifiedGroup.groups returns me an error: AttributeError: 'InstrumentedList' object has no attribute 'groups' Traceback (most recent call last): File "Mapping.py", line 119, in <module> print p.group.unifiedGroup.groups AttributeError: 'InstrumentedList' object has no attribute 'groups' What is wrong?

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  • Optimization of Function with Dictionary and Zip()

    - by eWizardII
    Hello, I have the following function: def filetxt(): word_freq = {} lvl1 = [] lvl2 = [] total_t = 0 users = 0 text = [] for l in range(0,500): # Open File if os.path.exists("C:/Twitter/json/user_" + str(l) + ".json") == True: with open("C:/Twitter/json/user_" + str(l) + ".json", "r") as f: text_f = json.load(f) users = users + 1 for i in range(len(text_f)): text.append(text_f[str(i)]['text']) total_t = total_t + 1 else: pass # Filter occ = 0 import string for i in range(len(text)): s = text[i] # Sample string a = re.findall(r'(RT)',s) b = re.findall(r'(@)',s) occ = len(a) + len(b) + occ s = s.encode('utf-8') out = s.translate(string.maketrans("",""), string.punctuation) # Create Wordlist/Dictionary word_list = text[i].lower().split(None) for word in word_list: word_freq[word] = word_freq.get(word, 0) + 1 keys = word_freq.keys() numbo = range(1,len(keys)+1) WList = ', '.join(keys) NList = str(numbo).strip('[]') WList = WList.split(", ") NList = NList.split(", ") W2N = dict(zip(WList, NList)) for k in range (0,len(word_list)): word_list[k] = W2N[word_list[k]] for i in range (0,len(word_list)-1): lvl1.append(word_list[i]) lvl2.append(word_list[i+1]) I have used the profiler to find that it seems the greatest CPU time is spent on the zip() function and the join and split parts of the code, I'm looking to see if there is any way I have overlooked that I could potentially clean up the code to make it more optimized, since the greatest lag seems to be in how I am working with the dictionaries and the zip() function. Any help would be appreciated thanks!

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  • Django: where do I call settings.configure?

    - by RexE
    The Django docs say that I can call settings.configure instead of having a DJANGO_SETTINGS_MODULE. I would like my website's project to do this. In what file should I put the call to settings.configure so that my settings will get configured at the right time? Edit in response to Daniel Roseman's comment: The reason I want to do this is that settings.configure lets you pass in the settings variables as a kwargs dict, e.g. {'INSTALLED_APPS': ..., 'TEMPLATE_DIRS': ..., ...}. This would allow my app's users to specify their settings in a dict, then pass that dict to a function in my app that augments it with certain settings necessary to make my app work, e.g. adding entries to INSTALLED_APPS. What I envision looks like this. Let's call my app "rexe_app". In wsgi.py, my app's users would do: import rexe_app my_settings = {'INSTALLED_APPS': ('a','b'), ...} updated_settings = rexe_app.augment_settings(my_settings) # now updated_settings is {'INSTALLED_APPS': ('a','b','c'), 'SESSION_SAVE_EVERY_REQUEST': True, ...} settings.configure(**updated_settings)

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  • Elegant Disjunctive Normal Form in Django

    - by Mike
    Let's say I've defined this model: class Identifier(models.Model): user = models.ForeignKey(User) key = models.CharField(max_length=64) value = models.CharField(max_length=255) Each user will have multiple identifiers, each with a key and a value. I am 100% sure I want to keep the design like this, there are external reasons why I'm doing it that I won't go through here, so I'm not interested in changing this. I'd like to develop a function of this sort: def get_users_by_identifiers(**kwargs): # something goes here return users The function will return all users that have one of the key=value pairs specified in **kwargs. Here's an example usage: get_users_by_identifiers(a=1, b=2) This should return all users for whom a=1 or b=2. I've noticed that the way I've set this up, this amounts to a disjunctive normal form...the SQL query would be something like: SELECT DISTINCT(user_id) FROM app_identifier WHERE (key = "a" AND value = "1") OR (key = "b" AND value = "2") ... I feel like there's got to be some elegant way to take the **kwargs input and do a Django filter on it, in just 1-2 lines, to produce this result. I'm new to Django though, so I'm just not sure how to do it. Here's my function now, and I'm completely sure it's not the best way to do it :) def get_users_by_identifiers(**identifiers): users = [] for key, value in identifiers.items(): for identifier in Identifier.objects.filter(key=key, value=value): if not identifier.user in users: users.append(identifier.user) return users Any ideas? :) Thanks!

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