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  • failure on creating a Scikits.TimeSeries object

    - by user311906
    Hi All I am trying to create a scikit.timeseries object starting from 2 datetime objects. If I understood correctly it should be possible to create a scikits.timeseries starting from datetime objects. I try the following code but it says that Insufficient parameters. The 2 datetime differs for few microseconds. In this case what should be the value for freq parameter? Is what I am trying allowed? In theory, since timeseries can be based on datetime objects it should be possible to hanlde up to microsecond , is this correct? I think that this is not really clear to me. Regards Eo import datetime import sckilits.timeseries as ts tm1 = datetime.datetime( 2010,1,1, 10,10,2, 123456 ) tm2 = datetime.datetime( 2010,1,1, 10,10,2, 345678 ) d = [ tm1, tm2 ] tseries = ts.time_series( dates=d ) tseries = ts.time_series( d )

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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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  • Differentiate gtk.Entry icons

    - by Ubersoldat
    I'm adding two icons to a gtk.Entry in PyGTK. The icons signals are handled by the following method def entry_icon_event(self, widget, position, event) I'm trying to differentiate between the two of them: <enum GTK_ENTRY_ICON_PRIMARY of type GtkEntryIconPosition> <enum GTK_ENTRY_ICON_SECONDARY of type GtkEntryIconPosition> How can I do this? I've been digging through the documentation of PyGTK but there's no object GtkEntryIconPosition nor any definition for this enums. Thanks

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  • combine lines from 2 prints to single line and insert into mysql database

    - by bleomycin
    Hello everyone i currently have this: import feedparser d = feedparser.parse('http://store.steampowered.com/feeds/news.xml') for i in range(10): print d.entries[i].title print d.entries[i].date How would i go about making it so that the title and date are on the same line? Also it doesn't need to print i just have that in there for testing, i would like to dump this output into a mysql db with the title and date, any help is greatly appreciated!

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  • How to check wether a path represented by a QString with german umlauts exists?

    - by MB
    Hey, i get a QString which represents a directory from a QLineEdit. Now i want to check wether a certain file exists in this directory. But if i try this with os.path.exists and os.path.join and get in trouble when german umlauts occur in the directory path: #the direcory coming from the user input in the QLineEdit #i take this QString to the local 8-Bit encoding and then make #a string from it target_dir = str(lineEdit.text().toLocal8Bit()) #the file name that should be checked for file_name = 'some-name.txt' #this fails with a UnicodeDecodeError when a umlaut occurs in target_dir os.path.exists(os.path.join(target_dir, file_name)) How would you check if the file exists, when you might encounter german umlauts?

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  • convert an int to list of individual digitals more faster?

    - by user478514
    All, I want define an int(987654321) <= [9, 8, 7, 6, 5, 4, 3, 2, 1] convertor, if the length of int number < 9, for example 10 the list will be [0,0,0,0,0,0,0,1,0] , and if the length 9, for example 9987654321 , the list will be [9, 9, 8, 7, 6, 5, 4, 3, 2, 1] >>> i 987654321 >>> l [9, 8, 7, 6, 5, 4, 3, 2, 1] >>> z = [0]*(len(unit) - len(str(l))) >>> z.extend(l) >>> l = z >>> unit [100000000, 10000000, 1000000, 100000, 10000, 1000, 100, 10, 1] >>> sum([x*y for x,y in zip(l, unit)]) 987654321 >>> int("".join([str(x) for x in l])) 987654321 >>> l1 = [int(x) for x in str(i)] >>> z = [0]*(len(unit) - len(str(l1))) >>> z.extend(l1) >>> l1 = z >>> l1 [9, 8, 7, 6, 5, 4, 3, 2, 1] >>> a = [i//x for x in unit] >>> b = [a[x] - a[x-1]*10 for x in range(9)] >>> if len(b) = len(a): b[0] = a[0] # fix the a[-1] issue >>> b [9, 8, 7, 6, 5, 4, 3, 2, 1] I tested above solutions but found those may not faster/simple enough than I want and may have a length related bug inside, anyone may share me a better solution for this kinds convertion? Thanks!

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  • Where is the help.py for Android's monkeyrunner

    - by Keyboardsurfer
    Hi, I just can't find the help.py file in order to create the API reference for the monkeyrunner. The command described at the Android references monkeyrunner <format> help.py <outfile> does not work when i call monkeyrunner html help.py /path/to/place/the/doc.html. It's quite obvious that the help.py file is not found and the monkeyrunner also tells me "Can't open specified script file". But a locate on my system doesn't bring me a help.py file that has anything to do with monkeyrunner or Android. So my question is: Where did they hide the help.py file for creating the API reference?

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  • django url matching

    - by ben
    can anyone see why this wouldn't be working. Fairly new to django so any help would be much appreciated actual url: http://127.0.0.1:8000/2010/may/12/my-second-blog-post/ urls.py: (r'(?P<year>d{4})/(?P<month>[a-z]{3})/(?P<day>w{1,2})/(?P<slug>[-w]+)/$', 'object_detail', dict(info_dict, slug_field='slug',template_name='blog/detail.html')),

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  • how to let the parser print help message rather than error and exit

    - by fluter
    Hi, I am using argparse to handle cmd args, I wanna if there is no args specified, then print the help message, but now the parse will output a error, and then exit. my code is: def main(): print "in abing/start/main" parser = argparse.ArgumentParser(prog="abing")#, usage="%(prog)s <command> [args] [--help]") parser.add_argument("-v", "--verbose", action="store_true", default=False, help="show verbose output") subparsers = parser.add_subparsers(title="commands") bkr_subparser = subparsers.add_parser("beaker", help="beaker inspection") bkr_subparser.set_defaults(command=beaker_command) bkr_subparser.add_argument("-m", "--max", action="store", default=3, type=int, help="max resubmit count") bkr_subparser.add_argument("-g", "--grain", action="store", default="J", choices=["J", "RS", "R", "T", "job", "recipeset", "recipe", "task"], type=str, help="resubmit selection granularity") bkr_subparser.add_argument("job_ids", nargs=1, action="store", help="list of job id to be monitored") et_subparser = subparsers.add_parser("errata", help="errata inspection") et_subparser.set_defaults(command=errata_command) et_subparser.add_argument("-w", "--workflows", action="store_true", help="generate workflows for the erratum") et_subparser.add_argument("-r", "--run", action="store_true", help="generate workflows, and run for the erratum") et_subparser.add_argument("-s", "--start-monitor", action="store_true", help="start monitor the errata system") et_subparser.add_argument("-d", "--daemon", action="store_true", help="run monitor into daemon mode") et_subparser.add_argument("erratum", action="store", nargs=1, metavar="ERRATUM", help="erratum id") if len(sys.argv) == 1: parser.print_help() return args = parser.parse_args() args.command(args) return how can I do that? thanks.

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  • Which class should store the lookup table?

    - by max
    The world contains agents at different locations, with only a single agent at any location. Each agent knows where he's at, but I also need to quickly check if there's an agent at a given location. Hence, I also maintain a map from locations to agents. I have a problem deciding where this map belongs to: class World, class Agent (as a class attribute) or elsewhere. In the following I put the lookup table, agent_locations, in class World. But now agents have to call world.update_agent_location every time they move. This is very annoying; what if I decide later to track other things about the agents, apart from their locations - would I need to add calls back to the world object all across the Agent code? class World: def __init__(self, n_agents): # ... self.agents = {} self.agent_locations = {} for id in range(n_agents): x, y = self.find_location() agent = Agent(self,x,y) self.agents.append(agent) self.agent_locations[x,y] = agent def update_agent_location(self, agent, x, y): del self.agent_locations[agent.x, agent.y] self.agent_locations[x, y] = agent def update(self): # next step in the simulation for agent in self.agents: agent.update() # next step for this agent # ... class Agent: def __init__(self, world, x, y): self.world = world self.x, self.y = x, y def move(self, x1, y1): self.world.update_agent_location(self, x1, y1) self.x, self.y = x1, y1 def update(): # find a good location that is not occupied and move there for x, y in self.valid_locations(): if not self.location_is_good(x, y): continue if self.world.agent_locations[x, y]: # location occupied continue self.move(x, y) I can instead put agent_locations in class Agent as a class attribute. But that only works when I have a single World object. If I later decide to instantiate multiple World objects, the lookup tables would need to be world-specific. I am sure there's a better solution... EDIT: I added a few lines to the code to show how agent_locations is used. Note that it's only used from inside Agent objects, but I don't know if that would remain the case forever.

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  • How refresh a DrawingArea in PyGTK ?

    - by Lialon
    I have an interface created with Glade. It contains a DrawingArea and buttons. I tried to create a Thread to refresh every X time my Canva. After a few seconds, I get error messages like: "X Window Server 0.0", "Fatal Error IO 11" Here is my code : import pygtk pygtk.require("2.0") import gtk import Canvas import threading as T import time import Map gtk.gdk.threads_init() class Interface(object): class ThreadCanvas(T.Thread): """Thread to display the map""" def __init__(self, interface): T.Thread.__init__(self) self.interface = interface self.started = True self.start() def run(self): while self.started: time.sleep(2) self.interface.on_canvas_expose_event() def stop(self): self.started = False def __init__(self): self.interface = gtk.Builder() self.interface.add_from_file("interface.glade") #Map self.map = Map.Map(2,2) #Canva self.canvas = Canvas.MyCanvas(self.interface.get_object("canvas"),self.game) self.interface.connect_signals(self) #Thread Canvas self.render = self.ThreadCanvas(self) def on_btnChange_clicked(self, widget): #Change map self.map.change() def on_interface_destroy(self, widget): self.render.stop() self.render.join() self.render._Thread__stop() gtk.main_quit() def on_canvas_expose_event(self): st = time.time() self.canvas.update(self.map) et = time.time() print "Canvas refresh in : %f times" %(et-st) def main(self): gtk.main() How can i fix these errors ?

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  • Selenium selected option in dropdown not displayed correctly

    - by luckyfool
    I have the following issue with Selenium Webdriver. There are two dropdown menus on a page i am testing "brand" and "items". The options of "items" depend on which brand you choose. I am trying to iterate through all possible choices and print brand-item pairs. I use two possible ways to pick an option from each dropdown menu Using Select(): def retryingSelectOption(name,n): result=False attempts=0 while attempts<5: try: element=Select(driver.find_element_by_name(name)) element.select_by_index(n) print element.all_selected_options[0].text result=True break except StaleElementReferenceException: pass attempts+=1 return result And using .click(): def retryingClickOption(name,n): result=False attempts=0 while attempts<5: try: driver.find_element_by_name(name).find_elements_by_tag_name("option")[n].click() result=True break except StaleElementReferenceException: pass attempts+=1 return result My problem is that at ,what seem to me as random moments (sometimes it works sometimes it does not), even though the above functions return True and printing out the selected option shows me the correct answer, the browser still displays the previous option. So basically Selenium tells me i have picked the right option but the browser displays the previous one.No idea what is wrong.

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  • Problem opening Solr *.jsp pages with urllib2.urlopen.

    - by nestling
    I'm trying to open a page at http://localhost:8983/solr/admin/stats.jsp but urllib2.urlopen returns a blank string. It works fine for solr/ and solr/admin, but for all the pages above /solr/admin/ I get nothing but a blank string. 76]: t = urllib2.urlopen('http://localhost:8983/solr/admin/stats.jsp') 77]: s = t.read() 78]: s 78]: 79]: type(s) 79]: <type 'str'> 80]: urllib2.urlopen('http://localhost:8983/solr/admin/registry.jsp').read() 80]: In [84]: urllib2.urlopen('http://localhost:8983/solr/admin/schema.jsp').read() Out[84]: I know this isn't a problem with urllib2, but beyond that I am at a loss. I wish solr (or jetty) had an easy to get to log file, so that perhaps it could tell me its side of the story.

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  • Filter across three tables using Django

    - by Vanessa MacDougal
    I have 3 django models, where the first has a foreign key to the second, and the second has a foreign key to the third. Like this: class Book(models.Model): year_published = models.IntField() author = models.ForeignKey(Author) class Author(models.Model): author_id = models.AutoField(primary_key=True) name = models.CharField(max_length=50) agent = models.ForeignKey(LitAgent) class LitAgent(models.Model): agent_id = models.AutoField(primary_key=True) name = models.CharField(max_length=50) I want to ask for all the literary agents whose authors had books published in 2006, for example. How can I do this in Django? I have looked at the documentation about filters and QuerySets, and don't see an obvious way. 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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  • Add string to another string

    - by daemonfire300
    Hi there, I currently encountered a problem: I want to handle adding strings to other strings very efficiently, so I looked up many methods and techniques, and I figured the "fastest" method. But I quite can not understand how it actually works: def method6(): return ''.join([`num` for num in xrange(loop_count)]) From source (Method 6) Especially the ([numfor num in xrange(loop_count)]) confused me totally.

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  • How can this code be made more Pythonic?

    - by usethedeathstar
    This next part of code does exactly what I want it to do. dem_rows and dem_cols contain float values for a number of things i can identify in an image, but i need to get the nearest pixel for each of them, and than to make sure I only get the unique points, and no duplicates. The problem is that this code is ugly and as far as I get it, as unpythonic as it gets. If there would be a pure-numpy-solution (without for-loops) that would be even better. # next part is to make sure that we get the rounding done correctly, and than to get the integer part out of it # without the annoying floatingpoint-error, and without duplicates fielddic={} for i in range(len(dem_rows)): # here comes the ugly part: abusing the fact that i overwrite dictionary keys if I get duplicates fielddic[int(round(dem_rows[i]) + 0.1), int(round(dem_cols[i]) + 0.1)] = None # also very ugly: to make two arrays of integers out of the first and second part of the keys field_rows = numpy.zeros((len(fielddic.keys())), int) field_cols = numpy.zeros((len(fielddic.keys())), int) for i, (r, c) in enumerate(fielddic.keys()): field_rows[i] = r field_cols[i] = c

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  • Can this django query be improved?

    - by Hobhouse
    Given a model structure like this: class Book(models.Model): user = models.ForeignKey(User) class Readingdate(models.Model): book = models.ForeignKey(Book) date = models.DateField() One book may have several readingdates. How do I list books having at least one readingdate within a specific year? I can do this: from_date = datetime.date(2010,1,1) to_date = datetime.date(2010,12,31) book_ids = Readingdate.objects\ .filter(date__range=(from_date,to_date))\ .values_list('book_id', flat=True) books_read_2010 = Book.objects.filter(id__in=book_ids) Is it possible to do this with one queryset, or is this the best way?

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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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