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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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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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  • 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 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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  • re.sub emptying list

    - by jmau5
    def process_dialect_translation_rules(): # Read in lines from the text file specified in sys.argv[1], stripping away # excess whitespace and discarding comments (lines that start with '##'). f_lines = [line.strip() for line in open(sys.argv[1], 'r').readlines()] f_lines = filter(lambda line: not re.match(r'##', line), f_lines) # Remove any occurances of the pattern '\s*<=>\s*'. This leaves us with a # list of lists. Each 2nd level list has two elements: the value to be # translated from and the value to be translated to. Use the sub function # from the re module to get rid of those pesky asterisks. f_lines = [re.split(r'\s*<=>\s*', line) for line in f_lines] f_lines = [re.sub(r'"', '', elem) for elem in line for line in f_lines] This function should take the lines from a file and perform some operations on the lines, such as removing any lines that begin with ##. Another operation that I wish to perform is to remove the quotation marks around the words in the line. However, when the final line of this script runs, f_lines becomes an empty lines. What happened? Requested lines of original file: ## English-Geek Reversible Translation File #1 ## (Moderate Geek) ## Created by Todd WAreham, October 2009 "TV show" <=> "STAR TREK" "food" <=> "pizza" "drink" <=> "Red Bull" "computer" <=> "TRS 80" "girlfriend" <=> "significant other"

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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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  • 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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  • 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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  • How can I load an MP3 or similar music file for display and analysis in wxWidgets?

    - by Jon Cage
    I'm developing a GUI in wxPython which allows a user to generate sequences of colours for some toys I'm building. Part of the program needs to load an MP3 (and potentially other formats further down the line) and display it to the user. That should be sufficient to get started but later I'd like to add features like identifying beats and some crude frequency analysis. Is there any simple way of loading / understanding an MP3's contents to display a plot of its amplitudes to the screen using wxWidgets? I later intend to port to C++/wxWidgets for speed and to avoid having to distribute wxPython.

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