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  • String manipulation appears to be inefficient

    - by user2964780
    I think my code is too inefficient. I'm guessing it has something to do with using strings, though I'm unsure. Here is the code: genome = FASTAdata[1] genomeLength = len(genome); # Hash table holding all the k-mers we will come across kmers = dict() # We go through all the possible k-mers by index for outer in range (0, genomeLength-1): for inner in range (outer+2, outer+22): substring = genome[outer:inner] if substring in kmers: # if we already have this substring on record, increase its value (count of num of appearances) by 1 kmers[substring] += 1 else: kmers[substring] = 1 # otherwise record that it's here once This is to search through all substrings of length at most 20. Now this code seems to take pretty forever and never terminate, so something has to be wrong here. Is using [:] on strings causing the huge overhead? And if so, what can I replace it with? And for clarity the file in question is nearly 200mb, so pretty big.

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  • I have a tab delimeted file that I want to convert into a mysql table

    - by user320835
    I have a tab delimeted file that I want to convert into a mysql table. there are 25 tab delimeted fields in the text file. I can get the values in when I construct the SQL statement word by word and get each value individually stated in the VALUES part but when I try to get the list as a whole it does not work. Here is the code. I couldn't figure it out. Any ideas? lines=open(path, "r").readlines() for line in lines[1:]: linex=line.strip().split("\t") linex.insert(0,'sometextindex') try: cursor.execute('INSERT INTO variants VALUES(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)',linex) except: print 'line number=',a,linex

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  • Interpreter more strict

    - by pacopepe
    Hi, Today, i lost a lot of time fixing a stupid error in my code. Very simplified, the problem was this: def f(): return 2 2 == f I forgot to write the parenthesis in the sentence, so I compared a pointer function with a number. Ok, my question: Is there any way to change the interpreter to be more stricted with the code? Show more warnings for example... Thanks ^^

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  • Remove substring from a string

    - by xRobot
    I want to remove the first characters from a string. Is there a function that work like this ?: . a = "BarackObama" print myfunction(4,a) "ckObama" b = "The world is mine" print myfunction(6,b) "rld is mine"

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  • Changes to multiple entities within a single transaction

    - by Nati
    Hy, I am trying to make changes to multiple entities within a single transaction in app engine platform. As I understand in order to succeed doing so, App Engine needs to know in advance which entities will be updated together, so it knows to store them in a way that supports transactions. And therefore, user must declare that an entity belongs to the same entity group as another entity when you create the entity. How do I declare that one entity belongs to another entity group in creation time? Thanks, Nati

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  • name of the class that contains the method code

    - by kdlp
    I'm trying to find the name of the class that contains method code. In the example underneath I use self.__class__.__name__, but of course this returns the name of the class of which self is an instance and not class that contains the test() method code. b.test() will print 'B' while I would like to get 'A'. I looked into the inspect module documentation but did not find anything directly useful. class A: def __init__(self): pass def test(self): print self.__class__.__name__ class B(A): def __init__(self): A.__init__(self) a = A() b = B() a.test() b.test()

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  • Is it me or is pygame.key.get_pressed() not working?

    - by user1321527
    okay, so I am making a basic space-ship game. I can't get rotation to work because it scrambles the bitmap, but that's for another question.Should I even use a gif? any other filetype suggestions? back to the actual point here, so: k = pygame.key.get_pressed() yeah, self explanatory. this doesn't work, as it returns each key as pressed. so, somewhere else: d = k[pygame.K_d] and another line: print d and another: if d: So, k returns as each key on the keyboard pressed. d returns 0 indefinitely, whether or not d is pressed. d is always 0. the statement about d therefore is never true. Why is this happening?

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  • I can't upload a file with CGIHTTPServer

    - by sdemingo
    Hi all, I'm using the CGIHTTPServer to implement a simple cgi server. I'm trying to upload a file by a form with the post method and the multipart/form-data enctype but I have problems when I recover the value of the fields in the cgi script. When the script catch the form fields, the value of the file is a MiniFieldStorage with two fields only (key and file name), and I can't recover the content of the file. As the API doc shows, this content is in value field of a StorageField but in the MiniFieldStorage this field isn't exits. ¿How can I recover a StorageField with the content of the file instead a MiniStorageField? ¿There are other method to upload a file using CGIHTTPServer? Thanks a lot

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  • Check exact match of a word in a list of words

    - by Flake
    I want to check if a word is in a list of words. word = "with" word_list = ["without", "bla", "foo", "bar"] I tried if word in set(list), but it is not yielding the wanted result due to the fact in is matching string rather than item. That is to say, "with" is a match in any of the words in the word_list but still if "with" in set(list) will say True. What is a simpler way for doing this check than manually iterate over the list?

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  • Should I use `import os.path` or `import os`?

    - by Denilson Sá
    According to the official documentation, os.path is a module. Thus, what is the preferred way of importing it? # Should I always import it explicitly? import os.path Or... # Is importing os enough? import os Please DON'T answer "importing os works for me". I know, it works for me too right now. What I want to know is any official recommendation about this issue. So, if you answer this question, please post your references.

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  • trying to work through a list in sections

    - by user1714887
    I have a list of lists sorted by the second value of the list (the groups). I now need to iterate through this to work on each "group" at a time. the data is [name, group, data1, data2, data3, data4]. I wasn't sure if I need a while or some other sort of loop, or maybe groupby but I've never used that. any help would be appreciated. for i in range (int(max_group)): x1 = [] x2 = [] x3 = [] x4 = [] if data[i][1] == i+1: x1.append(data[2]) x2.append(data[3]) x3.append(data[4]) x4.append(data[5]) print x1 print 'next' # these are just to test where we're at

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  • app-engine-rest-server to raise KeyError("name %s already used" % model_name)

    - by fx
    I'm playing with the project appengine-rest-server to create the REST webservices for all the existing models. I got a strange error, the first time I query the browser: http://localhost:8080/rest/metadata/user, it gives me the result: <xs:schema> - <xs:element name="user"> - <xs:complexType> - <xs:sequence> <xs:element maxOccurs="1" minOccurs="0" name="key" type="xs:normalizedString"/> <xs:element maxOccurs="1" minOccurs="0" name="surname" type="xs:string"/> <xs:element maxOccurs="1" minOccurs="0" name="firstname" type="xs:string"/> <xs:element maxOccurs="1" minOccurs="0" name="ages" type="xs:long"/> <xs:element maxOccurs="1" minOccurs="0" name="sex" type="xs:boolean"/> <xs:element maxOccurs="1" minOccurs="0" name="updatedDate" type="xs:dateTime"/> <xs:element maxOccurs="1" minOccurs="0" name="createdDate" type="xs:dateTime"/> </xs:sequence> </xs:complexType> </xs:element> </xs:schema> But refreshing the page, gives me this error: Traceback (most recent call last): File "/Users/foo/Documents/AppEngine/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/tools/dev_appserver.py", line 3185, in _HandleRequest self._Dispatch(dispatcher, self.rfile, outfile, env_dict) File "/Users/foo/Documents/AppEngine/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/tools/dev_appserver.py", line 3128, in _Dispatch base_env_dict=env_dict) File "/Users/foo/Documents/AppEngine/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/tools/dev_appserver.py", line 515, in Dispatch base_env_dict=base_env_dict) File "/Users/foo/Documents/AppEngine/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/tools/dev_appserver.py", line 2387, in Dispatch self._module_dict) File "/Users/foo/Documents/AppEngine/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/tools/dev_appserver.py", line 2297, in ExecuteCGI reset_modules = exec_script(handler_path, cgi_path, hook) File "/Users/foo/Documents/AppEngine/GoogleAppEngineLauncher.app/Contents/Resources/GoogleAppEngine-default.bundle/Contents/Resources/google_appengine/google/appengine/tools/dev_appserver.py", line 2195, in ExecuteOrImportScript script_module.main() File "/Users/foo/Documents/AppEngine/helloworld/main.py", line 48, in main rest.Dispatcher.add_models({"user": UserModel}) File "/Users/foo/Documents/AppEngine/helloworld/rest/__init__.py", line 845, in add_models cls.add_model(model_name, model_type) File "/Users/foo/Documents/AppEngine/helloworld/rest/__init__.py", line 863, in add_model raise KeyError("name %s already used" % model_name) KeyError: 'name user already used' Can someone give me the explanation on why it happens? Restarting the server, run on the browser again I get the xml result, but refreshing causes the error. Is it a bug in the appengine-rest-server application or it is in my code? My helloworld application is available for download here.

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  • Named pipe is using 100% CPU

    - by willwill
    I'm starting the script with ./file.py < pipe >> logfile and the script is: while True: try: I = raw_input().strip().split() except EOFError: continue doSomething() How could I better handle named pipe? This script always run at 100% CPU and it need to be real-time so I cannot use time.sleep.

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  • Mako "Missing parentheses in %def"

    - by michaelmior
    In trying to add a cached section to a Mako template, I get the error listed in the above question. Adding () to the end gets rid of the error, but I see no content on my page. Any help is appreciated! <%def name="test" cached="True" cache_timeout="60" cache_type="file"> Test /%def>

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  • How do you know where macports installs python packages to?

    - by xmaslist
    I am running macports to install scipy and such on OS X leopard with python 2.7. The install runs successfully, but running python and trying to import the packages I've installed, they're not found. What I'm running is: sudo python_select python27 sudo port install py27-wxpython py27-numpy py27-matplotlib sudo port install py27-scipy py27-ipython Opening up python in interactive mode (it is the correct version of python), I type 'import scipy' and get a module not found error. What gives? How can I find out where it is installing the packages to instead?

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  • Why is Python 3.1.3 in the header listed as a syntax error?

    - by squashua
    Hi, I'm a newbie programmer so I'll do my best to clearly ask my question. I'm running Python scripts in Mac 10.6.5 and now trying to write and save to a text file (following instructions in HeadsUp Python book). Whenever I hit function+F5 (as instructed) I get the same "invalid syntax" error and Idle highlights the "1" in "Python 3.1.3" of the header. Here's the header to which I'm referring: Python 3.1.3 (r313:86882M, Nov 30 2010, 09:55:56) [GCC 4.0.1 (Apple Inc. build 5494)] on darwin Type "copyright", "credits" or "license()" for more information. Extremely frustrating. I've checked and rechecked the code but this doesn't seem to be code related because the "syntax error" is in regards to the header text that posts in every Idle/Python session. Help anyone? Thanks, Squash

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  • Animate and form rows, arrays, AS3

    - by VideoDnd
    Question How can I animate and form rows together? Explanation One 'for loop' is for animation, the other 'for loop' is for making rows. I want to understand how to use arrays and create a row of sprite animations. 'for loop' for animation //FRAMES ARRAY //THIS SETS UP MY ANIMATION FOR TIMER EVENT var frames:Array = [ new Frame1(), new Frame2(), new Frame3(), new Frame4(), new Frame5(), new Frame6(), new Frame7(), new Frame8(), new Frame9(), new Frame0(), ]; for each (var frame:Sprite in frames) { addChild(frame); } 'for loop' for rows //THIS MAKES A ROW OF DISPLAY OBJECTS var numberOfClips:Number = 11; var xStart:Number = 0; var yStart:Number = 0; var xVal:Number = xStart; var xOffset:Number = 2; for (var $:Number=0; $<numberOfClips; $++) { //DUDE ARRAY var dude:Array = frames; dude.y = yStart +11; dude.x = xVal +55; xVal = dude.x + dude.width + this.xOffset; } timer var timer:Timer = new Timer(100); timer.addEventListener(TimerEvent.TIMER, countdown); function countdown(event:TimerEvent) { var currentFrame:int = timer.currentCount % frames.length; for (var i:int = 0; i < frames.length; ++i) { frames[i].visible = (i == currentFrame); } } timer.start(); counter experiment My new class I'm working on loops through 10 different display objects that are numbers. For those following, I'm trying to make something like NumbersView.

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  • Setting up OpenGL camera with off-center perspective

    - by user5484
    Hi, I'm using OpenGL ES (in iOS) and am struggling with setting up a viewport with an off-center distance point. Consider a game where you have a character in the left hand side of the screen, and some controls alpha'd over the left-hand side. The "main" part of the screen is on the right, but you still want to show whats in the view on the left. However when the character moves "forward" you want the character to appear to be going "straight", or "up" on the device, and not heading on an angle to the point that is geographically at the mid-x position in the screen. Here's the jist of how i set my viewport up where it is centered in the middle: // setup the camera // glMatrixMode(GL_PROJECTION); glLoadIdentity(); const GLfloat zNear = 0.1; const GLfloat zFar = 1000.0; const GLfloat fieldOfView = 90.0; // can definitely adjust this to see more/less of the scene GLfloat size = zNear * tanf(DEGREES_TO_RADIANS(fieldOfView) / 2.0); CGRect rect; rect.origin = CGPointMake(0.0, 0.0); rect.size = CGSizeMake(backingWidth, backingHeight); glFrustumf(-size, size, -size / (rect.size.width / rect.size.height), size / (rect.size.width / rect.size.height), zNear, zFar); glMatrixMode(GL_MODELVIEW); // rotate the whole scene by the tilt to face down on the dude const float tilt = 0.3f; const float yscale = 0.8f; const float zscale = -4.0f; glTranslatef(0.0, yscale, zscale); const int rotationMinDegree = 0; const int rotationMaxDegree = 180; glRotatef(tilt * (rotationMaxDegree - rotationMinDegree) / 2, 1.0f, 0.0f, 0.0f); glTranslatef(0, -yscale, -zscale); static float b = -25; //0; static float c = 0; // rotate by to face in the direction of the dude float a = RADIANS_TO_DEGREES(-atan2f(-gCamera.orientation.x, -gCamera.orientation.z)); glRotatef(a, 0.0, 1.0, 0.0); // and move to where it is glTranslatef(-gCamera.pos.x, -gCamera.pos.y, -gCamera.pos.z); // draw the rest of the scene ... I've tried a variety of things to make it appear as though "the dude" is off to the right: - do a translate after the frustrum to the x direction - do a rotation after the frustrum about the up/y-axis - move the camera with a biased lean to the left of the dude Nothing i do seems to produce good results, the dude will either look like he's stuck on an angle, or the whole scene will appear tilted. I'm no OpenGL expert, so i'm hoping someone can suggest some ideas or tricks on how to "off-center" these model views in OpenGL. Thanks!

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  • Is there any reason to use C++ instead of C, Perl, Python, etc.?

    - by Ehsan
    As a Linux (server side) developer, I don't know where and why should I use C++. When I'm going to performance, the first and last choice is C. When "performance" isn't the main issue, programming languages like Perl and Python would be good choices. Almost all of open source applications I know in this area has been written in C, Perl and Python, Bash script, AWK and even PHP, but no one goes to use C++. I'm not discussing about some other areas like GUI or web application, I'm just talking about Linux and about CLI and daemons. Is there any satisfiable reason to use C++?

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  • Sortie de la quatrième beta de PySide 1.0.0, le binding Python de Qt : corrections de bogues et exécutable Windows au menu

    Sortie de PySide 1.0.0 beta 3 Elle corrige 35 bogues qualifiés de haute priorité du binding Python pour le framework Qt Par Jiyuu et dourouc05 le 07/01/2010 Nokia vient d'annoncer la sortie de la troisième beta de son binding Python du framework Qt. Cette nouvelle beta est principalement considérée comme une version de maintenance, corrigeant trente-cinq bogues de la deuxième beta, ces bogues étant qualifiés de haute priorité. Des versions corrigées de apiextractor, shiboken et libpyside, partie de la chaîne d'outils servant à la génération du binding, sont aussi disponibles. Actuellement, seule les sources de cette version sont disponibles ; des versions binaires devraient être d...

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