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  • Loop over a file and write the next line if a condition is met

    - by 111078384259264152964
    Having a hard time fixing this or finding any good hints about it. I'm trying to loop over one file, modify each line slightly, and then loop over a different file. If the line in the second file starts with the line from the first then the following line in the second file should be written to a third file. !/usr/bin/env python with open('ids.txt', 'rU') as f: with open('seqres.txt', 'rU') as g: for id in f: id=id.lower()[0:4]+'_'+id[4] with open(id + '.fasta', 'w') as h: for line in g: if line.startswith(''+ id): h.write(g.next()) All the correct files appear, but they are empty. Yes, I am sure the if has true cases. :-) "seqres.txt" has lines with an ID number in a certain format, each followed by a line with data. The "ids.txt" has lines with the ID numbers of interest in a different format. I want each line of data with an interesting ID number in its own file. Thanks a million to anyone with a little advice!

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  • Problem building PyGTK on CentOS

    - by Marcelo Cantos
    I am trying to build PyGTK on CentOS for a non-standard Python (2.6, vs the out-of-the-box 2.4). It requires that I first build pygobject. pygobject-2.18.0 fails at the configure step. The error messages is as follows: checking for GLIB - version >= 2.14.0... no *** Could not run GLIB test program, checking why... *** The test program failed to compile or link. See the file config.log for the *** exact error that occured. This usually means GLIB is incorrectly installed. configure: error: maybe you want the pygobject-2-4 branch? I have downloaded, built and successfully installed glib. The config.log file contains the following output: configure:6893: gcc -E conftest.c conftest.c:13:28: error: ac_nonexistent.h: No such file or directory What am I doing wrong?

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  • Any implementations of graph st-ordering or ear-decomposition?

    - by chang
    I'm in the search for an implementation of an ear-decomposition algorithm (http://www.ics.uci.edu/~eppstein/junkyard/euler/ear.html). I examined networkx and didn't find one. Although the algorithm layout is vaguely in my mind, I'd like to see some reference implementation, too. I'm aware of Ulrik Brandes publication on a linear time Eager st-ordering algorithm, which results in an ear decomposition as a side product, if I understand correctly (it even includes pseudocode, which I'm trying to base my implementation on). Side problem: First step could be an st-ordering of a graph. Are there any implementations for st-ordering algorithms you know? Thanks for your input. I'd really like to contribute e.g. to networkx by implementing the ear-decomposition algorithm in python.

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  • SQLAlchemy custom sorting algorithms when using SQL indexes

    - by David M
    Is it possible to write custom collation functions with indexes in SQLAlchemy? SQLite for example allows specifying the sorting function at a C level as sqlite3_create_collation(). An implementation of some of the Unicode collation algorithm has been provided by James Tauber here, which for example sorts all the "a"'s close together whether they have accents on them or not. Other examples of why this might be useful is for different alphabet orders (languages other than English) and sorting numeric values (sorting 10 after 9 rather than codepoint order.) Is this possible in SQLAlchemy? If not, is it supported by the pysqlite3 or MySQLdb modules, or for any other SQL database modules supported by python for that matter? Any information would be greatly appreciated.

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  • How do I get the position of a result in the list after an order_by?

    - by Bob Bob
    I'm trying to find an efficient way to find the rank of an object in the database related to it's score. My naive solution looks like this: rank = 0 for q in Model.objects.all().order_by('score'): if q.name == 'searching_for_this' return rank rank += 1 It should be possible to get the database to do the filtering, using order_by: Model.objects.all().order_by('score').filter(name='searching_for_this') But there doesn't seem to be a way to retrieve the index for the order_by step after the filter. Is there a better way to do this? (Using python/django and/or raw SQL.) My next thought is to pre-compute ranks on insert but that seems messy.

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  • Database query optimization

    - by hdx
    Ok my Giant friends once again I seek a little space in your shoulders :P Here is the issue, I have a python script that is fixing some database issues but it is taking way too long, the main update statement is this: cursor.execute("UPDATE jiveuser SET username = '%s' WHERE userid = %d" % (newName,userId)) That is getting called about 9500 times with different newName and userid pairs... Any suggestions on how to speed up the process? Maybe somehow a way where I can do all updates with just one query? Any help will be much appreciated! PS: Postgres is the db being used.

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  • django templating system inheritance issue

    - by Suhail
    hi, i am having issues with my django templating system, i have a base.html file, which contains the content which will be common on all the web pages of the web site, the base.html file fetches some dynamic content, like the categories and the archives, which are passed to it by a python file, which fetches the categories and the archives data from a mysql database. the issue when i inherit this base.html file in other html files like index.html: {% extends "base.html" %} and when when i call the main index URL for ex: http://mywebsite.com/index/ the index page gets loaded, but the categories and the archives data that should get loaded from the base.html file does not. what am i doing wrong, please help.

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  • Importing Sqlite data into Google App Engine

    - by Keck
    I have a relatively extensive sqlite database that I'd like to import into my Google App Engine python app. I've created my models using the appengine API which are close, but not quite identical to the existing schema. I've written an import script to load the data from sqlite and create/save new appengine objects, but the appengine environment blocks me from accessing the sqlite library. This script is only to be run on my local app engine instance, and from there I hope to push the data to google. Am I approaching this problem the wrong way, or is there a way to import the sqlite library while running in the local instance's environment?

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  • Best data-structure to use for two ended sorted list

    - by fmark
    I need a collection data-structure that can do the following: Be sorted Allow me to quickly pop values off the front and back of the list Remain sorted after I insert a new value Allow a user-specified comparison function, as I will be storing tuples and want to sort on a particular value Thread-safety is not required Optionally allow efficient haskey() lookups (I'm happy to maintain a separate hash-table for this though) My thoughts at this stage are that I need a priority queue and a hash table, although I don't know if I can quickly pop values off both ends of a priority queue. I'm interested in performance for a moderate number of items (I would estimate less than 200,000). Another possibility is simply maintaining an OrderedDictionary and doing an insertion sort it every-time I add more data to it. Furthermore, are there any particular implementations in Python. I would really like to avoid writing this code myself.

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  • Image Processing, joining the small images to form the main image

    - by n0idea
    Good morning everyone, Actually I'm having a small issue in image processing and I'm in need of some help. First of all, let me explain what i want to do, i have an image that was split into 4 other small images. I currently have like 6 small images that i need to figure out which ones are part of the real image. Second, what i currently know is that that i should compare these images edges or last column with the first column of the other image. I'm not sure yet what exactly should be done, anyone is able to put me on the same tracks, with some detailed hints and how to compare the edges of 2 images. Some links and example codes will be help full. One more thing, how am i able to read .Raw images using java, c# or python ?

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  • Pylons and Facebook

    - by Nayan Jain
    The following is my oauth template top.location.href='https://graph.facebook.com/oauth/authorize?client_id=${config['facebook.appid']}&redirect_uri=${config['facebook.callbackurl']}&display=page&scope=publish_stream'; Click here to authorize this application When I hit the page I am prompted to login (desired), upon login I am redirected in a loop between a permissions page and an app page. My controller looks like: class RootController(BaseController): def __before__(self): tmpl_context.user = None if request.params.has_key('session'): access_token = simplejson.loads(request.params['session'])['access_token'] graph = facebook.GraphAPI(access_token) tmpl_context.user = graph.get_object("me") def index(self): if not tmpl_context.user: return render('/oauth_redirect.mako') return render('/index.mako') I'm guessing my settings are off somewhere, probably with the callback. Not to sure if it is an issue with my code or the python sdk for facebook.

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  • What exactly is a Monad?

    - by WeNeedAnswers
    Can someone please explain to me what a Monad is. I think I grasp Monoids and I grasp that they basically control the input of state into a system. I just look at the text in Haskell and glaze over. A simple example in python would be great. My current understanding is that a Monoid is a procedural piece of code that needs to be read from top to bottom in sequence with the output being the input for the function. I think that I may even got that wrong, but hey I am here to learn.

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  • How does git-diff generate hunk descriptions?

    - by RobM
    (git version 1.6.5.7) When I run git diff the output has a nice scope hint after the line numbers for my Python scripts, e.g.: diff --git a/file.py b/file.py index 024f5bb..c3b5c56 100644 --- a/file.py +++ b/file.py @@ -14,6 +14,8 @@ TITF: Test Infrastructure Tags Format ... @@ -1507,13 +1533,16 @@ class Tags( object ): ... Note that the line numbers are followed by TITF: Test Infrastructure Tags Format and class Tags( object ):. The first patch applies to module scope and the description TITF: Test Infrastructure Tags Format is the module's description. The second patch applies to a method of the Tags class. How does git generate these descriptions? How can I tweak them to show the method name that the patch applies to?

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  • Parsing a list of dictionaries passed as a POST parameter

    - by andyashton
    I have a list of python dictionaries that look like this: sandwiches = [ {'bread':'wheat', 'topping':'tomatoes', 'meat':'bacon'}, {'bread':'white', 'topping':'peanut butter', 'meat':'bacon'}, {'bread':'sourdough', 'topping':'cheese', 'meat':'bacon'} ] I want to pass this as a POST parameter to another Django app. What does the client app need to do to iterate through the list? I want to do something like: for sandwich in request.POST['sandwiches']: print "%s on %s with %s is yummy!" % (sandwich['meat'], sandwich['bread'], sandwich['topping']) But I don't seem to have a list of dicts when my data arrives at my client app.

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  • What exactly does raw microphone data represent?

    - by esperantist
    I'm using PyAudio, a PortAudio wrapper for Python. I'm getting data from a microphone. Data which is represented by a continuous stream of bytes divided into chunks (of a size determined by me). I've tried to plot the signal, assuming the bytes represent the current signal amplitude, but I get an interesting image that I can't easily describe. ^^ It seems to be composed of two waves, one shifted from the other. What exactly do the particular bytes represent, and how does this change when I'm recording only one channel, instead of two? Any explanations, suggestions, code snippets, anything, very welcome! (I'm new at this.) Thanks!

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  • Find the closest vector

    - by Alexey Lebedev
    Hello! Recently I wrote the algorithm to quantize an RGB image. Every pixel is represented by an (R,G,B) vector, and quantization codebook is a couple of 3-dimensional vectors. Every pixel of the image needs to be mapped to (say, "replaced by") the codebook pixel closest in terms of euclidean distance (more exactly, squared euclidean). I did it as follows: class EuclideanMetric(DistanceMetric): def __call__(self, x, y): d = x - y return sqrt(sum(d * d, -1)) class Quantizer(object): def __init__(self, codebook, distanceMetric = EuclideanMetric()): self._codebook = codebook self._distMetric = distanceMetric def quantize(self, imageArray): quantizedRaster = zeros(imageArray.shape) X = quantizedRaster.shape[0] Y = quantizedRaster.shape[1] for i in xrange(0, X): print i for j in xrange(0, Y): dist = self._distMetric(imageArray[i,j], self._codebook) code = argmin(dist) quantizedRaster[i,j] = self._codebook[code] return quantizedRaster ...and it works awfully, almost 800 seconds on my Pentium Core Duo 2.2 GHz, 4 Gigs of memory and an image of 2600*2700 pixels:( Is there a way to somewhat optimize this? Maybe the other algorithm or some Python-specific optimizations.

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  • Storing cookielib cookies in a database

    - by Mridang Agarwalla
    Hi, I'm using the cookielib module to handle HTTP cookies when using the urllib2 module in Python 2.6 in a way similar to this snippet: import cookielib, urllib2 cj = cookielib.CookieJar() opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) r = opener.open("http://example.com/") I'd like to store the cookies in a database. I don't know whats better - serialize the CookieJar object and store it or extract the cookies from the CookieJar and store that. I don't know which one's better or how to implement either of them. I should be also be able to recreate the CookieJar object. Could someone help me out with the above? Thanks in advance.

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  • BeautifulSoup: Get the contents of a specific table

    - by Adam Matan
    Hi, My local airport disgracefully blocks users without IE, and looks awful. I want to write a Python scripts that would get the contents of the Arrival and Departures pages every few minutes, and show them in a more readable manner. My tools of choice are mechanize for cheating the site to believe I use IE, and BeautifulSoup for parsing page to get the flights data table. Quite honestly, I got lost in the BeautifulSoup documentation, and can't understand how to get the table (whose title I know) from the entire document, and how to get a list of rows from that table. Any ideas? Adam

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  • PyDev and Django: how to restart dev server?

    - by Rosarch
    I'm new to Django. I think I'm making a simple mistake. I launched the dev server with Pydev: RClick on project Django Custom command runserver The server came up, and everything was great. But now I'm trying to stop it, and can't figure out how. I stopped the process in the PyDev console, and closed Eclipse, but web pages are still being served from http://127.0.0.1:8000. I launched and quit the server from the command line normally: python manage.py runserver But the server is still up. What am I doing wrong here?

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  • Dynamically creating page definitions in Cherrypy

    - by Hugh
    Hi, I've been looking around the CherryPy documentation, but can't quite get my head around what I want to do. I suspect it might be more of a Python thing than a CherryPy thing... My current class looks something like this: import managerUtils class WebManager: def A(self, **kwds): return managerUtils.runAction("A", kwds) A.enabled = True def B(self, **kwds): return managerUtils.runAction("B", kwds) B.enabled = True def C(self, **kwds): return managerUtils.runAction("C", kwds) C.enabled = True Obviously there's a lot of repetition in here. in managerUtils.py, I have a dict that's something like: actions = {'A': functionToRunForA, 'B': functionToRunForB, 'C': functionToRunForC} Okay, so that's a slightly simplistic view of it, but I'm sure you get the idea. I want to be able to do something like: import managerUtils class WebManager: def __init__(self): for action in managerUtils.actions: f = registerFunction(action) f.enabled = True Any ideas of how to do this?

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  • wanting to move up from ms access, thinking .net? visual studio?

    - by Tristan Lear
    So I wrote a project-management program for a small business using Microsoft Access 2007. Now they've requested lots of additional features (timekeeping, privileged data tiers ...) I personally use Linux, but the whole office uses Windows. I'm relatively new to programming but like to teach myself using projects like this. I'm right on the edge on this -- I can't really tell what the path of least resistance here is: do I stay in access + VBA and teach myself a dying, annoying language -- while struggling against all the limitations of Access? Or do I move to something else? Python seems simple enough ... Whatever I use, i need to be able to offer a GUI.

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  • st-ordering library function?

    - by chang
    I'm in the search for an implementation of an ear-decomposition algorithm (http://www.ics.uci.edu/~eppstein/junkyard/euler/ear.html). I examined networkx and didn't find one. Although the algorithm layout is vaguely in my mind, I'd like to see some reference implementation, too. Side problem: First step could be an st-ordering of a graph. Are there any implementations for st-ordering algorithms you know? Thanks for your input. I'd really like to contribute e.g. to networkx by implementing the ear-decomposition algorithm in python.

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  • how to create local dynamic varables

    - by xielingyun
    this is my code, i want to use eval() to get the rule status and eval() nead local varables, there is many classes inherit class base, so i should to rewrite get_stat() in every class.i just want to avoid this, an idea is to create dynamic varables in get_stat(),eg. in class b it dynamic create var a and b how to create dynamic varables in function? or any other way to avoid this stupid idea i use python 3.2.3, locals() does not work class base(object): def check(self): stat = get_stat() def get_stat(self): pass class b(base): rule = 'a > 5 and b < 3' a = 0 b = 0 def update_data(self, a, b): self.a = a self.b = b def get_stat(self): a = self.a b = self.b return eval(rule) class b(base): rule = 'd > 5 and e < 3' d = 0 e = 0 def update_data(self, d, e): self.d = d self.e = e def get_stat(self): d = self.d e = self.e return eval(rule)

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  • Errors detected when loading a vim plugin from .vimrc

    - by Tejinder
    I have installed vim 7.3 on debian system along with some vimrc i have downloaded from internet. It used to work fine on my other debian machine but here i get these error messages while i load the vim editor. Here are the errors: Error detected while processing /home/tejinder/.vim/plugin/gundo.vim: line 196: E319: Sorry, the command is not available in this version: python << ENDPYTHON line 197: E492: Not an editor command: def asciiedges(seen, rev, parents): line 199: E121: Undefined variable: rev E15: Invalid expression: rev not in seen: line 221: E133: :return not inside a function line 231: E133: :return not inside a function line 233: E133: :return not inside a function line 235: E133: :return not inside a function line 238: E690: Missing "in" after :for line 347: E690: Missing "in" after :for line 356: E690: Missing "in" after :for line 453: E690: Missing "in" after :for line 464: E690: Missing "in" after :for line 469: E133: :return not inside a function line 795: E170: Missing :endfor Press ENTER or type command to continue If anyone could figure out thats going on, please guide me. Thanks a lot. Here is vimrc source: https://github.com/mitsuhiko/dotfiles/tree/master/vim

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  • Beginner having a problem with classes

    - by David
    I'm working through O'Reilly's "Learning Python" and having a problem with classes. I think I understand the concept, but in practice have stumbled upon this problem. Fron page 88-89: >>> class Worker: def __innit__(self, name, pay): self.name=name self.pay=pay def lastName(self): return self.name.split()[-1] def giveRaise(self, percent): self.pay*=(1.0+percent) Then the book says "Calling the class like a function generates instances of a new type ...etc" and gives this example. bob = Worker('Bob Smith', 50000) This gives me this error: TypeError: this constructor takes no arguments. And then I start muttering profanities. So what am I doing wrong here? Thanks for the help.

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