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  • How to extract a couple marked strings from a line (python)

    - by GoJian
    My Friends, I spent quite some time on this one... but cannot yet figure out a better way to do it. I am coding in python, by the way. So, here is a line of text in a file I am working with, for example: "ref|ZP_01631227.1| 3-dehydroquinate synthase [Nodularia spumigena CCY9414]..." How can I extract the two strings "ZP_01631227.1" and "Nodularia spumigena CCY9414" from the line? The pairs of "| |" and brackets are like markers so we know we want to get the strings in between the two... I guess I can probably loop over all the characters in the line and do it the hard way. It just takes so much time... Wondering if there is a python library or other smart ways to do it nicely? Thanks to all!

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  • Python: mysqldb install error

    - by Grenko
    So i've been pulling my hair out trying to install the mysqldb package. When i run the build i get a long transcript of errors, heres just part of it, i would posit it all but its huge list of errors [rv@med240-183 MySQL-python-1.2.3c1]$ sudo python setup.py build [sudo] password for rv: running build running build_py copying MySQLdb/release.py -> build/lib.linux-i686-2.6/MySQLdb running build_ext building '_mysql' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i586 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -Dversion_info=(1,2,3,'gamma',1) -D__version__=1.2.3c1 -I/usr/include/mysql -I/usr/include/python2.6 -c _mysql.c -o build/temp.linux-i686-2.6/_mysql.o -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -fasynchronous-unwind-tables -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fwrapv -fPIC -DUNIV_LINUX _mysql.c:36:23: error: my_config.h: No such file or directory _mysql.c:38:19: error: mysql.h: No such file or directory Any ideas?

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  • python: calling constructor from dictionary?

    - by Jason S
    I'm not quite sure of the terminology here so please bear with me.... Let's say I have a constructor call like this: machineSpecificEnvironment = Environment( TI_C28_ROOT = 'C:/appl/ti/ccs/4.1.1/ccsv4/tools/compiler/c2000', JSDB = 'c:/bin/jsdb/jsdb.exe', PYTHON_PATH = 'c:/appl/python/2.6.4', ) except I would like to replace that by an operation on a dictionary provided to me: keys = {'TI_C28_ROOT': 'C:/appl/ti/ccs/4.1.1/ccsv4/tools/compiler/c2000', 'JSDB': 'c:/bin/jsdb/jsdb.exe', 'PYTHON_PATH': 'c:/appl/python/2.6.4'} machineSpecificEnvironment = Environment( ... what do I put here? it needs to be a function of "keys" ... ) How can I do this?

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  • Convert Google results object (pure js) to Python object

    - by colwilson
    So I'm trying to use Google Map suggest API to request place name suggestions. Unfortunately I can't find the docs for this bit. Here is an example URI: http://maps.google.com/maps/suggest?q=lon&cp=3&ll=55.0,-3.5&spn=11.9,1.2&hl=en&gl=uk&v=2 which returns: {suggestion:[{query:"London",... I want to use this in python (2.5). Now in proper JSON there would have been quotations around the keys like so: {"suggestion":[{"query":"London",... and I could have used simplejson or something, but as it is I'm a bit stuck. There are two possible solutions here; either I can get to the API code and find an option to return proper JSON, or I do that in python. Any ideas please.

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  • Creating Instance of Python Extension Type in C

    - by Brad Zeis
    I am writing a simple Vector implementation as a Python extension module in C that looks mostly like this: typedef struct { PyObject_HEAD double x; double y; } Vector; static PyTypeObject Vector_Type = { ... }; It is very simple to create instances of Vector while calling from Python, but I need to create a Vector instance in the same extension module. I looked in the documentation but I couldn't find a clear answer. What's the best way to do this?

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  • Python, implementing proxy support for a socket based application (not urllib2)

    - by Terry Felkrow
    Hey guys, I am little stumped: I have a simple messenger client program (pure python, sockets), and I wanted to add proxy support (http/s, socks), however I am a little confused on how to go about it. I am assuming that the connection on the socket level will be done to the proxy server, at which point the headers should contain a CONNECT + destination IP (of the chat server) and authentication, (if proxy requires so), however the rest is a little beyond me. How is the subsequent connection handled, specifically the reading/writing, etc... Are there any guides on proxy support implementation for socket based (tcp) programming in Python? Thank you

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  • [SOLVED]Port C's fread(&struct,....) to Python

    - by user287669
    Hey, I'm really struggling with this one. I'am trying to port a small piece of someone else's code to Python and this is what I have: typedef struct { uint8_t Y[LUMA_HEIGHT][LUMA_WIDTH]; uint8_t Cb[CHROMA_HEIGHT][CHROMA_WIDTH]; uint8_t Cr[CHROMA_HEIGHT][CHROMA_WIDTH]; } __attribute__((__packed__)) frame_t; frame_t frame; while (! feof(stdin)) { fread(&frame, 1, sizeof(frame), stdin); // DO SOME STUFF } Later I need to access the data like so: frame.Y[x][y] So I made a Class 'frame' in Python and inserted the corresponding variables(frame.Y, frame.Cb, frame.Cr). I have tried to sequentially map the data from Y[0][0] to Cr[MAX][MAX], even printed out the C struct in action but didn't manage to wrap my head around the method used to put the data in there. I've been struggling overnight with this and have to get back to the army tonight, so any immediate help is very welcome and appreciated. Thanks

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  • Python IPC, popen too slow

    - by UnableToLoad
    i need to run a subprocess (./myProgram) form python script and get output, actually i do this: import subprocess proc = subprocess.Popen('./generate_out', shell=False, stdout=subprocess.PIPE, ) while proc.poll() is None: out = proc.stdout.readline() data = doStuff(out) print(data) but is slow, sometimes pass a lot of time between the output produced by ./generate_out and the print(data), knowing that my doStuff() function is very fast, i think there is some buffer slowing down my pipe... Notes: ./generate_out, generates potentially an unlimited number of lines of finite length each. It seems that when too few chars are put in the pipe between the two processes nothing happens, then when enough is produced i get a huge print (non the expected behaviour!) sometimes i wait many seconds (10-20 and more) between generate_out print and python print) what can i do? maybe communicate() is faster? anithing else? Thank you a lot!

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  • Integrate Python Projects Into Xcode

    - by Vynile
    Hi! I'm a Mac user, and one of my hobbies is programming. I use Xcode, the integrated IDE of Mac OS X. I started to learn Python programming langage, and I want to use Xcode for developing my scripts. I searched for weeks in the internet, but I didn't find something interesting. Firstly, I want to update the integrated interpreter of Mac OS X, that is on 2.6 version. And secondly, I want to create a Python project on Xcode easily, like I do with C & C++ projects. Can you help me? I really need help! Cordially.

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  • Alternative to nesting for loops in Python

    - by davenz
    I've read that one of the key beliefs of Python is that flat nested. However, if I have several variables counting up, what is the alternative to multiple for loops? My code is for counting grid sums and goes as follows: def horizontal(): for x in range(20): for y in range(17): temp = grid[x][y: y + 4] sum = 1 for n in temp: sum += int(n) return sum This seems to me like it is too heavily nested. Firstly, what is considered to many nested loops in Python ( I have certainly seen 2 nested loops before). Secondly, if this is too heavily nested, what is an alternative way to write this code?

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  • Embedding Python in C: Having problems importin local modules

    - by Drew
    I'm needing to run Python scripts within a C-based app. I am able to import standard modules from the Python libraries i.e.: PyRun_SimpleString("import sys") But when I try to import a local module 'can' PyRun_SimpleString("import can") returns the error msg: Traceback (most recent call last): File "", line 1, in ImportError: No module named can When I type the command "import can" in iPython, the system is able to find it. How can I link my app with can? I've tried setting PYTHONPATH to my working directory. Thanks.

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  • Doxygen C++ comment string parser in python?

    - by Sebastian
    Does anybody know of a python module to parse a doxygen style C++ comment string? I mean a string like this (simple example): /** * A constructor. * A more elaborate description of the constructor. * @param param1 test1 * @param param2 test2 */ and I would like to extract the brief, the long description, the parameters, the return value etc. I'm currently doing this using string methods and regular expressions but my solution is not very robust. Alternatively can anybody recommend an easy to use python parser lib that I can set up quickly? Thanks in advance

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  • how to load a module within python debugger

    - by MK
    This looks like something simple but I could not find the answer so far - I have just learnt python and need to start learning pdb. In my module I have the usual if __name__ == __main_ trick to execute some code when the module is run as a program. So far I have been running it via python -m mymod arg1 arg2 syntax Now I want to do exactly the same thing from inside pdb. Normally in C, I would just do gdb mybinary followed by run arg1 arg2 But I cannot figure out how to achieve the same thing in pdb. I am sure there has to be a simple way to achieve this but it is taking me too long to search for it.. Thanks for your help!

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  • Is there are standard way to store a database schema outside a python app

    - by acrosman
    I am working on a small database application in Python (currently targeting 2.5 and 2.6) using sqlite3. It would be helpful to be able to provide a series of functions that could setup the database and validate that it matches the current schema. Before I reinvent the wheel, I thought I'd look around for libraries that would provide something similar. I'd love to have something akin to RoR's migrations. xml2ddl doesn't appear to be meant as a library (although it could be used that way), and more importantly doesn't support sqlite3. I'm also worried about the need to move to Python 3 one day given the lack of recent attention to xml2ddl. Are there other tools around that people are using to handle this?

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  • Python in AWS Elastic Beasntalk: Private package dependencies

    - by Adam Matan
    I would like to deploy a Python Flask application on beanstalk. The application depends on external packages (e.g. geopy) and internal packages (e.g. adam_geography). The manual Create a requirements.txt file and place it in the top-level directory of your source bundle. This would probably fetch geopy and its dependencies, but would not fetch adam_geography which is available from a custom repo inside my VPC. How do I specify/upload private, internal Python package dependencies in a Beanstalk application?

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  • Installing mySQL on mac for use with python

    - by Paul Patterson
    I am aware that there are umpteen similar questions here, and on other forums, but none of them have been able to help me. I simply want to install mySQL on my mac (running snow leopard 10.6.5) for use with Python. So far I have: 1) downloaded and installed [mysql-5.5.8-osx10.6-x86_64.dmg] (I have also accidentally downloaded and installed [mysql-5.1.54-osx10.6-x86_64.dmg]) 2) downloaded and installed [mySQL-python-1.2.3] 3) added the following to my .bash_profile: [export PATH=$PATH:/usr/local/mysql/bin] but when i run:import mySQLdb in terminal I am met with the following message: Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named mySQLdb Can anyone help?

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  • Python - network buffer handling question...

    - by Patrick Moriarty
    Hi, I want to design a game server in python. The game will mostly just be passing small packets filled with ints, strings, and bytes stuffed into one message. As I'm using a different language to write the game, a normal packet would be sent like so: Writebyte(buffer, 5); // Delimit type of message Writestring(buffer, "Hello"); Sendmessage(buffer, socket); As you can see, it writes the bytes to the buffer, and sends the buffer. Is there any way to read something like this in python? I am aware of the struct module, and I've used it to pack things, but I've never used it to actually read something with mixed types stuck into one message. Thanks for the help.

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  • Newbie question about file formatting in Python

    - by user568041
    I'm writing a simple program in Python 2.7 using pycURL library to submit file contents to pastebin. Here's the code of the program: #!/usr/bin/env python2 import pycurl, os def send(file): print "Sending file to pastebin...." curl = pycurl.Curl() curl.setopt(pycurl.URL, "http://pastebin.com/api_public.php") curl.setopt(pycurl.POST, True) curl.setopt(pycurl.POSTFIELDS, "paste_code=%s" % file) curl.setopt(pycurl.NOPROGRESS, True) curl.perform() def main(): content = raw_input("Provide the FULL path to the file: ") open = file(content, 'r') send(open.readlines()) return 0 main() The output pastebin looks like standard Python list: ['string\n', 'line of text\n', ...] etc. Is there any way I could format it so it looks better and it's actually human-readable? Also, I would be very happy if someone could tell me how to use multiple data inputs in POSTFIELDS. Pastebin API uses paste_code as its main data input, but it can use optional things like paste_name that sets the name of the upload or paste_private that sets it private.

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  • How can i add encoding to the python generated CSV file

    - by user1958218
    I am following this post http://stackoverflow.com/a/9016545 and i want to know that how can i do that in Python. I don't know how can i insert BOM data in there This is my current code response = HttpResponse(content_type='text/csv') response['Content-Type'] = 'application/octet-stream' response['Content-Disposition'] = 'attachment; filename="results.csv"' writer = UnicodeWriter(response, quoting=csv.QUOTE_ALL, encoding="utf-8") I want to convert to utf -16 . BOm data is this but don't know how to insert it From here http://stackoverflow.com/a/4440143 echo "\xEF\xBB\xBF"; // UTF-8 BOM But i want it for python and utf-16 I tried opening that csv in notepad and insert \xef\xbb\xb in beginning and excel displayed that correctly. But it is also visible before first column. How can i hide that because user wont like that

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  • Implementation Details as a "Document" ( In generic terms) - Python, C++

    - by mgj
    Hi..:) For documentation and presentation purposes, we often find professionals/students creating SRS, coding guidelines etc. for these things there is some kind of a checklist which one could use to appropriately match what could relate to a specific case and accordingly one does a documentation for each. On those grounds could you please give me some sort of a checklist( any points/guidelines) one could use for going about Implementation( in the form of Implementation Details) in Python and C++ . Although this might sound specific as the query is "Implementation Details" and is different for different cases as one goes about the REAL implementation, I just want a SET of guidelines one should follow ( Preferably In Python, C++ specific, even for any other language is Welcome) if this( Implementation Details ) has to also be documented or presented. Hope the question is clear, I am sorry if it still sounds ambiguous, I guess this is the best I could do to frame my query. Thank you for your time...:)

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  • Check if a MediaWiki page exists (Python)

    - by compie
    I'm working on a Python script that transforms this: foo bar Into this: [[Component foo]] [[bar]] The script checks (per input line) if the page "Component foo" exists. If it exists then a link to that page is created, if it doesn't exist then a direct link is created. The problem is that I need a quick & cheap way to check if a lot of wiki pages exist.I don't want to (try to) download all the 'Component' pages. I already figured out a fast way to do this by hand: Edit a new wiki page. paste all the 'component' links into the page, press preview, and then save the resulting preview HTML page. The resulting HTML file contains a different link for existing pages than for non-existing pages. So to rephrase my question: How can I save a mediawiki preview page in Python?

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