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  • Can anyone tell me why these lines are not working?

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO_init_.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • [Python] OR in regular expression?

    - by www.yegorov-p.ru
    Hello. I have text file with several thousands lines. I want to parse this file into database and decided to write a regexp. Here's part of file: blablabla checked=12 unchecked=1 blablabla unchecked=13 blablabla checked=14 As a result, I would like to get something like (12,1) (0,13) (14,0) Is it possible?

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  • How to download file from particular url???

    - by greshi gupta
    NSURL * url = @"http://192.168.100.161/UploadWhiteB/wh.txt"; NSData * data = [NSData dataWithContentsOfURL:url]; if (data != nil) { NSLog(@"\nis not nil"); NSString *readdata = [[NSString alloc] initWithContentsOfURL:(NSData *)data ]; I write this code to download a file from given url... but i get an error on line NSData * data = [NSData dataWithContentsOfURL:url]; uncaught exception....so please help me out..

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  • PowerShell and interactive external programs

    - by CC
    Hi all I'm attempting to write a PowerShell script that, among other things, runs two external programs, harvesting the output of one and providing it to the other. The problem is that the second program is interactive and asks for: - a password - an option (1, 2, or 3) - an option (Y or N) - output of external program 1 Note also that this is on XP with PowerShell v1 and .net v2.0 (no I can't upgrade) Any ideas how I would do this? CC

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  • Can Android OS be programmed to interface with a external device via the mini-USB port?

    - by user322865
    Basic example, if I bought a chipset with a light socket and bulb soldered to the chipset; then put a USB cable with the mini-USB plug on the end to get plugged into the android phone. Can I write a Java application to turn on/off the light, get the status of the light(on/off) and maybe power a super-small led/bulb with power from the phone itself? Any insight at all would be greatly appreciated. Thank you

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  • Different cache concurrent strategies for root entity and its collection (Hibernate with EHCache)?

    - by grigory
    Given example from Hibernate docs and modifying it so that root level entity (Customer) is read-only while one of its collections (tickets) is read-write: @Entity @Cache(usage = CacheConcurrencyStrategy.READ_ONLY) public class Customer { ... @OneToMany(...) @Cache(usage = CacheConcurrencyStrategy.READ_WRITE) public SortedSet<Ticket> getTickets() { return tickets; } ... } Would collection of tickets get refreshed when accessing customer from cache?

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  • PHP codinh in real world

    - by user261002
    I know how to write program in PHP and implementation of MVC model. but I really want to practice coding like the coding in real world??? I was wondering is there any specific example or book which can show me the tricks or logic and the way professional programmers consider about coding???

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  • Oracle join query

    - by Jasim
    There are three tables in my db ITEM_MASTER, PRICE_MASTER, COMP_MASTER ITEM_MASTER STORE_CODE ITEM_CODE ITEM_DESC 011 914004 desccc PRICE_MASTER STORE_CODE ITEM_CODE COMP_CODE 011 914004 01 011 914004 02 011 914004 03 011 914004 04 COMP_MASTER COMP_CODE COMP_DESC STORE_CODE 01 comp1 011 02 comp2 011 03 comp3 011 04 comp4 011 I want to get all these for an ITEM_CODE in single query STORE_CODE ITEM_CODE ITEM_DESC COMP_DESC1 COMP_DESC2 COMP_DESC3 COMP_DESC4 011 914004 desccc comp1 comp2 comp3 comp4 How can i write a oracle SQL query for this??

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  • boost.asio error on read from socket.

    - by niXman
    The following code of the client: typedef boost::array<char, 10> header_packet; header_packet header; boost::system::error_code error; ... /** send header */ boost::asio::write( _socket, boost::asio::buffer(header, header.size()), boost::asio::transfer_all(), error ); /** send body */ boost::asio::write( _socket, boost::asio::buffer(buffer, buffer.length()), boost::asio::transfer_all(), error ); of the server: struct header { boost::uint32_t header_length; boost::uint32_t id; boost::uint32_t body_length; }; static header unpack_header(const header_packet& data) { header hdr; sscanf(data.data(), "%02d%04d%04d", &hdr.header_length, &hdr.id, &hdr.body_length); return hdr; } void connection::start() { boost::asio::async_read( _socket, boost::asio::buffer(_header, _header.size()), boost::bind( &connection::read_header_handler, shared_from_this(), boost::asio::placeholders::error ) ); } /***************************************************************************/ void connection::read_header_handler(const boost::system::error_code& e) { if ( !e ) { std::cout << "readed header: " << _header.c_array() << std::endl; std::cout << constants::unpack_header(_header); boost::asio::async_read( _socket, boost::asio::buffer(_body, constants::unpack_header(_header).body_length), boost::bind( &connection::read_body_handler, shared_from_this(), boost::asio::placeholders::error ) ); } else { /** report error */ std::cout << "read header finished with error: " << e.message() << std::endl; } } /***************************************************************************/ void connection::read_body_handler(const boost::system::error_code& e) { if ( !e ) { std::cout << "readed body: " << _body.c_array() << std::endl; start(); } else { /** report error */ std::cout << "read body finished with error: " << e.message() << std::endl; } } On the server side the method read_header_handler() is called, but the method read_body_handler() is never called. Though the client has written down the data in a socket. The header is readed and decoded successfully. What's the error?

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  • .htaccess | Adding A Second Vanity URL

    - by Necro.
    I want to take my .htaccess file and add a second rule for another vanity URL as I already have one declaring the page. So how would I write it so I can go to my page, and the next vanity being a variable for a profile? Ex:// mywebsite.com/page/profile Here is my current .htaccess file. RewriteEngine On RewriteBase / RewriteRule ^([a-zA-Z0-9-]+)$ index.php?p=$1 [L] RewriteRule ^([a-zA-Z0-9-]+)/$ index.php?p=$1 [L]

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  • Writing a spec for helper with Ruby on Rails and RSpec

    - by TK
    I have been writing specs for controllers and models, but I have never written a helper spec. I have no idea where I start. I have the following snippet in application_helper.rb def title(page_title) content_for(:title) { page_title } end How should I write a helper spec on the code? Also if there's any open-source Rails app to show good helper testing/specing, do let me know.

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  • How do I create a Django ModelForm, so that it's fields are sometimes required, sometimes not?

    - by Graf
    Ok, here is the question. Imagine I have a ModelForm which have only two fields. like this one: class ColorForm(forms.Form): color_by_name = forms.CharField() color = forms.IntegerField(widget = forms.Select(choices=COLOR_CHOICES)) So a user can either input a color name, a choose it from a list. Color is required, but that doesn't mean, that user should enter it manually. There do I put validation, so that my code checks if user selected color in dropdownlist and if not then he should write it manually?

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  • Help with data retrieval MACRO

    - by Andrei Ciobanu
    Hello, given the following structure: struct nmslist_elem_s { nmptr data; struct nmslist_elem_s *next; }; typedef struct nmslist_elem_s nmslist_elem; Where: typedef void* nmptr; Is it possible to write a MACRO that retrieves the data from the element and cast it to the right type: MACRO(type, element) that expands to *((type*)element->data). For example for int, i would need something like this: *((int*)(element->data)) .

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  • Emacs align-regexp on = but not ==

    - by Karl
    I am working in Haskell and frequently come across code similar to the following: func i j | i == j = i | otherwise = j I want to align on the '=' character using align-regexp but don't have the elisp knowhow. I have tried just doing " = " without the quotes, but this inserts an unwanted space character before each '='. I have found a proposed solution here but I can't seem to get that to do anything at all. Please help me write a function or hard-coded macro that will allow me to set a keybinding for this.

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