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  • Imputing missing data in aligned sequences

    - by Kwame Oduro
    I want a simple perl script that can help me impute missing nucleotides in aligned sequences: As an example, my old_file contains the following aligned sequences: seq1 ATGTC seq2 ATGTC seq3 ATNNC seq4 NNGTN seq5 CTCTN So I now want to infer all Ns in the file and get a new file with all the Ns inferred based on the majority nucleotide at a particular position. My new_file should look like this: seq1 ATGTC seq2 ATGTC seq3 ATGTC seq4 ATGTC seq5 CTCTC A script with usage: "impute_missing_data.pl old_file new_file" or any other approach will be helpful to me. Thank you.

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  • Connect to MySQL in Ruby using NetBeans

    - by Varun
    I've downloaded the "dbd-mysql-0.4.4.zip" and linked it to my project. While I try to run a demo code from NetBeans the very first line require "dbi" gives me an error. Is there a different way to do it? I also tried jruby setup.rb config --with=dbi,dbd_mysql from the command prompt and it gave me the following error: config: unknown option --with=dbi,dbd_mysql Try 'ruby setup.rb --help' for detailed usage. Any suggestions please?

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  • magento https error

    - by Ela
    when i made https enabled in secure url and front end secure url usage to yes in magento the checkout page becomes not found. Should i need to do anything more? where i have to place my ssl certificates. please help me in this

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  • Visual Studio Solution: static or shared projects?

    - by goodrone
    When a whole project (solution) consists of multiple subprojects (.vcproj), what is a preferable way to tie them: as static libraries or as shared libraries? Assuming that those subprojects are not used elsewhere, the shared libraries approach shouldn't decrease memory usage or load time.

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  • Are there any FREE Xaml Diff/Merge tools available?

    - by Ahikam
    I am searching a free diff tool with support of native syntax and markup for XAML, but failed to find one. I like Altova's DiffDog but it's paid. CodeCompare is an useful tool. It has some worth with its integration into VisualStudio and usage of native editors. It's a perfect solution for XML! However, it does not support XAML editors. Who can recommend a diff tool for XAML?

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  • Android googlemap Out of memory

    - by Xiaofeng
    Hi, I made an android application with googlemap api, and draw some 16x16 png (about 200 count) on overlay. When I move or zoom on/in mapview, "out of memory" error occurs very often. I also used the googlemap appication in my htc itself. Seams that it uses about 14+MB memmory, and never happens "out of memory". How to save memmory usage in a googlemap api, or how to enlarge android api memmory limit. Thanks a lot!

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  • What alternatives to __attribute__ exist on 64-bit kernels?

    - by Saifi Khan
    Hi: Is there any alternative to non-ISO gcc specific extension __attribute__ on 64-bit kernels ? Three types that i've noticed are: function attributes, type attributes and variable attributes. eg. i'd like to avoid using __attribute__((__packed__)) for structures passed over the network, even though some gcc based code do use it. Any suggestions or pointers on how to entirely avoid __attribute__ usage in C systems/kernel code ? thanks Saifi.

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  • ByPassing Google App Engine SDK to allow black listed classes

    - by ivanceras
    Is there a way to circumbent google app engine sdk to allow the usage of classes that are not present in the GAE JRE white list? I know the app that I would be building will not run in appspot, but at least in my development server, I need to access a postgresql database(java.net.socket.*) and generate some files(java.io.FileWriter) in my development server.

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  • How to use length indicator in a C++ program

    - by cj
    I want to make a program in C++ that reads a file where each field will have a number before it that indicates how long it is. The problem is I read every record in object of a class; how do I make the attributes of the class dynamic? For example if the field is "john" it will read it in a 4 char array. I don't want to make an array of 1000 elements as minimum memory usage is very important.

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  • variable argument list in windows va_list

    - by shrikant
    hi, I wanted to have function which will accept as foo(...) { } usage of this would be foo(1,2,3); foo(1) foo(1,2,3,4,5,5,6); va_list can be used but again for that I have to pass foo(int count, ...), as this at run time i dont know how many argument i have. any pointer would be appreciated Thanks

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  • Using CONNECT BY to get all parents and one child in Hierarchy through SQL query in Oracle

    - by s khan
    I was going through some previous posts on CONNECT BY usage. What I need to find is that what to do if I want to get all the parents (i.e, up to root) and just one child for a node, say 4. It seems Like I will have to use union of the following two:- SELECT * FROM hierarchy START WITH id = 4 CONNECT BY id = PRIOR parent union SELECT * FROM hierarchy WHERE LEVEL =<2 START WITH id = 4 CONNECT BY parent = PRIOR id Is there a better way to do this, some workaround that is more optimized?

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  • How to automatically monitor and limit resource of process on Windows

    - by Nat
    On Linux, normally I use ptrace function to trace all syscall, and kill the process if the it tries to do anything harmful to my machine, such as system("shutdown -s -t 00") or so. Is there a way for me to do this on Windows? EDIT: I want to write Sandbox program to limit time and memory usage of its child that can work on both Windows and Linux, and now it can only run on Linux via ptrace

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  • The single most useful Emacs feature

    - by Readonly
    My primary editor is Emacs, but my usage habits and knowledge of features has barely changed over the last few years. What are the Emacs features that you use on a daily basis? Are there any little-known Emacs features that you find very useful? Edit: Made this into the recommended poll format...please put one feature per answer from now on.

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  • Why would someone use WHERE 1=1 AND <conditions> in a SQL clause?

    - by Bogdan Maxim
    Why would someone use WHERE 1=1 AND <conditions> in a SQL clause (Either SQL obtained through concatenated strings, either view definition) I've seen somewhere that this would be used to protect against SQL Injection, but it seems very weird. If there is injection WHERE 1 = 1 AND injected OR 1=1 would have the same result as injected OR 1=1. Later edit: What about the usage in a view definition?

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  • using # instead of . in API documentation

    - by landon9720
    In API documentation, and sometimes even used in discussions here on Stack Overflow, I sometimes see the pound (#) character used instead of the dot (.) as the separator between the class name and the method name. For example: Settings#maxPageSize I'm wondering what this usage means, and where it comes from?

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  • Merge decorator function as class

    - by SyetemHog
    How to make this merge function as class decorator? def merge(*arg, **kwarg): # get decorator args & kwargs def func(f): def tmp(*args, **kwargs): # get function args & kwargs kwargs.update(kwarg) # merge two dictionaries return f(*args, **kwargs) # return merged data return tmp return func Usage: @other_decorator # return *args and **kwarg @merge(list=['one','two','three']) # need to merge with @other_decorator def test(*a, **k): # get merged args and kwargs print 'args:', a print 'kwargs:', k

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  • Heap Behavior in C++

    - by wowus
    Is there anything wrong with the optimization of overloading the global operator new to round up all allocations to the next power of two? Theoretically, this would lower fragmentation at the cost of higher worst-case memory consumption, but does the OS already have redundant behavior with this technique, or does it do its best to conserve memory? Basically, given that memory usage isn't as much of an issue as performance, should I do this?

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  • Using many mutex locks

    - by hanno
    I have a large tree structure on which several threads are working at the same time. Ideally, I would like to have an individual mutex lock for each cell. I looked at the definition of pthread_mutex_t in bits/pthreadtypes.h and it is fairly short, so the memory usage should not be an issue in my case. However, is there any performance penalty when using many (let's say a few thousand) different pthread_mutex_ts for only 8 threads?

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