GATB - create or manipulate data of Sequence

Question

[wfd]

Hi there,

For my recent GATB project I'd like to either create a Sequence object [with comment(id and such), possibly quality and a given string] or manipulate the sequence string of an existing Sequence. However, while there are setters for quality and comment, I do not know how to set the data itself. Is there a way to do it?

I tried creating a sequence using a dummy bank with just one sequence like this;

 Sequence str2seq(string str){
      IBank *dummyBank = new BankStrings(str.c_str(), NULL);
      LOCAL (dummyBank);
      Iterator<Sequence> *it = dummyBank->iterator();
      LOCAL (it);
      it->first();
      Sequence seq = it->item();
      seq.setComment("DUMMYCOMMENT"); 
      return seq;
 }

But the returned Sequence is corrupted - pointers, I guess?

Thanks for your help

Answer 1

[pierre.peterlongo]

Hi,

From the GATB documentation, you will find many snipets examples.

You code could be

  #include <gatb/gatb_core.hpp>

 Sequence str2seq(std::string str){


    BankFasta dummyBank (str);
    BankFasta::Iterator it (dummyBank);
    for (it.first(); !it.isDone(); it.next())
    {

        std::cout << "[" << it->getDataSize() << "] " << it->getComment()  << std::endl;
        it->setComment("DUMMYCOMMENT"); 

        std::cout << it->toString() << std::endl;
    }
 }

 int main (int argc, char* argv[]){
    if(argc != 2)
    {
        printf("%s filename\n",argv[0]);
        exit(1);
    }

    // We get the file name from the user arguments
    const char* filename = argv[1] ;

    str2seq(filename);

 }

[wfd]

seems to work, thanks!