Question: GATB - create or manipulate data of Sequence
gravatar for wfd
10 months ago by
wfd0 wrote:

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);
      Sequence seq = it->item();
      return seq;

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

Thanks for your help

gatb • 351 views
ADD COMMENTlink modified 9 months ago by pierre.peterlongo820 • written 10 months ago by wfd0
gravatar for pierre.peterlongo
9 months ago by
pierre.peterlongo820 wrote:


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();

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

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

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

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


ADD COMMENTlink modified 9 months ago • written 9 months ago by pierre.peterlongo820

seems to work, thanks!

ADD REPLYlink modified 9 months ago • written 9 months ago by wfd0
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