C++ parse GTF file

Question

[scchess]

I am looking for a library to parse a GTF file in C++. I'm using htslib for SAM/BAM, and it works well. However, I am not aware of any library that can handle GTF format for me. Is there a good library that I can use to parse GTF file, or should implement a parser myself?

Answer 1

[Alex Reynolds]

I have C code for parsing GTF in convert2bed on my Github page: https://github.com/alexpreynolds/convert2bed

The relevant function parses an input buffer into a c2b_gtf_t struct. You could leave out the last line of the conversion function, if you do not need BED output.

Answer 2

[Devon Ryan]

What do you need the library to do? I have a C library that can parse a GTF files and create an interval trees of it, if that's what you need.

Answer 3

[Zev.Kronenberg]

It isn't a full blown library, but it's a start:

https://github.com/zeeev/coverup/blob/master/lib/genCodeClass.hpp

I'd be happy to pull in changes.

Here is an example of looping over the GTF:

 gcClass gtf ("data/gencode.v23.annotation.gtf");

  gtf.index();
  gtf.loadIndex();

  bool flag = true;

  while(true){
    gene gf;
    gene * transcript;
    flag = gtf.getNextGene(gf);
    if(!flag){
      break;
    }
    if(!gf.isProteinCoding()){
      continue;
    }
    gf.getLongestChild(&transcript);

    if(gf.getSeqid().compare("chr1") != 0){
      break;
   }​

}

Answer 4

[dendrov.kan]

This is part of our core library, but it is may be helpful for you:
https://local.ugene.unipro.ru/svn/ugene/trunk/src/corelibs/U2Formats/src/GTFFormat.h
https://local.ugene.unipro.ru/svn/ugene/trunk/src/corelibs/U2Formats/src/GTFFormat.cpp

Note the implementation of methods parseDocument and parseAndValidateLine.