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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/lineBasedFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/KERNEL/system.h>
#include <BALL/STRUCTURE/peptides.h>
#include "version.h"
using namespace BALL;
int main(int argc, char* argv[])
{
// instantiate CommandlineParser object
CommandlineParser parpars("ExtractProteinSequence", "extracts fasta sequence", VERSION, String(__DATE__), "Get Data");
parpars.registerMandatoryInputFile("i", "input pdb file from which to extract ");
parpars.registerMandatoryOutputFile("o", "output fasta file");
parpars.registerOptionalStringParameter("c", "chain specifier");
// the manual
String man = String("This tool extracts the fasta sequence from a given pdb file.");
parpars.setToolManual(man);
parpars.setSupportedFormats("i", "pdb");
parpars.setSupportedFormats("o", "fasta");
// parse the command line
parpars.parse(argc, argv);
PDBFile in_file;
in_file.open(parpars.get("i"), std::ios::in);
if (!in_file)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("i") << " for input." << std::endl;
exit(2);
}
//TODO switch to the BALL FastaFile format if available
LineBasedFile out_file;
out_file.open(parpars.get("o"), std::ios::out);
if (!out_file)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("o") << " for output." << std::endl;
exit(2);
}
System system;
in_file >> system;
in_file.close();
for (ProteinIterator it = system.beginProtein(); +it; ++it)
{
ChainConstIterator c_it = it->beginChain();
for (; +c_it ; ++c_it)
{
// get the chain's sequence
String seq = Peptides::GetSequence(*c_it);
out_file << "> " << it->getName() + ":" + c_it->getName() << std::endl << seq << std::endl;
}
}
out_file.close();
Log << "wrote file " << parpars.get("o") << std::endl;
return 0;
}
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