int main (int argc, char* argv[])
{
/** We create a command line parser. */
OptionsParser parser ("BankFilter");
parser.push_back (new OptionOneParam (STR_URI_INPUT, "bank reference", true));
parser.push_back (new OptionOneParam (STR_URI_SEQ_IDS, "file holding indexes of bank", true));
try
{
/** We parse the user options. */
IProperties* options = parser.parse (argc, argv);
/** We read the list of indexes. */
set<size_t> indexes;
FILE* file = fopen (options->getStr(STR_URI_SEQ_IDS).c_str(), "r");
if (file != 0)
{
char buffer[128];
while (fgets (buffer, sizeof(buffer), file)) { indexes.insert (atoi(buffer)); }
fclose (file);
}
cout << "found " << indexes.size() << " indexes" << endl;
/** We open the output bank. */
string outputBankUri = options->getStr(STR_URI_INPUT) + "_" + System::file().getBaseName (options->getStr(STR_URI_SEQ_IDS));
IBank* outputBank = Bank::open (outputBankUri);
LOCAL (outputBank);
/** We loop the input bank. */
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
LOCAL (inputBank);
/** We use another iterator for filtering out some sequences. */
FilterIterator<Sequence,FilterFunctor> itSeq (inputBank->iterator(), FilterFunctor(indexes));
/** We loop the sequences. */
for (itSeq.first(); !itSeq.isDone(); itSeq.next())
{
outputBank->insert (itSeq.item());
}
/** We flush the output bank. */
outputBank->flush();
}
catch (OptionFailure& e)
{
return e.displayErrors (cout);
}
catch (Exception& e)
{
cerr << "EXCEPTION: " << e.getMessage() << endl;
}
}
int main (int argc, char* argv[])
{
/** We create a command line parser. */
OptionsParser parser ("BankStats");
parser.push_back (new OptionOneParam (STR_URI_INPUT, "bank input", true));
try
{
/** We parse the user options. */
IProperties* options = parser.parse (argc, argv);
std::string filename = options->getStr(STR_URI_INPUT);
//! [snippet16_bank]
// We get an instance of IBank from the URI.
IBank* bank = Bank::open (filename);
//! [snippet16_seq]
// We create an iterator on the bank
Iterator<Sequence>* it = bank->iterator();
// We iterate the sequences of the bank
for (it->first(); !it->isDone(); it->next())
{
// We get a shortcut on the current sequence and its data
Sequence& seq = it->item();
Data& data = seq.getData();
// We dump some information about the sequence.
std::cout << "comment " << seq.getComment() << std::endl;
// We dump each nucleotide. NOTE: the output depends on the data encoding
for (size_t i=0; i<data.size(); i++) { std::cout << data[i]; } std::cout << std::endl;
}
//! [snippet16_seq]
// The bank and the iterator have been allocated on the heap, so we have to delete them
delete it;
delete bank;
//! [snippet16_bank]
}
catch (OptionFailure& e)
{
return e.displayErrors (std::cout);
}
catch (Exception& e)
{
std::cerr << "EXCEPTION: " << e.getMessage() << std::endl;
}
}
int main (int argc, char* argv[])
{
if (argc < 2)
{
std::cerr << "you must provide a bank." << std::endl;
return EXIT_FAILURE;
}
// We declare an input Bank and use it locally
IBank* inputBank = Bank::open (argv[1]);
LOCAL (inputBank);
// We create an iterator over this bank.
Iterator<Sequence>* it = inputBank->iterator();
LOCAL (it);
// We loop over sequences in a "push" fashion (a functor is called for each sequence)
Functor fct;
it->iterate (fct);
}
// START Application
int main (int argc, char* argv[])
{
// We check that the user provides at least one option: a Fasta/FastQ file.
// Online GATB-Tutorial: this argument is automatically filled in with an
// appropriate file.
if (argc < 2)
{
std::cerr << "Please, provide a sequence file." << std::endl;
return EXIT_FAILURE;
}
// We define a try/catch block in case some method fails (bad filename for instance)
try
{
// We declare an input Bank and use it locally
IBank* inputBank = Bank::open (argv[1]);
LOCAL (inputBank);
// We create an iterator over this bank using some filtering system
FilterIterator<Sequence,QualityFilter> it (inputBank->iterator(), QualityFilter());
// We loop over sequences.
for (it.first(); !it.isDone(); it.next())
{
// Shortcut
Sequence& seq = it.item();
// We dump the sequence quality
std::cout << "[" << seq.getQuality() << "] " << computeMeanPhredScore(seq.getQuality()) << std::endl;
}
}
catch (Exception& e)
{
std::cerr << "EXCEPTION: " << e.getMessage() << std::endl;
}
}
int main (int argc, char* argv[])
{
if (argc < 2)
{
std::cerr << "you must provide a bank." << std::endl;
return EXIT_FAILURE;
}
// We define a try/catch block in case some method fails
try
{
// We declare an input Bank and use it locally
IBank* inputBank = Bank::open (argv[1]);
LOCAL (inputBank);
// Note also that we have to parameterize the SubjectIterator by the kind of iterated
// items (Sequence) and the processing that has to be done on each iteration (ProgressFunctor).
SubjectIterator<Sequence> iter (inputBank->iterator(), 10);
// We create some listener to be notified every 10 iterations and attach it to the iterator.
iter.addObserver (new ProgressFunctor());
// We loop over sequences.
for (iter.first(); !iter.isDone(); iter.next())
{
// Note that we do nothing inside the sequence iterating loop about the progression management.
// In other words, we don't "pollute" the code inside this loop by presentation concerns and
// we can therefore focus on the job to be done on the iterated sequences.
}
}
catch (Exception& e)
{
std::cerr << "EXCEPTION: " << e.getMessage() << std::endl;
}
}