string * FASTA_Parser::getSequence() {
string line;
string * rna_sequence = new string();
if (expected_sequence_length > 0) {
rna_sequence->reserve(expected_sequence_length);
}
//cerr << "getSequence" << endl;
//cout <<"line: "<< line << endl;
while (*rna_stream) {
std::getline(*rna_stream, line);
//cerr << "y:" << line << endl;
if (line.length() == 0) {
continue;
}
if (line[0] == '#' ) {
continue;
}
if (line[line.size() - 1] == '\r') {
line.resize(line.size() - 1);
}
if (line[0] == '>' ) {
this->description_line = getFASTADescription(line);
if (getOnlyIdentfier) {
this->description_line = getFASTADescription(line);
} else {
this->description_line = line;
}
have_read_descr = false;
rna_sequence->reserve(rna_sequence->length());
return rna_sequence;
} else {
int lastpos = line.length()-1;
if (line[lastpos] == '\n') {
line.erase(lastpos); // remove trailing newline
}
//rna_sequence->append("@");
rna_sequence->append(line);
}
}
//file_closed = true;
if (fp != 0) {
pclose(fp);
fp = 0;
}
rna_sequence->reserve(rna_sequence->length());
return rna_sequence;
}
bool FASTA_Parser::getNextDescriptionLine(string& descr) {
//cerr << "getNextDescriptionLine" << endl;
if ( *rna_stream == false ) {
return false;
}
// jump over sequence to next description line
if (have_read_descr == true) {
bool found_descr=false;
string line;
while (*rna_stream) {
std::getline(*rna_stream, line);
//cerr << "x:" << line << endl;
if (line.length() == 0) {
continue;
}
if (line[0] == '#' ) {
continue;
}
if (line[line.size() - 1] == '\r') {
line.resize(line.size() - 1);
}
if (line[0] == '>' ) {
found_descr=true;
//exit(1);
this->description_line = getFASTADescription(line);
if (getOnlyIdentfier) {
this->description_line = getFASTADescription(line);
} else {
this->description_line = line;
}
break;
}
}
if (! found_descr) {
return false;
}
}
have_read_descr = true;
descr = this->description_line;
return true;
}
void FASTA_Parser::start(string command, bool getOnlyIdentfier) {
this->getOnlyIdentfier=getOnlyIdentfier;
expected_sequence_length=0;
fp = popen(command.c_str(), "r");
if (fp == NULL) {
cerr << "error: " << command << endl;
exit(EXIT_FAILURE);
}
namespace io = boost::iostreams;
io::file_descriptor_flags flags= io::close_handle;
fpstream = new io::stream_buffer<io::file_descriptor_source>(fileno(fp), flags);
rna_stream = new std::istream(fpstream);
//rna_stream = std::ifstream(fpstream);
//rna_stream.open(fpstream, ifstream::in);
string line;
while (1) {
std::getline(*rna_stream, line);
if (rna_stream->eof()) {
return;
}
if (line.length() == 0) {
continue;
}
if (line[0] == '#' ) {
continue;
}
break;
}
if (line.length() < 2) {
cerr << "FASTA_Parser: error parsing" << endl;
}
if (line[0] != '>') {
cerr << "FASTA_Parser: error parsing" << endl;
}
if (getOnlyIdentfier) {
this->description_line = getFASTADescription(line);
} else {
this->description_line = line;
}
have_read_descr = false;
}
bool FASTA_Parser::getNextDescriptionLine(string& descr) {
//cerr << "getNextDescriptionLine" << endl;
//if ( *rna_stream == false ) {
//std::istream & rna_stream_ref = *rna_stream;
sequence = 0;
if ( rna_stream->fail() ) {
return false;
}
// jump over sequence to next description line
if (have_read_descr == true) {
bool found_descr=false;
string line;
while (not rna_stream->fail()) {
std::getline(*rna_stream, line);
//cerr << "x:" << line << endl;
if (line.length() == 0) {
continue;
}
if (line[0] == '#' ) {
continue;
}
if (line[0] == '>' ) {
found_descr=true;
//exit(1);
//this->description_line = getFASTADescription(line);
if (getOnlyIdentfier) {
this->description_line = getFASTADescription(line);
} else {
this->description_line = line;
}
break;
}
}
if (! found_descr) {
return false;
}
}
descr = this->description_line;
have_read_descr = true;
return true;
}
string * FASTA_Parser::getSequence() {
string line;
if (sequence != 0) {
cerr << "error: sequence has already been read via getSequence()" << endl;
exit(1);
}
sequence = new string();
if (expected_sequence_length > 0) {
sequence->reserve(expected_sequence_length);
}
//cerr << "getSequence" << endl;
//cout <<"line: "<< line << endl;
while (true) {
std::getline(*rna_stream, line);
if (rna_stream->fail()) {
break;
}
//cout << "fail: " << rna_stream->fail() << endl;
//cerr << "y:" << line << endl;
if (line.length() == 0) {
continue;
}
if (line[0] == '#' ) {
continue;
}
if (line[0] == '>' ) {
//this->description_line = getFASTADescription(line);
if (getOnlyIdentfier) {
this->description_line = getFASTADescription(line);
} else {
this->description_line = line;
}
have_read_descr = false;
sequence->reserve(sequence->length());
return sequence;
} else {
int lastpos = line.length()-1;
if (line[lastpos] == '\n') {
line.erase(lastpos); // remove trailing newline
}
//sequence->append("@");
//cout << "append" << endl;
sequence->append(line);
}
}
//file_closed = true;
if (fp != 0) {
pclose(fp);
fp = 0;
}
sequence->reserve(sequence->length());
return sequence;
}
