int read_sequences(Auto_Unzip & input, int num_seq, Mask sequences[], Fasta::FASTQ_encoding format_type, bool gui_output) {
if (&input == NULL)
return 0;
Fasta read;
read.set_FASTQ_type(format_type);
int n_seq = 0;
{
mutex::scoped_lock lock(read_mutex);
istream & in = input.filtered();
while (not input.eof() and n_seq < num_seq) {
in >> read;
if (read.length() > MAX_READ_LENGTH) {
cerr << "Read " << read.get_id() << " too long. Max allowed read size is " << MAX_READ_LENGTH << endl;
exit(5);
}
//Reset and take a ref
Mask & r = sequences[n_seq] = Mask();
r.set_id(read.get_id());
r.set_sequence(read.get_sequence());
r.set_quality(read.get_quality());
n_seq++;
}
output_progress(input, gui_output);
}
return n_seq;
}
int read_sequences(Auto_Unzip & first, Auto_Unzip & second, int num_seq, Mask sequences[], Fasta::FASTQ_encoding format_type, bool gui_output) {
if (&first == NULL or &second == NULL)
return 0;
Fasta read;
read.set_FASTQ_type(format_type);
int n_seq = 0;
{
mutex::scoped_lock lock(read_mutex);
istream & first_in = first.filtered();
istream & second_in = second.filtered();
while (not first.eof() and not second.eof() and (n_seq + 1) < num_seq) {
first_in >> read;
if (read.length() > MAX_READ_LENGTH) {
cerr << "Read " << read.get_id() << " too long. Max allowed read size is " << MAX_READ_LENGTH << endl;
exit(5);
}
Mask & rf = sequences[n_seq];
rf.set_id(read.get_id());
rf.set_sequence(read.get_sequence());
rf.set_quality(read.get_quality());
n_seq++;
second_in >> read;
if (read.length() > MAX_READ_LENGTH) {
cerr << "Read " << read.get_id() << " too long. Max allowed read size is " << MAX_READ_LENGTH << endl;
exit(5);
}
Mask & rs = sequences[n_seq];
rs.set_id(read.get_id());
rs.set_sequence(read.get_sequence());
rs.set_quality(read.get_quality());
n_seq++;
//CHECK!!
if (rf.id.compare(0, rf.id.size() - 1, rs.id, 0, rs.id.size() - 1) != 0) {
ERROR_CHANNEL << "wrong paired reads IDs: '" << rf.id << "' and '" << rs.id << '\'' << endl;
exit(2);
}
}
output_progress(first, gui_output);
}
return n_seq;
}
int main( int argc, char *argv[])
{
// Options
bool showHelp = false;
string cutSeq = "AAGCTT";
string genomeFile;
string bedFile = "stdout";
string faFile = "ends.fa";
CHRPOS readLen = 20;
// Show help when has no options
if(argc <= 1)
{
Help();
return 0;
}
// Parsing options
for(int i = 1; i < argc; i++)
{
int parameterLength = (int)strlen(argv[i]);
if((PARAMETER_CHECK("-h", 2, parameterLength)) || (PARAMETER_CHECK("--help", 5, parameterLength)))
showHelp=true;
else if((PARAMETER_CHECK("-g", 2, parameterLength)) || (PARAMETER_CHECK("--genome", 8, parameterLength)))
{
if ((++i) < argc)
genomeFile = argv[i];
}
else if((PARAMETER_CHECK("-c", 2, parameterLength)) || (PARAMETER_CHECK("--cut_seq", 9, parameterLength)))
{
if ((++i) < argc)
cutSeq = argv[i];
}
else if ((PARAMETER_CHECK("-b", 2, parameterLength)) || (PARAMETER_CHECK("--bed_output", 12, parameterLength)))
{
if ((++i) < argc)
bedFile=argv[i];
}
else if ((PARAMETER_CHECK("-f", 2, parameterLength)) || (PARAMETER_CHECK("--fa_output", 11, parameterLength)))
{
if ((++i) < argc)
faFile=argv[i];
}
else if ((PARAMETER_CHECK("-r", 2, parameterLength)) || (PARAMETER_CHECK("--read_len", 10, parameterLength)))
{
if ((++i) < argc)
readLen = StringUtils::toValue<CHRPOS>(argv[i]);
}
else
{
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// Show help if no proper auguments.
if (showHelp)
{
Help();
return 0;
}
// Statistical variables
map <string, int, less<string> > bedCount;
map <string, CHRPOS, less<string> > bedSum;
map <string, CHRPOS, less<string> > faSize;
// Variables
CHRPOS lindex,rindex;
int siteLen=cutSeq.size();
bool flag;
Fasta curFa;
SeqReader fhfa(genomeFile);
Writer bedOutput(bedFile);
Writer faOutput(faFile);
// open files
fhfa.open();
bedOutput.open();
faOutput.open();
// Read the genome file.
while (fhfa.getNext(curFa))
{
// Statistics
bedCount[curFa.id]=0;
bedSum[curFa.id]=0;
faSize[curFa.id]=curFa.length();
// Find next recognition site.
lindex=rindex=0;
flag=true;
while (flag)
{
rindex=curFa.seq.find(cutSeq,lindex);
if(rindex==CHRPOS(string::npos))
{
rindex=curFa.seq.size();
flag=false;
}
(*(bedOutput.Printer())) << curFa.id << "\t" << lindex << "\t" << rindex << "\t" << (lindex+rindex)/2 << endl;
if (rindex - lindex >= 2*readLen)
{
bedCount[curFa.id]++;
bedSum[curFa.id]+=rindex-lindex;
(*(faOutput.Printer())) << ">" << curFa.id << "_" << (lindex+rindex)/2 << "_L" << endl;
(*(faOutput.Printer())) << curFa.seq.substr(lindex,readLen) << endl;
(*(faOutput.Printer())) << ">" << curFa.id << "_" << (lindex+rindex)/2 << "_R" << endl;
(*(faOutput.Printer())) << curFa.seq.substr(rindex-readLen,readLen) << endl;
}
lindex=rindex+siteLen;
}
}
// close files
fhfa.close();
bedOutput.close();
faOutput.close();
// print statistics into log file
Writer log(cutSeq+".log");
log.open();
log.close();
return 0;
}
void Module_DCREATE::compute_master(const Options & options) {
string prefix_temp = options.output_file + string("_temp");
DEFAULT_CHANNEL << '[' << my_rank << "] reading input" << endl;
// Read all the Fasta files and check for duplicate names
vector<Fasta *> multi_fasta;
set<string> names;
pair<set<string>::iterator,bool> ret;
bool all_ok = true;
size_t sum = 0;
for (vector<string>::const_iterator iter = options.input_files.begin(); iter != options.input_files.end(); iter++) {
Auto_Unzip input(iter->c_str());
while (not input.eof()) {
Fasta * temp = new Fasta();
input.filtered() >> *temp;
sum += temp->length();
multi_fasta.push_back(temp);
ret = names.insert(temp->get_id());
if (ret.second == false) {
ERROR_CHANNEL << "Error: name \"" << temp->get_id() << "\" already exists!" << endl;
all_ok = false;
}
}
}
if (not all_ok) {
for (int node = 1; node < nprocs; node++)
send_sequences_to_slave(node, 0, 0, string(), string());
return;
}
DEFAULT_CHANNEL << '[' << my_rank << "] sorting" << endl;
// sort by length
if (options.balancing)
sort(multi_fasta.begin(), multi_fasta.end(), sort_reverse_function);
DEFAULT_CHANNEL << '[' << my_rank << "] preparing header" << endl;
// prepare file for header
stringstream header_name;
header_name << options.output_file << "_h.dht";
ofstream o(header_name.str().c_str());
for (vector<Fasta *>::iterator iter = multi_fasta.begin(); iter != multi_fasta.end(); iter++)
o << (*iter)->get_id() << '\t' << (*iter)->get_sequence().size() << endl;
o.close();
DEFAULT_CHANNEL << '[' << my_rank << "] preparing temporary files" << endl;
// prepare sets and create temp files
size_t bins = nprocs;
size_t bin_length[bins];
ofstream outputs[bins];
for (size_t i = 0; i < bins; i++) {
bin_length[i] = 0;
stringstream filename;
filename << prefix_temp << '_' << (i+1) << ".fasta";
temp_files.push_back(filename.str());
outputs[i].open(filename.str().c_str());
}
DEFAULT_CHANNEL << '[' << my_rank << "] writing to files" << endl;
// write to files
for (vector<Fasta *>::iterator iter = multi_fasta.begin(); iter != multi_fasta.end(); iter++) {
size_t min_pos = 0;
size_t t_min = sum;
for (size_t i = 0; i < bins; i++)
if (bin_length[i] < t_min) {
min_pos = i;
t_min = bin_length[min_pos];
}
bin_length[min_pos] += (*iter)->length();
outputs[min_pos] << **iter;
}
for (size_t i = 0; i < bins; i++) {
outputs[i].close();
}
DEFAULT_CHANNEL << '[' << my_rank << "] sending to slaves" << endl;
// send to slaves
for (size_t i = 1; i < bins; i++) {
stringstream filename_input;
stringstream filename_output;
filename_input << prefix_temp << '_' << (i+1) << ".fasta";
filename_output << options.output_file << '_' << (i+1) << ".eht";
send_sequences_to_slave(i, options.k, options.blockLength, filename_input.str(), filename_output.str());
}
DEFAULT_CHANNEL << '[' << my_rank << "] clearing memory" << endl;
// clear memory
for (vector<Fasta *>::iterator iter = multi_fasta.begin(); iter != multi_fasta.end(); iter++)
delete *iter;
DEFAULT_CHANNEL << '[' << my_rank << "] computing" << endl;
// compute by master process
stringstream filename_input;
stringstream filename_output;
filename_input << prefix_temp << "_1.fasta";
filename_output << options.output_file << "_1.eht";
compute_hash(options.k,options.blockLength,filename_input.str().c_str(), filename_output.str().c_str(),false); //TODO handle methyl_hash
DEFAULT_CHANNEL << '[' << my_rank << "] finishing" << endl;
stringstream filename_numberfile;
filename_numberfile << options.output_file << "_n.dht";
ofstream nf(filename_numberfile.str().c_str());
if (!nf) {
ERROR_CHANNEL << "I cannot open file " << filename_numberfile.str() << " for writing!" << endl;
exit(6);
}
nf << nprocs << endl;
}