Beispiel #1
0
int runMe(int argc, char* argv[]) {

    ArgProcessor args(argc, argv);
    if(args.isArgSet("--help") ||
       (!(args.isArgSet("--reads")
          &&
          ( args.isArgSet("--kmers") || args.isArgSet("--kmers_from_reads") )
          )) ) {
        cerr << usage(args) << endl << endl;
        exit(1);
    }

    string reads_fasta_file = args.getStringVal("--reads");
    
    bool is_DS = (! args.isArgSet("--SS"));
    if(args.isArgSet("--kmer_size")) {
        KMER_SIZE = args.getIntVal("--kmer_size");
        if(KMER_SIZE < 20) {
            cerr << "Error, min kmer size is 20";
            exit(2);
        }
    }
    if(args.isArgSet("--monitor")) {
        IRKE_COMMON::MONITOR = args.getIntVal("--monitor");
    }
    if (args.isArgSet("--num_threads")) {
        int num_threads = args.getIntVal("--num_threads");
        if (num_threads < MAX_THREADS) {
            omp_set_num_threads(num_threads);
        }
        else {
            // set to max
            omp_set_num_threads(MAX_THREADS);
        }
    }
    
    if(omp_get_max_threads() > MAX_THREADS) {
        omp_set_num_threads(MAX_THREADS);
    }
    KmerCounter kcounter (KMER_SIZE, is_DS);

    if (args.isArgSet("--kmers")) {
        string kmers_fasta_file = args.getStringVal("--kmers");
        populate_kmer_counter_from_kmers(kcounter, kmers_fasta_file);
    }
    else {
        string kmer_read_source_fasta_file = args.getStringVal("--kmers_from_reads");
        populate_kmer_counter_from_reads(kcounter, kmer_read_source_fasta_file);
    }
    
    Fasta_reader fasta_reader(reads_fasta_file);
    bool write_coverage_info = args.isArgSet("--capture_coverage_info");
    
    int start_time = time(NULL);

    #pragma omp parallel
    while (true) {

        if (! fasta_reader.hasNext())
            break;
        
        int myTid = omp_get_thread_num();
        
        Fasta_entry fe = fasta_reader.getNext();
        string sequence = fe.get_sequence();
        if(sequence == "")
            continue;

        string header = fe.get_header();
        vector<unsigned int> kmer_coverage = compute_kmer_coverage(sequence, kcounter);
        unsigned int median_cov = median_coverage(kmer_coverage);
        float mean_cov = mean(kmer_coverage);
        float stdev = stDev(kmer_coverage);
        float pct_stdev_of_avg = stdev/mean_cov*100;
        stringstream stats_text;
                
        stats_text << median_cov << "\t"
                   << mean_cov << "\t"
                   << stdev << "\t"
                   << pct_stdev_of_avg << "\t"
                   << fe.get_accession();

        stats_text << "\tthread:" << myTid;
        
        if(write_coverage_info) {
            // add the coverage info
            stats_text << "\t";
            for (size_t i = 0; i < kmer_coverage.size(); i++) {
                stats_text<< kmer_coverage[i];
                if(i != kmer_coverage.size() - 1) {
                    stats_text<< ",";
                }
            }
        }
        stats_text << endl;
        
        #pragma omp critical 
        {
            cout << stats_text.str();
        }
        
        if (mean_cov < 0) {
            cerr << "ERROR, cannot have negative coverage!!" << endl;
            exit(1);
        }
        
    }

    int end_time = time(NULL);

    cerr << "STATS_GENERATION_TIME: " << (end_time - start_time) << " seconds." << endl;
    
    return(0);
}
int main(int argc, char* argv[]) {
    ArgProcessor args(argc, argv);
    if(args.isArgSet("--help") ||
       (!(args.isArgSet("--reads") && args.isArgSet("--kmers")))) {
        cerr << usage(args) << endl << endl;
        exit(1);
    }
    string reads_fasta_file = args.getStringVal("--reads");
    string kmers_fasta_file = args.getStringVal("--kmers");
    bool is_DS = (! args.isArgSet("--SS"));
    if(args.isArgSet("--kmer_size")) {
        KMER_SIZE = args.getIntVal("--kmer_size");
        if(KMER_SIZE < 20) {
            cerr << "Error, min kmer size is 20";
            exit(2);
        }
    }
    if(args.isArgSet("--monitor")) {
        IRKE_COMMON::MONITOR = args.getIntVal("--monitor");
    }
    if(omp_get_max_threads() > MAX_THREADS) {
        omp_set_num_threads(MAX_THREADS);
    }
    KmerCounter kcounter (KMER_SIZE, is_DS);
    populate_kmer_counter(kcounter, kmers_fasta_file);
    Fasta_reader fasta_reader(reads_fasta_file);
    ofstream* filewriter = NULL;
    ofstream* covwriter = NULL;
    bool write_coverage_info = args.isArgSet("--capture_coverage_info");
    while (true) {
        Fasta_entry fe = fasta_reader.getNext();
        string sequence = fe.get_sequence();
        if(sequence == "") break;
        string header = fe.get_header();
        vector<unsigned int> kmer_coverage = compute_kmer_coverage(sequence, kcounter);
        unsigned int median_cov = median_coverage(kmer_coverage);
        float mean_cov = mean(kmer_coverage);
        float stdev = stDev(kmer_coverage);
        float pct_stdev_of_avg = stdev/mean_cov*100;
        stringstream stats_text;
        stats_text << median_cov << "\t"
                   << mean_cov << "\t"
                   << stdev << "\t"
                   << pct_stdev_of_avg << "\t"
                   << fe.get_accession();
        if(write_coverage_info) {
            // add the coverage info
            stats_text << "\t";
            for (int i = 0; i < kmer_coverage.size(); i++) {
                stats_text<< kmer_coverage[i];
                if(i != kmer_coverage.size() - 1) {
                    stats_text<< ",";
                }
            }
        }
        stats_text << endl;
        cout << stats_text.str();

        if (mean_cov < 0) {
            cerr << "ERROR, cannot have negative coverage!!" << endl;
            exit(1);
        }
        
    }
    return(0);
}