bool IRKE::sequence_path_exists(string &sequence, unsigned int min_coverage, float min_entropy, float min_connectivity,
vector<unsigned int> &coverage_counter)
{
unsigned int kmer_length = kcounter.get_kmer_length();
if (sequence.length() < kmer_length) {
return (false);
}
bool path_exists = true;
string prev_kmer = sequence.substr(0, kmer_length);
if (contains_non_gatc(prev_kmer) || !kcounter.kmer_exists(prev_kmer)) {
path_exists = false;
coverage_counter.push_back(0);
}
else {
unsigned int kmer_count = kcounter.get_kmer_count(prev_kmer);
coverage_counter.push_back(kmer_count);
float entropy = compute_entropy(prev_kmer);
if (kmer_count < min_coverage || entropy < min_entropy) {
path_exists = false;
}
}
for (unsigned int i = 1; i <= sequence.length() - kmer_length; i++) {
string kmer = sequence.substr(i, kmer_length);
if (contains_non_gatc(kmer) || !kcounter.kmer_exists(kmer)) {
path_exists = false;
coverage_counter.push_back(0);
}
else {
unsigned int kmer_count = kcounter.get_kmer_count(kmer);
coverage_counter.push_back(kmer_count);
float entropy = compute_entropy(kmer);
if (kmer_count < min_coverage || entropy < min_entropy) {
path_exists = false;
}
}
if (path_exists && !exceeds_min_connectivity(kcounter, prev_kmer, kmer, min_connectivity)) {
path_exists = false;
}
prev_kmer = kmer;
}
return (path_exists);
}
vector<unsigned int> compute_kmer_coverage(string& sequence, KmerCounter& kcounter) {
vector<unsigned int> coverage;
if(IRKE_COMMON::MONITOR) {
cerr << "processing sequence: " << sequence << endl;
}
for (int i = 0; i <= (int) sequence.length() - KMER_SIZE; i++) {
// cerr << "i: " << i << ", <= " << sequence.length() - KMER_SIZE << endl;
string kmer = sequence.substr(i, KMER_SIZE);
if(IRKE_COMMON::MONITOR >= 2) {
for (int j = 0; j <= i; j++) {
cerr << " ";
}
cerr << kmer << endl;
}
unsigned int kmer_count = 0;
if(!contains_non_gatc(kmer)) {
kmer_count = kcounter.get_kmer_count(kmer);
}
// Note, in the jellyfish run, we restrain it to min kmer coverage of 2.
// If we don't find a kmer catalogued, it must have a kmer count of 1.
if (kmer_count < 1) {
kmer_count = 1;
}
coverage.push_back(kmer_count);
}
return(coverage);
}
vector<unsigned int> compute_kmer_coverage(string& sequence, KmerCounter& kcounter) {
if(IRKE_COMMON::MONITOR) {
cerr << "processing sequence: " << sequence << endl;
}
if (sequence.length() < KMER_SIZE)
{
// Can't rely on length() - KMER_SIZE for this as length is unsigned
cerr << "Sequence: " << sequence << "is smaller than " << KMER_SIZE << " base pairs, skipping" << endl;
return vector<unsigned int>();
}
vector<unsigned int> coverage;
for (size_t i = 0; i <= sequence.length() - KMER_SIZE; i++) {
// cerr << "i: " << i << ", <= " << sequence.length() - KMER_SIZE << endl;
string kmer = sequence.substr(i, KMER_SIZE);
if(IRKE_COMMON::MONITOR >= 2) {
for (size_t j = 0; j <= i; j++) {
cerr << " ";
}
cerr << kmer << endl;
}
unsigned int kmer_count = 0;
if(!contains_non_gatc(kmer)) {
kmer_count = kcounter.get_kmer_count(kmer);
}
// Note, in the jellyfish run, we restrain it to min kmer coverage of 2.
// If we don't find a kmer catalogued, it must have a kmer count of 1.
if (kmer_count < 1) {
kmer_count = 1;
}
coverage.push_back(kmer_count);
}
return(coverage);
}
int run (int argc, char* argv[]) {
if (argc < 3) {
stringstream s;
s << "Usage: " << argv[0] << " file.fasta kmer_length [DS_mode]" << endl << endl;
cerr << s.str();
return(1);
}
string fasta_filename (argv[1]);
unsigned int kmer_length = atoi(argv[2]);
bool DS_mode = (argc >= 3) ? true : false;
Fasta_reader fasta_reader(fasta_filename);
Ktree ktree;
long read_counter = 0;
while (fasta_reader.hasNext()) {
read_counter++;
if (read_counter % 1000 == 0) {
cerr << "\rread[" << read_counter << "] ";
}
Fasta_entry fe = fasta_reader.getNext();
string accession = fe.get_accession();
string sequence = fe.get_sequence();
// cerr << "Processing: " << sequence << endl;
if (sequence.length() < kmer_length + 1) {
continue;
}
for (unsigned int i = 0; i <= sequence.length() - kmer_length; i++) {
string kmer = sequence.substr(i, kmer_length);
if (! contains_non_gatc(kmer)) {
ktree.add_kmer(kmer);
if (DS_mode) {
kmer = revcomp(kmer);
ktree.add_kmer(kmer);
}
}
}
}
ktree.report_kmer_counts();
return(0);
}