void Assemble(HashGraph &hash_graph)
{
cout << "kmers " << hash_graph.num_vertices() << " "<< hash_graph.num_edges() << endl;
int kmer_size = hash_graph.kmer_size();
double min_cover = max(1, (kmer_size == option.mink ? option.min_count : option.min_support));
Histgram<int> hist = hash_graph.coverage_histgram();
double expected_coverage = hist.mean();
deque<Sequence> contigs;
deque<ContigInfo> contig_infos;
hash_graph.Assemble(contigs, contig_infos);
hash_graph.clear();
{
HashGraph tmp_hash_graph;
tmp_hash_graph.swap(hash_graph);
}
ContigGraph contig_graph(kmer_size, contigs, contig_infos);
contigs.clear();
contig_infos.clear();
contig_graph.RemoveDeadEnd(option.min_contig);
int bubble = contig_graph.RemoveBubble();
cout << "merge bubble " << bubble << endl;
contig_graph.MergeSimilarPath();
if (!option.is_no_coverage)
contig_graph.RemoveLocalLowCoverage(min_cover, option.min_contig, 0.1);
contig_graph.SortVertices();
contig_graph.GetContigs(contigs, contig_infos);
WriteSequence(option.graph_file(kmer_size), contigs);
contigs.clear();
contig_infos.clear();
if (!option.is_no_coverage)
{
double ratio = (kmer_size < option.maxk) ? 0.5 : 0.2;
if (ratio < 2.0 / expected_coverage)
ratio = 2.0 / expected_coverage;
contig_graph.IterateLocalCoverage(option.min_contig, ratio, min_cover, 1e100, 1.1);
contig_graph.MergeSimilarPath();
}
deque<Sequence> multi_contigs;
deque<ContigInfo> multi_contig_infos;
contig_graph.SortVertices();
contig_graph.GetContigs(multi_contigs, multi_contig_infos);
PrintN50(multi_contigs);
//WriteSequence(option.contig_file(kmer_size), multi_contigs);
WriteContig(option.contig_file(kmer_size), multi_contigs, multi_contig_infos, FormatString("contig-%d", kmer_size));
//WriteContigInfo(option.contig_info_file(kmer_size), multi_contig_infos);
}
void IterateHashGraph(AssemblyInfo &assembly_info, int new_kmer_size, int min_support, HashGraph &hash_graph, deque<Sequence> &old_contigs)
{
int old_kmer_size = hash_graph.kmer_size();
deque<ShortSequence> &reads = assembly_info.reads;
deque<Sequence> &long_reads = assembly_info.long_reads;
vector<bool> &read_flags = assembly_info.read_flags;
vector<bool> &long_read_flags = assembly_info.long_read_flags;
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)old_contigs.size(); ++i)
hash_graph.InsertUncountKmers(old_contigs[i]);
hash_graph.AddAllEdges();
deque<Sequence> contigs;
hash_graph.Assemble(contigs);
hash_graph.clear();
uint64_t sum = 0;
int d = new_kmer_size - old_kmer_size;
for (unsigned i = 0; i < contigs.size(); ++i)
{
if ((int)contigs[i].size() - old_kmer_size + 1 >= 2*d + 2)
sum += 2*d + 2;
else if ((int)contigs[i].size() >= old_kmer_size)
sum += contigs[i].size() - old_kmer_size + 1;
}
HashGraph old_hash_graph(old_kmer_size);
old_hash_graph.reserve(sum);
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)contigs.size(); ++i)
{
Sequence seq;
seq.Assign(contigs[i], 0, min(new_kmer_size, (int)contigs[i].size()));
old_hash_graph.InsertKmers(seq);
seq.Assign(contigs[i], max(0, (int)contigs[i].size() - new_kmer_size), min(new_kmer_size, (int)contigs[i].size()));
old_hash_graph.InsertKmers(seq);
}
//cout << "old kmer " << old_hash_graph.num_vertices() << endl;
hash_graph.set_kmer_size(new_kmer_size);
#pragma omp parallel for
for (int64_t i = 0; i < (int64_t)reads.size(); ++i)
{
if (!read_flags[i])
continue;
Sequence seq(reads[i]);
InsertIterativeKmers(old_hash_graph, seq, hash_graph);
}
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)long_reads.size(); ++i)
{
if (!long_read_flags[i])
continue;
InsertIterativeKmers(old_hash_graph, long_reads[i], hash_graph);
}
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)assembly_info.ref_contigs.size(); ++i)
InsertIterativeKmers(old_hash_graph, assembly_info.ref_contigs[i], hash_graph);
old_hash_graph.clear();
{
HashGraph tmp_hash_graph;
tmp_hash_graph.swap(old_hash_graph);
}
hash_graph.RefreshVertices(min_support);
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)old_contigs.size(); ++i)
hash_graph.InsertUncountKmers(old_contigs[i]);
hash_graph.ClearCount();
InsertExistKmers(assembly_info, hash_graph);
}
void process_commands(std::string preface) {
for (;;) try {
std::string command = menu_prompt(preface);
if (command == "an") {
std::string n = ics::prompt_string(" Enter node name");
g.add_node(n);
}
else if (command == "ae") {
std::string o = ics::prompt_string(" Enter origin node name");
std::string d = ics::prompt_string(" Enter destination node name");
int v = ics::prompt_int (" Enter value for this edge ");
g.add_edge(o,d,v);
}
else if (command == "rn") {
std::string n = ics::prompt_string(" Enter node name");
g.remove_node(n);
}
else if (command == "re") {
std::string o = ics::prompt_string(" Enter origin node name");
std::string d = ics::prompt_string(" Enter destination node name");
g.remove_edge(o,d);
}
else if (command == "x")
g.clear();
else if (command == "=") {
ics::HashGraph<int> g2(ics::prompt_graph());
g = g2;
}
else if (command == "m")
std::cout << " empty() = " << g.empty() << std::endl;
else if (command == "#n")
std::cout << " node_count() = " << g.node_count() << std::endl;
else if (command == "#e")
std::cout << " edge_count() = " << g.edge_count() << std::endl;
else if (command == "n") {
std::string n = ics::prompt_string(" Enter node name");
std::cout << " has_node(...) = " << g.has_node(n) << std::endl;
}
else if (command == "e") {
std::string o = ics::prompt_string(" Enter origin node name");
std::string d = ics::prompt_string(" Enter destination node name");
std::cout << " has_edge(...) = " << g.has_edge(o,d) << std::endl;
}
else if (command == "v") {
std::string o = ics::prompt_string(" Enter origin node name");
std::string d = ics::prompt_string(" Enter destination node name");
std::cout << " edge_value(...) = " << g.edge_value(o,d) << std::endl;
}
else if (command == "i") {
std::string n = ics::prompt_string(" Enter node name");
std::cout << " in_degree(...) = " << g.in_degree(n) << std::endl;
}
else if (command == "o") {
std::string n = ics::prompt_string(" Enter node name");
std::cout << " out_degree(...) = " << g.out_degree(n) << std::endl;
}
else if (command == "d") {
std::string n = ics::prompt_string(" Enter node name");
std::cout << " degree(...) = " << g.degree(n) << std::endl;
}
else if (command == "<")
std::cout << preface+" << = " << g << std::endl;
else if (command == "r") {
std::cout << " g == g = " << (g == g) << std::endl;
std::cout << " g != g = " << (g != g) << std::endl;
ics::HashGraph<int> g2(ics::prompt_graph());
std::cout << " g == g2 = " << (g == g2) << std::endl;
std::cout << " g != g2 = " << (g != g2) << std::endl;
}
else if (command == "l") {
std::string separator = prompt_string(" Enter separator used in file");
std::ifstream in_file;
ics::safe_open(in_file," Enter file name to read graph from","graph.txt");
g.load(in_file,separator);
}
else if (command == "s") {
std::string separator = prompt_string(" Enter separator to use in file");
std::ofstream out_file;
out_file.open(ics::prompt_string(" Enter file name to store graph in").c_str());
if (out_file.fail())
std::cout << " Illegal file name" << std :: endl;
else
g.store(out_file,separator);
}
else if (command == "q")
break;
else
std::cout << preface+"\""+command+"\" is unknown command" << std::endl;
} catch (ics::IcsError& e) {
std::cout << preface+" " << e.what() << std::endl;
}
}
void Assemble(HashGraph &hash_graph)
{
cout << "kmers " << hash_graph.num_vertices() << " "<< hash_graph.num_edges() << endl;
int kmer_size = hash_graph.kmer_size();
double min_cover = max(1, (kmer_size == option.mink ? option.min_count : option.min_support));
Histgram<int> hist = hash_graph.coverage_histgram();
//double expected_coverage = hist.mean();
deque<Sequence> contigs;
deque<ContigInfo> contig_infos;
hash_graph.Assemble(contigs, contig_infos);
hash_graph.clear();
{
HashGraph tmp_hash_graph;
tmp_hash_graph.swap(hash_graph);
}
ContigGraph contig_graph(kmer_size, contigs, contig_infos);
contigs.clear();
contig_infos.clear();
if (!option.is_no_coverage)
{
contig_graph.RemoveStandAlone(kmer_size);
int bubble = contig_graph.RemoveBubble();
cout << "merge bubble " << bubble << endl;
contig_graph.RemoveLocalLowCoverage(min_cover, option.min_contig, 0.1);
}
contig_graph.SortVertices();
contig_graph.GetContigs(contigs, contig_infos);
WriteSequence(option.graph_file(kmer_size), contigs);
contigs.clear();
contig_infos.clear();
if (!option.is_no_coverage)
{
double ratio = 0.25;
deque<Sequence> multi_contigs;
deque<ContigInfo> multi_contig_infos;
contig_graph.GetContigs(multi_contigs, multi_contig_infos);
PrintN50(multi_contigs);
contig_graph.Trim(10);
contig_graph.MergeSimilarPath();
contig_graph.GetContigs(multi_contigs, multi_contig_infos);
contig_graph.InitializeTable();
contig_graph.IterateComponentCoverage2(option.min_contig, ratio, min_cover, 1e100, 1.1, max_component_size);
contig_graph.GetContigs(multi_contigs, multi_contig_infos);
contig_graph.Trim(10);
contig_graph.Prune(kmer_size);
contig_graph.GetContigs(multi_contigs, multi_contig_infos);
contig_graph.MergeSimilarPath();
}
deque<Sequence> multi_contigs;
deque<ContigInfo> multi_contig_infos;
contig_graph.SortVertices();
contig_graph.GetContigs(multi_contigs, multi_contig_infos);
PrintN50(multi_contigs);
WriteSequence(option.contig_file(kmer_size), multi_contigs);
WriteContigInfo(option.contig_info_file(kmer_size), multi_contig_infos);
deque<Sequence> transcripts;
FindIsoforms(contig_graph, transcripts);
int index = 0;
for (unsigned i = 0; i < transcripts.size(); ++i)
{
if (transcripts[i].size() >= 300)
transcripts[index++] = transcripts[i];
}
transcripts.resize(index);
PrintN50(transcripts);
WriteSequence(option.transcript_file(kmer_size), transcripts, FormatString("transcript-%d", kmer_size));
}