// Simulate single-end sequencing from a fragment.
void SequencingSimulator::_simulateBSTreatment(seqan::Dna5String & methFragment,
TFragment const & frag,
MethylationLevels const & levels,
bool reverse)
{
methFragment = frag;
for (unsigned pos = 0; pos != length(frag); ++pos)
{
double level = reverse ? levels.levelR(pos + beginPosition(frag)) : levels.levelF(pos + beginPosition(frag));
if ((!reverse && methFragment[pos] != 'C') || (reverse && methFragment[pos] != 'G')) // Skip all non-cyteline chars
{
SEQAN_ASSERT_EQ_MSG(level, 0.0,
"Methylation for non-C should be 0 (pos+beginPosition(frag)=%d, reverse=%u",
pos + beginPosition(frag), reverse);
continue;
}
// Decide whether methFragment[pos] is methylated. If this is the case then we leave it untouched.
seqan::Pdf<seqan::Uniform<double> > pdf(0, 1);
if (pickRandomNumber(methRng, pdf) < level)
continue;
// Otherwise, pick whether we will convert.
if (pickRandomNumber(methRng, pdf) < seqOptions->bsSeqOptions.bsConversionRate)
methFragment[pos] = reverse ? 'A' : 'T';
}
}
void check_cutted_frags(CharString frag, std::vector<table_entry*> &links,
map<unsigned long long, string> &chains, unsigned int min_length){
if(length(frag) > min_length){
std::queue<int> l_link;
std::queue<int> r_link;
Pattern<CharString, ShiftOr > pattern(frag);
for(unsigned int i=0; i<links.size(); ++i){
CharString text = links[i]->get_short_read()->get_RNA_seq_sequence();
Finder<CharString> finder(text);
find(finder,pattern);
if(beginPosition(finder) < min_length){
//std::cout << "L link " << i << ::std::endl;
l_link.push(i);
}
if(endPosition(finder) > length(text) - min_length){
//std::cout << "R link" << ::std::endl;
r_link.push(i);
}
}
if(l_link.size() != 0 && r_link.size() != 0){
string head;
assign(head,frag);
for(unsigned int z=0; z<min_length*2 - length(frag);++z){
head.append("A");
}
if(chains.find(fingerprint(head)) == chains.end()){
chains[fingerprint(head)] = toCString(frag);
//std::cerr << "CUT: " << frag << " " << length(frag) << std::endl;
}else{
//std::cerr << "Problem:" << std::endl;
//std::cerr << chains[fingerprint(head)] << std::endl;
//std::cerr << toCString(frag) << std::endl;
}
//::std::cout << toCString(frag) << ::std::endl;
while(!l_link.empty()){
links[l_link.front()]->push_D_link(fingerprint(head));
l_link.pop();
}
while(!r_link.empty()){
links[r_link.front()]->push_A_link(fingerprint(head));
r_link.pop();
}
}
}
}
iterator& begin() const {
iterator it(this, beginPosition());
itbegin = it;
return itbegin;
}
void check_overlapping_nodes(::std::vector<table_entry*> & links, map<unsigned long long, string> & chains, int len,
::std::map<unsigned long long, unsigned long long>& mapping, unsigned int min_overlap,
int ov_perc){
::std::map<unsigned long long, string>::iterator chain_it;
::std::map<unsigned long long, string>::iterator chain_it_2;
::std::vector<small_frag> short_blocks;
stack<unsigned int> s;
queue<unsigned long long> q;
for(chain_it = chains.begin(); chain_it != chains.end(); ++chain_it){
for(chain_it_2 = chains.begin(); chain_it_2 != chains.end(); ++chain_it_2){
unsigned int ov = overlappedStringLength(chain_it->second,chain_it_2->second);
if(chain_it != chain_it_2 && ov < (ov_perc*chain_it->second.length())/100 &&
(ov_perc*ov < chain_it_2->second.length())/100 && ov > min_overlap){
bool new_node = false;
CharString pat_text=prefix(chain_it_2->second,ov);
//::std::cout << chain_it->second << ::std::endl;
//::std::cout << chain_it_2->second << ::std::endl;
//::std::cout << ov << ::std::endl;
Pattern<CharString, ShiftAnd> pattern(pat_text);
for(unsigned int i=0; i<links.size();++i){
CharString link_read = links[i]->get_short_read()->get_RNA_seq_sequence();
Finder<CharString> finder(link_read);
if(find(finder,pattern) && (
prefix(link_read,beginPosition(finder)) == infix(chain_it->second,chain_it->second.length()-ov-beginPosition(finder),chain_it->second.length()-ov) ||
suffix(link_read,length(link_read) - endPosition(finder)) == infix(chain_it_2->second,ov,ov+endPosition(finder)))){
//::std::cout << link_read << ::std::endl;
//::std::cout << prefix(link_read,beginPosition(finder)) << ::std::endl;
//::std::cout << infix(chain_it->second,chain_it->second.length()-ov-beginPosition(finder),chain_it->second.length()-ov) << ::std::endl;
//::std::cout << suffix(link_read,length(link_read) - endPosition(finder)) << ::std::endl;
//::std::cout << infix(chain_it_2->second,ov,ov+endPosition(finder)) << ::std::endl;
new_node = true;
}
}
if(new_node){
small_frag f;
f.frag_links.D_chain = chain_it->first;
f.frag_links.A_chain = chain_it_2->first;
f.frag = prefix(chain_it_2->second,ov);
short_blocks.push_back(f);
}
}else{
if(chain_it != chain_it_2 && ov>=(ov_perc*chain_it->second.length())/100){
//::std::cout << "Chain_it sub-node of Chain_it_2" << ::std::endl;
//::std::cout << "Chain_it " << chain_it->second << ::std::endl;
//::std::cout << "Chain_it_2 " << chain_it_2->second << ::std::endl;
//::std::cout << ov << ::std::endl;
q.push(chain_it->first);
}else{
if(chain_it != chain_it_2 && ov>=(ov_perc*chain_it_2->second.length())/100){
//::std::cout << "Chain_it_2 sub-node of Chain_it" << ::std::endl;
//::std::cout << "Chain_it " << chain_it->second << ::std::endl;
//::std::cout << "Chain_it_2 " <<chain_it_2->second << ::std::endl;
//::std::cout << ov << ::std::endl;
q.push(chain_it_2->first);
}
}
}
}
}
for(unsigned int i=0; i<short_blocks.size(); ++i){
bool sub_seq = false;
for(unsigned int k=0; k<short_blocks.size(); ++k){
if(short_blocks[i].frag == short_blocks[k].frag && i<k){
links_pair erased_links;
erased_links.D_chain = short_blocks[i].frag_links.D_chain;
erased_links.A_chain = short_blocks[i].frag_links.A_chain;
short_blocks[k].other_links.push_back(erased_links);
sub_seq = true;
}
if(i!=k && (::seqan::length(short_blocks[i].frag)) < (::seqan::length(short_blocks[k].frag))){
Finder<CharString> finder(short_blocks[k].frag);
Pattern<CharString, ShiftAnd> pattern(short_blocks[i].frag);
if(find(finder,pattern)){
links_pair erased_links;
erased_links.D_chain = short_blocks[i].frag_links.D_chain;
erased_links.A_chain = short_blocks[i].frag_links.A_chain;
//::std::cout << i << k << " - " << beginPosition(finder) << " " << endPosition(finder) << ::std::endl;
short_blocks[k].other_links.push_back(erased_links);
sub_seq = true;
}
}
}
if(sub_seq){
s.push(i);
}
}
while(!s.empty()){
short_blocks.erase(short_blocks.begin()+s.top());
s.pop();
}
while(!q.empty()){
chains.erase(q.front());
q.pop();
}
for(unsigned int i=0; i<short_blocks.size(); ++i){
//::std::cout << short_blocks[i].frag << " " << length(short_blocks[i].frag) << ::std::endl;
string ch = "";
for(unsigned int z = 0; z<len-length(short_blocks[i].frag); ++z){
ch.append("A");
}
ch.append(toCString(short_blocks[i].frag));
//if(chains.find(fingerprint(ch)) == chains.end()){//Start_If_5
//chains[fingerprint(ch)] = ::seqan::toCString(short_blocks[i].frag);
//::std::cout << ::seqan::toCString(short_blocks[i].frag) <<" "<< length(short_blocks[i].frag)<<::std::endl;
//mapping[fingerprint(ch)] = fingerprint(ch);
//Add the first link
string first_half;
assign(first_half,prefix(chains[short_blocks[i].frag_links.D_chain],len));
string new_link_1 = first_half;
new_link_1.append(ch);
table_entry* link_1 = new table_entry(new_link_1,fingerprint(first_half),fingerprint(ch));
link_1->push_D_link(short_blocks[i].frag_links.D_chain);
link_1->push_A_link(short_blocks[i].frag_links.A_chain);
links.push_back(link_1);
/*
//Add the second link
string second_half;
assign(second_half,prefix(chains[short_blocks[i].frag_links.A_chain],len));
string new_link_2 = ch;
new_link_2.append(second_half);
table_entry* link_2 = new table_entry(new_link_2,fingerprint(ch),fingerprint(second_half));
link_2->push_D_link(short_blocks[i].frag_links.D_chain);
link_2->push_A_link(short_blocks[i].frag_links.A_chain);
links.push_back(link_2);
*/
//::std::cout<<links[short_blocks[i].frag_links.D_chain]->get_short_read()->get_RNA_seq_sequence()<<::std::endl;
//::std::cout<<links[short_blocks[i].frag_links.A_chain]->get_short_read()->get_RNA_seq_sequence()<<::std::endl;
for(unsigned int j=0; j<short_blocks[i].other_links.size(); ++j){//Start_For_6
string second_half;
assign(first_half,prefix(chains[short_blocks[i].other_links[j].D_chain],len));
string new_link_2 = second_half;
new_link_2.append(ch);
table_entry* link_2 = new table_entry(new_link_2,fingerprint(second_half),fingerprint(ch));
link_2->push_D_link(short_blocks[i].other_links[j].D_chain);
link_2->push_A_link(short_blocks[i].other_links[j].A_chain);
links.push_back(link_1);
}//End_For_6
//}//End_If_5
}
}
void linking_refinement(::std::vector<table_entry*> & links, map<unsigned long long, string> & chains, unsigned int len,
::std::map<unsigned long long, unsigned long long> & mapping){
for(unsigned int i=0; i<links.size(); ++i){
//Linkato solo a dx
if(links[i]->size_D_link() == 0 && links[i]->size_A_link() != 0){
//::std::cout << "D link" << ::std::endl;
CharString p = ::seqan::prefix(links[i]->get_short_read()->get_RNA_seq_sequence(),len);
Pattern<CharString, ShiftOr > pattern(p);
::std::map<unsigned long long, string>::iterator chain_it;
::std::set<unsigned long long> modif_chains;
for(chain_it = chains.begin(); chain_it != chains.end(); ++chain_it){
CharString text = chain_it->second;
Finder<CharString> finder(text);
if(modif_chains.find(chain_it->first) == modif_chains.end() && find(finder,pattern)){
links[i]->push_D_link(chain_it->first);
if(chain_it->second.length()- endPosition(finder) > len){
//::std::cout << "D " << (i+1) << " " << beginPosition(finder) << ::std::endl;
CharString pre = ::seqan::prefix(chain_it->second, beginPosition(finder) + len);
string str_pre = ::seqan::toCString(pre);
CharString suf = ::seqan::suffix(chain_it->second, beginPosition(finder) + len);
string str_suf = ::seqan::toCString(suf);
//::std::cout << chain_it->second << " - " << chain_it->second.length() << ::std::endl;
//Sono sicuro che sia > len dato che la estraggo da un prefisso
//di lunghezza len...
chains[chain_it->first] = str_pre;
//::std::cout << str_pre << " - " << str_pre.length() << ::std::endl;
modif_chains.insert(chain_it->first);
//...ma il suffissopotrebbe essere piu' corto di len
string head;
if(str_suf.length() >= len){
head = ::seqan::toCString(::seqan::prefix(suf,len));
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}else{
head = str_suf;
for(unsigned int z=0; z<len-str_suf.length();++z){
head.append("A");
}
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}
//::std::cout << str_suf << " - " << str_suf.length() << ::std::endl << ::std::endl;
modif_chains.insert(fingerprint(head));
for(unsigned int z=0; z<links.size();++z){
for(int k=0; k<links[z]->size_D_link();++k){
if(links[z]->at_D_link(k) == chain_it->first){
links[z]->at_D_link(k) = fingerprint(head);
}
}
}
//Aggiungere un link tra le due catene create
CharString l_part = chains[chain_it->first];
string new_link = ::seqan::toCString(::seqan::suffix(l_part,length(l_part) - len));
unsigned long long f_l = fingerprint(new_link);
new_link.append(head);
table_entry* t_new = new table_entry(new_link,f_l,fingerprint(head));
t_new->push_D_link(chain_it->first);
t_new->push_A_link(fingerprint(head));
links.push_back(t_new);
}
}
}
}
//Linkato solo a sx
if(links[i]->size_A_link() == 0 && links[i]->size_D_link() != 0){
//::std::cout << "A link" << ::std::endl;
CharString p = ::seqan::suffix(links[i]->get_short_read()->get_RNA_seq_sequence(),len);
Pattern<CharString, ShiftOr > pattern(p);
::std::map<unsigned long long, string>::iterator chain_it;
::std::set<unsigned long long> modif_chains;
for(chain_it = chains.begin(); chain_it != chains.end(); ++chain_it){
CharString text = chain_it->second;
Finder<CharString> finder(text);
if(modif_chains.find(chain_it->first) == modif_chains.end() && find(finder,pattern)){
//if(find(finder,pattern)){
//::std::cout << "1 - if " << beginPosition(finder) << " " << endPosition(finder) << ::std::endl;
if(beginPosition(finder) == 0){
links[i]->push_A_link(chain_it->first);
}
if(endPosition(finder) > len){
//::std::cout << "A " << (i+1) << " " << beginPosition(finder) << ::std::endl;
CharString pre = ::seqan::prefix(chain_it->second, beginPosition(finder) + len);
string str_pre = ::seqan::toCString(pre);
CharString suf = ::seqan::suffix(chain_it->second, beginPosition(finder) + len);
string str_suf = ::seqan::toCString(suf);
chains[chain_it->first] = str_pre;
//::std::cout << str_pre << " - " << str_pre.length() << ::std::endl;
modif_chains.insert(chain_it->first);
string head;
if(str_suf.length() >= len){
head = ::seqan::toCString(::seqan::prefix(suf,len));
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}else{
head = str_suf;
for(unsigned int z=0; z<len-str_suf.length();++z){
head.append("A");
}
chains[fingerprint(head)] = str_suf;
mapping[fingerprint(head)] = fingerprint(head);
}
//::std::cout << str_suf << " - " << str_suf.length() << ::std::endl << ::std::endl;
modif_chains.insert(fingerprint(head));
for(unsigned int z=0; z<links.size();++z){
for(int k=0; k<links[z]->size_D_link();++k){
if(links[z]->at_D_link(k) == chain_it->first){
links[z]->at_D_link(k) = fingerprint(head);
}
}
}
//Aggiungere un link tra le due catene create
CharString l_part = chains[chain_it->first];
string new_link = ::seqan::toCString(::seqan::suffix(l_part,length(l_part) - len));
unsigned long long f_l = fingerprint(new_link);
new_link.append(head);
table_entry* t_new = new table_entry(new_link,f_l,fingerprint(head));
t_new->push_D_link(chain_it->first);
t_new->push_A_link(fingerprint(head));
links.push_back(t_new);
links[i]->push_A_link(fingerprint(head));
}
}
}
}
}
//::std::cout << chains.size() << ::std::endl;
}
