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#ifndef TRANSCRIPT_H_
#define TRANSCRIPT_H_
#include<cstdio>
#include<cstdlib>
#include<cassert>
#include<string>
#include<vector>
#include<fstream>
#include<sstream>
#include "utils.h"
/**
If no genome is provided, seqname field is used to store the allele name.
*/
struct Interval {
int start, end;
Interval(int start, int end) {
this->start = start;
this->end = end;
}
};
class Transcript {
public:
Transcript() {
length = 0;
structure.clear();
strand = 0;
seqname = gene_id = transcript_id = "";
gene_name = transcript_name = "";
left = "";
}
Transcript(const std::string& transcript_id, const std::string& gene_id, const std::string& seqname,
const char& strand, const std::vector<Interval>& structure, const std::string& left,
const std::string& transcript_name = "", const std::string& gene_name = "") : structure(structure), strand(strand),
seqname(seqname), gene_id(gene_id), transcript_id(transcript_id), gene_name(gene_name), transcript_name(transcript_name) {
//eliminate prefix spaces in string variable "left"
int pos = 0;
int len = left.length();
while (pos < len && left[pos] == ' ') ++pos;
this->left = left.substr(pos);
length = 0;
int s = structure.size();
for (int i = 0; i < s; i++) length += structure[i].end + 1 - structure[i].start;
}
bool operator< (const Transcript& o) const {
return gene_id < o.gene_id || (gene_id == o.gene_id && transcript_id < o.transcript_id) || (gene_id == o.gene_id && transcript_id == o.transcript_id && seqname < o.seqname);
}
const std::string& getTranscriptID() const { return transcript_id; }
const std::string& getTranscriptName() const { return transcript_name; }
const std::string& getGeneID() const { return gene_id; }
const std::string& getGeneName() const { return gene_name; }
const std::string& getSeqName() const { return seqname; }
char getStrand() const { return strand; }
const std::string& getLeft() const { return left; }
int getLength() const { return length; }
const std::vector<Interval>& getStructure() const { return structure; }
void extractSeq (const std::string&, std::string&) const;
void read(std::ifstream&);
void write(std::ofstream&);
private:
int length; // transcript length
std::vector<Interval> structure; // transcript structure , coordinate starts from 1
char strand;
std::string seqname, gene_id, transcript_id; // follow GTF definition
std::string gene_name, transcript_name;
std::string left;
};
//gseq : genomic sequence
void Transcript::extractSeq(const std::string& gseq, std::string& seq) const {
seq = "";
int s = structure.size();
size_t glen = gseq.length();
if (structure[0].start < 1 || (size_t)structure[s - 1].end > glen) {
fprintf(stderr, "Transcript %s is out of chromosome %s's boundary!\n", transcript_id.c_str(), seqname.c_str());
exit(-1);
}
switch(strand) {
case '+':
for (int i = 0; i < s; i++) {
seq += gseq.substr(structure[i].start - 1, structure[i].end - structure[i].start + 1); // gseq starts from 0!
}
break;
case '-':
for (int i = s - 1; i >= 0; i--) {
for (int j = structure[i].end; j >= structure[i].start; j--) {
seq += getOpp(gseq[j - 1]);
}
}
break;
default: assert(false);
}
assert(seq.length() > 0);
}
void Transcript::read(std::ifstream& fin) {
int s;
std::string tmp;
std::istringstream strin;
getline(fin, tmp);
strin.str(tmp);
getline(strin, transcript_id, '\t');
getline(strin, transcript_name);
getline(fin, tmp);
strin.clear(); strin.str(tmp);
getline(strin, gene_id, '\t');
getline(strin, gene_name);
getline(fin, seqname);
fin>>tmp>>length;
assert(tmp.length() == 1 && (tmp[0] == '+' || tmp[0] == '-'));
strand = tmp[0];
structure.clear();
fin>>s;
for (int i = 0; i < s; i++) {
int start, end;
fin>>start>>end;
structure.push_back(Interval(start, end));
}
getline(fin, tmp); //get the end of this line
getline(fin, left);
}
void Transcript::write(std::ofstream& fout) {
int s = structure.size();
fout<< transcript_id;
if (transcript_name != "") fout<< '\t'<< transcript_name;
fout<< std::endl;
fout<< gene_id;
if (gene_name != "") fout<< '\t'<< gene_name;
fout<< std::endl;
fout<<seqname<<std::endl;
fout<<strand<<" "<<length<<std::endl;
fout<<s;
for (int i = 0; i < s; i++) fout<<" "<<structure[i].start<<" "<<structure[i].end;
fout<<std::endl;
fout<<left<<std::endl;
}
#endif /* TRANSCRIPT_H_ */
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