16 seqname = source = feature = "";
19 strand = 0; //strand is a char variable
21 gene_id = transcript_id = "";
25 bool operator<(const GTFItem& o) const {
26 if (gene_id != o.gene_id) return gene_id < o.gene_id;
27 if (transcript_id != o.transcript_id) return transcript_id < o.transcript_id;
28 return start < o.start;
31 void my_assert(char value, std::string& line, const std::string& msg) {
33 fprintf(stderr, ".gtf file might be corrupted!\n");
34 fprintf(stderr, "Stop at line : %s\n", line.c_str());
35 fprintf(stderr, "Error Message: %s\n", msg.c_str());
40 void parse(std::string line) {
41 std::istringstream strin(line);
44 getline(strin, seqname, '\t');
45 getline(strin, source, '\t');
46 getline(strin, feature, '\t');
47 getline(strin, tmp, '\t');
48 start = atoi(tmp.c_str());
49 getline(strin, tmp, '\t');
50 end = atoi(tmp.c_str());
51 getline(strin, score, '\t');
52 getline(strin, tmp, '\t');
53 my_assert((tmp.length() == 1 && (tmp[0] == '+' || tmp[0] == '-')), line, "Strand is neither '+' nor '-'!");
55 getline(strin, frame, '\t');
57 getline(strin, tmp, ';'); tmp = cleanStr(tmp);
58 my_assert((tmp.substr(0, 7) == "gene_id"), line, "Identifier should be gene_id!");
59 tmp = cleanStr(tmp.substr(7));
60 my_assert((tmp[0] == '"' && tmp[tmp.length() - 1] == '"'), line, "Textual attributes should be surrounded by doublequotes!");
61 gene_id = tmp.substr(1, tmp.length() - 2);
63 getline(strin, tmp, ';'); tmp = cleanStr(tmp);
64 my_assert((tmp.substr(0, 13) == "transcript_id"), line, "Identifier should be transcript_id!");
65 tmp = cleanStr(tmp.substr(13));
66 my_assert((tmp[0] == '"' && tmp[tmp.length() - 1] == '"'), line, "Textual attributes should be surrounded by doublequotes!");
67 transcript_id = tmp.substr(1, tmp.length() - 2);
72 std::string getSeqName() { return seqname; }
73 std::string getSource() { return source; }
74 std::string getFeature() { return feature; }
75 int getStart() { return start; }
76 int getEnd() { return end; }
77 char getStrand() { return strand; }
78 std::string getScore() { return score; } // float, integer or "." ; let downstream programs parse it
79 std::string getFrame() { return frame; } // 0, 1, 2, or "."; let downstream programs parse it
80 std::string getGeneID() { return gene_id; }
81 std::string getTranscriptID() { return transcript_id; }
82 std::string getLeft() { return left; }
84 void setGeneID(const std::string& gene_id) {
85 this->gene_id = gene_id;
88 std::string toString() {
90 std::ostringstream strout;
91 strout<<seqname<<'\t'<<source<<'\t'<<feature<<'\t'<<start<<'\t'<<end<<'\t'<<score<<'\t'<<strand<<'\t'<<frame<<'\t';
92 strout<<"gene_id \""<<gene_id<<"\"; transcript_id \""<<transcript_id<<"\";"<<left;
99 std::string seqname, source, feature;
104 std::string gene_id, transcript_id;