#include "utils.h"
class GTFItem {
- public:
-
- GTFItem() {
- seqname = source = feature = "";
- score = "";
- start = end = 0;
- strand = 0; //strand is a char variable
- frame = "";
- gene_id = transcript_id = "";
- left = "";
- }
-
- bool operator<(const GTFItem& o) const {
- if (gene_id != o.gene_id) return gene_id < o.gene_id;
- if (transcript_id != o.transcript_id) return transcript_id < o.transcript_id;
- return start < o.start;
- }
-
- void my_assert(char value, std::string& line, const std::string& msg) {
- if (!value) {
- fprintf(stderr, ".gtf file might be corrupted!\n");
- fprintf(stderr, "Stop at line : %s\n", line.c_str());
- fprintf(stderr, "Error Message: %s\n", msg.c_str());
- exit(-1);
- }
- }
-
- void parse(std::string line) {
- std::istringstream strin(line);
- std::string tmp;
-
- getline(strin, seqname, '\t');
- getline(strin, source, '\t');
- getline(strin, feature, '\t');
- getline(strin, tmp, '\t');
- start = atoi(tmp.c_str());
- getline(strin, tmp, '\t');
- end = atoi(tmp.c_str());
- getline(strin, score, '\t');
- getline(strin, tmp, '\t');
- my_assert((tmp.length() == 1 && (tmp[0] == '+' || tmp[0] == '-')), line, "Strand is neither '+' nor '-'!");
- strand = tmp[0];
- getline(strin, frame, '\t');
-
- getline(strin, left); // assign attributes and possible comments into "left"
-
- strin.clear(); strin.str(left);
- bool find_gene_id = false, find_transcript_id = false;
-
- while (getline(strin, tmp, ';') && (!find_gene_id || !find_transcript_id)) {
- tmp = cleanStr(tmp);
- size_t pos = tmp.find(' ');
- my_assert((pos != std::string::npos), line, "Cannot separate the identifier from the value for attribute " + tmp + "!");
- std::string identifier = tmp.substr(0, pos);
-
- if (identifier == "gene_id") {
- my_assert(!find_gene_id, line, "gene_id appear more than once!");
- tmp = cleanStr(tmp.substr(pos));
- my_assert((tmp[0] == '"' && tmp[tmp.length() - 1] == '"'), line, "Textual attributes should be surrounded by doublequotes!");
- gene_id = tmp.substr(1, tmp.length() - 2);
- find_gene_id = true;
- } else if (identifier == "transcript_id") {
- my_assert(!find_transcript_id, line, "transcript_id appear more than once!");
- tmp = cleanStr(tmp.substr(pos));
- my_assert((tmp[0] == '"' && tmp[tmp.length() - 1] == '"'), line, "Textual attributes should be surrounded by doublequotes!");
- transcript_id = tmp.substr(1, tmp.length() - 2);
- find_transcript_id = true;
- }
- }
-
- my_assert(find_gene_id, line, "Cannot find gene_id!");
- my_assert(find_transcript_id, line, "Cannot find transcript_id!");
- }
-
- std::string getSeqName() { return seqname; }
- std::string getSource() { return source; }
- std::string getFeature() { return feature; }
- int getStart() { return start; }
- int getEnd() { return end; }
- char getStrand() { return strand; }
- std::string getScore() { return score; } // float, integer or "." ; let downstream programs parse it
- std::string getFrame() { return frame; } // 0, 1, 2, or "."; let downstream programs parse it
- std::string getGeneID() { return gene_id; }
- std::string getTranscriptID() { return transcript_id; }
- std::string getLeft() { return left; }
-
- void setGeneID(const std::string& gene_id) {
- this->gene_id = gene_id;
- }
-
- std::string toString() {
- std::string val;
- std::ostringstream strout;
- strout<<seqname<<'\t'<<source<<'\t'<<feature<<'\t'<<start<<'\t'<<end<<'\t'<<score<<'\t'<<strand<<'\t'<<frame<<'\t';
- strout<<"gene_id \""<<gene_id<<"\"; transcript_id \""<<transcript_id<<"\";"<<left;
- val = strout.str();
-
- return val;
- }
-
- private:
- std::string seqname, source, feature;
- std::string score;
- int start, end;
- char strand;
- std::string frame;
- std::string gene_id, transcript_id;
- std::string left;
+public:
+
+ GTFItem() {
+ seqname = source = feature = "";
+ score = "";
+ start = end = 0;
+ strand = 0; //strand is a char variable
+ frame = "";
+ gene_id = transcript_id = "";
+ left = "";
+ }
+
+ bool operator<(const GTFItem& o) const {
+ if (gene_id != o.gene_id) return gene_id < o.gene_id;
+ if (transcript_id != o.transcript_id) return transcript_id < o.transcript_id;
+ return start < o.start;
+ }
+
+ void my_assert(char value, std::string& line, const std::string& msg) {
+ if (!value) {
+ fprintf(stderr, ".gtf file might be corrupted!\n");
+ fprintf(stderr, "Stop at line : %s\n", line.c_str());
+ fprintf(stderr, "Error Message: %s\n", msg.c_str());
+ exit(-1);
+ }
+ }
+
+ void parse(std::string line) {
+ std::istringstream strin(line);
+ std::string tmp;
+
+ getline(strin, seqname, '\t');
+ getline(strin, source, '\t');
+ getline(strin, feature, '\t');
+ getline(strin, tmp, '\t');
+ start = atoi(tmp.c_str());
+ getline(strin, tmp, '\t');
+ end = atoi(tmp.c_str());
+ getline(strin, score, '\t');
+ getline(strin, tmp, '\t');
+ my_assert((tmp.length() == 1 && (tmp[0] == '+' || tmp[0] == '-')), line, "Strand is neither '+' nor '-'!");
+ strand = tmp[0];
+ getline(strin, frame, '\t');
+
+ getline(strin, left); // assign attributes and possible comments into "left"
+
+ strin.clear(); strin.str(left);
+ bool find_gene_id = false, find_transcript_id = false;
+
+ while (getline(strin, tmp, ';') && (!find_gene_id || !find_transcript_id)) {
+ tmp = cleanStr(tmp);
+ size_t pos = tmp.find(' ');
+ my_assert((pos != std::string::npos), line, "Cannot separate the identifier from the value for attribute " + tmp + "!");
+ std::string identifier = tmp.substr(0, pos);
+
+ if (identifier == "gene_id") {
+ my_assert(!find_gene_id, line, "gene_id appear more than once!");
+ tmp = cleanStr(tmp.substr(pos));
+ my_assert((tmp[0] == '"' && tmp[tmp.length() - 1] == '"'), line, "Textual attributes should be surrounded by doublequotes!");
+ gene_id = tmp.substr(1, tmp.length() - 2);
+ find_gene_id = true;
+ } else if (identifier == "transcript_id") {
+ my_assert(!find_transcript_id, line, "transcript_id appear more than once!");
+ tmp = cleanStr(tmp.substr(pos));
+ my_assert((tmp[0] == '"' && tmp[tmp.length() - 1] == '"'), line, "Textual attributes should be surrounded by doublequotes!");
+ transcript_id = tmp.substr(1, tmp.length() - 2);
+ find_transcript_id = true;
+ }
+ }
+
+ my_assert(feature != "exon" || find_gene_id, line, "Cannot find gene_id!");
+ my_assert(feature != "exon" || find_transcript_id, line, "Cannot find transcript_id!");
+ if (!find_gene_id && feature != "exon") { printf("Warning: line \" %s \" does not contain a gene_id attribute! Since this line will not be used for reference construction, it is skipped. But if you think this GTF file is corrupted, you should find a complelete GTF file instead and rebuild the reference.\n", line.c_str()); }
+ if (!find_transcript_id && feature != "exon") { printf("Warning: line \" %s \" does not contain a transcript_id attribute! Since this line will not be used for reference construction, it is skipped. But if you think this GTF file is corrupted, you should find a complelete GTF file instead and rebuild the reference.\n", line.c_str()); }
+ }
+
+ std::string getSeqName() { return seqname; }
+ std::string getSource() { return source; }
+ std::string getFeature() { return feature; }
+ int getStart() { return start; }
+ int getEnd() { return end; }
+ char getStrand() { return strand; }
+ std::string getScore() { return score; } // float, integer or "." ; let downstream programs parse it
+ std::string getFrame() { return frame; } // 0, 1, 2, or "."; let downstream programs parse it
+ std::string getGeneID() { return gene_id; }
+ std::string getTranscriptID() { return transcript_id; }
+ std::string getLeft() { return left; }
+
+ void setGeneID(const std::string& gene_id) {
+ this->gene_id = gene_id;
+ }
+
+ std::string toString() {
+ std::string val;
+ std::ostringstream strout;
+ strout<<seqname<<'\t'<<source<<'\t'<<feature<<'\t'<<start<<'\t'<<end<<'\t'<<score<<'\t'<<strand<<'\t'<<frame<<'\t';
+ strout<<"gene_id \""<<gene_id<<"\"; transcript_id \""<<transcript_id<<"\";"<<left;
+ val = strout.str();
+
+ return val;
+ }
+
+private:
+ std::string seqname, source, feature;
+ std::string score;
+ int start, end;
+ char strand;
+ std::string frame;
+ std::string gene_id, transcript_id;
+ std::string left;
};
#endif
projects / rsem.git / blobdiff