X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=GTFItem.h;h=e0499be9139ab226a1643aea47e379e92af275f4;hp=4e502706b88bb55767ff4f7ddf98797bdf8680c7;hb=910250881a4c3e48a33aa427b82131acda914da3;hpb=da827678b21e94c74fd17c9b8683edb60f73e814

diff --git a/GTFItem.h b/GTFItem.h
index 4e50270..e0499be 100644
--- a/GTFItem.h
+++ b/GTFItem.h
@@ -10,114 +10,116 @@
 #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