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/* Copyright (c) 2015
Bo Li (University of California, Berkeley)
bli25@berkeley.edu
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA
*/
#ifndef GTFITEM_H_
#define GTFITEM_H_
#include<cstdio>
#include<cctype>
#include<cstdlib>
#include<cassert>
#include<string>
#include<sstream>
class GTFItem {
public:
GTFItem() {
seqname = source = feature = "";
score = "";
start = end = 0;
strand = 0; //strand is a char variable
frame = "";
gene_id = transcript_id = "";
gene_name = transcript_name = "";
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 parse(const 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');
gtf_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"
}
void parseAttributes(const std::string& line) {
assert(feature == "exon");
gene_id = transcript_id = "";
gene_name = transcript_name = "";
int nleft = 4;
int pos, lpos = 0, rpos, left_len = left.length();
std::string identifier;
while (nleft > 0 && get_an_attribute(lpos, rpos, left_len)) {
// locate identifier
pos = lpos;
while (pos < rpos && !isspace(left[pos])) ++pos;
gtf_assert(isspace(left[pos]), line, "Cannot locate the identifier from attribute " + left.substr(lpos, rpos + 1 - lpos) + "!");
identifier = left.substr(lpos, pos - lpos);
// prepare for the next attribute
lpos = rpos + 1;
// locate value
++pos;
while (pos < rpos && isspace(left[pos])) ++pos;
if (left[pos] != '"') pos = rpos;
--rpos;
while (rpos > pos && isspace(left[rpos])) --rpos;
if (rpos > pos && left[rpos] != '"') rpos = pos;
// test if the identifier is interested
if (identifier == "gene_id") {
gtf_assert(gene_id == "", line, "gene_id appear more than once!");
gtf_assert(rpos - pos > 1 , line, "Attribute " + identifier + "'s value should be surrounded by double quotes and cannot be empty!");
gene_id = left.substr(pos + 1, rpos - pos - 1);
--nleft;
}
else if (identifier == "transcript_id") {
gtf_assert(transcript_id == "", line, "transcript_id appear more than once!");
gtf_assert(rpos - pos > 1 , line, "Attribute " + identifier + "'s value should be surrounded by double quotes and cannot be empty!");
transcript_id = left.substr(pos + 1, rpos - pos - 1);
--nleft;
}
else if (identifier == "gene_name" && gene_name == "" && rpos - pos > 1) {
gene_name = left.substr(pos + 1, rpos - pos - 1);
--nleft;
}
else if (identifier == "transcript_name" && transcript_name == "" && rpos - pos > 1) {
transcript_name = left.substr(pos + 1, rpos - pos - 1);
--nleft;
}
}
gtf_assert(gene_id != "", line, "Cannot find gene_id!");
gtf_assert(transcript_id != "", line, "Cannot find transcript_id!");
}
const std::string& getSeqName() const { return seqname; }
const std::string& getSource() const { return source; }
const std::string getFeature() const { return feature; }
int getStart() const { return start; }
int getEnd() const { return end; }
char getStrand() const { return strand; }
const std::string& getScore() const { return score; } // float, integer or "." ; let downstream programs parse it
const std::string& getFrame() const { return frame; } // 0, 1, 2, or "."; let downstream programs parse it
const std::string& getGeneID() const { return gene_id; }
const std::string& getTranscriptID() const { return transcript_id; }
const std::string& getGeneName() const { return gene_name; }
const std::string& getTranscriptName() const { return transcript_name; }
const std::string getLeft() { return left; }
void setGeneID(const std::string& gene_id) {
this->gene_id = gene_id;
}
std::string toString() {
std::ostringstream strout("");
strout<< seqname<< '\t'<< source<< '\t'<< feature<< '\t'<< start<< '\t'<< end<< '\t'<< score<< '\t'<< strand<< '\t'<< frame<< '\t'<< left;
return strout.str();
}
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 gene_name, transcript_name;
std::string left;
bool get_an_attribute(int& lpos, int& rpos, int left_len) {
bool in_quote;
while (lpos < left_len && isspace(left[lpos])) ++lpos; // remove leading white spaces
rpos = lpos; in_quote = false;
while (rpos < left_len && (left[rpos] != ';' || in_quote)) {
if (left[rpos] == '"') in_quote ^= true;
++rpos;
}
return rpos < left_len;
}
void gtf_assert(bool expr, const std::string& line, const std::string& msg) {
if (!expr) {
fprintf(stderr, "The 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);
}
}
};
#endif
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