uint loadGTF(SjdbClass &sjdbLoci, Parameters *P) {//load gtf file, add junctions to P->sjdb //returns number of added junctions if (P->sjdbOverhang>0 && P->sjdbGTFfile!="-") { ifstream sjdbStreamIn ( P->sjdbGTFfile.c_str() ); if (sjdbStreamIn.fail()) { ostringstream errOut; errOut << "FATAL error, could not open file sjdbGTFfile=" << P->sjdbGTFfile <<"\n"; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P); }; std::map <string,uint> transcriptIDnumber; uint exonN=0; while (sjdbStreamIn.good()) {//count the number of exons string chr1,ddd2,featureType; sjdbStreamIn >> chr1 >> ddd2 >> featureType; if (chr1.substr(0,1)!="#" && featureType==P->sjdbGTFfeatureExon) { exonN++; }; sjdbStreamIn.ignore(1000000000,'\n'); //ignore the rest of the line }; uint* exonLoci=new uint [exonN*GTF_exonLoci_size]; char* transcriptStrand = new char [exonN]; vector <string> transcriptID; exonN=0;//re-calculate sjdbStreamIn.clear(); sjdbStreamIn.seekg(0,ios::beg); while (sjdbStreamIn.good()) { string oneLine,chr1,ddd2,featureType; getline(sjdbStreamIn,oneLine); istringstream oneLineStream (oneLine); oneLineStream >> chr1 >> ddd2 >> featureType; if (chr1.substr(0,1)!="#" && featureType==P->sjdbGTFfeatureExon) {//exonic line, process if (P->sjdbGTFchrPrefix!="-") chr1=P->sjdbGTFchrPrefix + chr1; if (P->chrNameIndex.count(chr1)==0) {//chr not in Genome P->inOut->logMain << "WARNING: while processing sjdbGTFfile=" << P->sjdbGTFfile <<": chromosome '"<<chr1<<"' not found in Genome fasta files for line:\n"; P->inOut->logMain << oneLine <<"\n"<<flush; continue; //do not process exons/transcripts on missing chromosomes }; uint ex1,ex2; char str1; oneLineStream >> ex1 >> ex2 >> ddd2 >> str1 >> ddd2; //read all fields except the last string oneLine1; getline(oneLineStream, oneLine1);//get the last field replace(oneLine1.begin(),oneLine1.end(),';',' ');//to separate attributes replace(oneLine1.begin(),oneLine1.end(),'=',' ');//for GFF3 processing oneLineStream.str(oneLine1); oneLineStream.clear(); string trID(""), attr1(""); while (oneLineStream.good()) { oneLineStream >> attr1; if (attr1==P->sjdbGTFtagExonParentTranscript) { oneLineStream >> trID; trID.erase(remove(trID.begin(),trID.end(),'"'),trID.end()); trID.erase(remove(trID.begin(),trID.end(),';'),trID.end()); // cout <<trID<<endl; }; }; if (trID=="") {//no transcript ID P->inOut->logMain << "WARNING: while processing sjdbGTFfile=" << P->sjdbGTFfile <<": no transcript_id for exon feature for line:\n"; P->inOut->logMain << oneLine <<"\n"<<flush; } else { transcriptIDnumber.insert(std::pair <string,uint> (trID,(uint) transcriptIDnumber.size()));//insert new element if necessary with a new numeric value if (transcriptID.size() < transcriptIDnumber.size()) transcriptID.push_back(trID); if (str1=='+') { transcriptStrand[transcriptIDnumber[trID]]=1; } else if (str1=='-') { transcriptStrand[transcriptIDnumber[trID]]=2; } else { transcriptStrand[transcriptIDnumber[trID]]=0; }; }; exonLoci[GTF_exonTrID(exonN)]=transcriptIDnumber[trID]; exonLoci[GTF_exonStart(exonN)]=ex1+P->chrStart[P->chrNameIndex[chr1]]-1; exonLoci[GTF_exonEnd(exonN)]=ex2+P->chrStart[P->chrNameIndex[chr1]]-1; ++exonN; };//if (chr1.substr(0,1)!="#" && featureType=="exon") };//
uint loadGTF(SjdbClass &sjdbLoci, Parameters *P, string dirOut) {//load gtf file, add junctions to P->sjdb //returns number of added junctions if (P->sjdbOverhang>0 && P->sjdbGTFfile!="-") { time_t rawTime; time(&rawTime); P->inOut->logMain << timeMonthDayTime(rawTime) <<" ..... Processing annotations GTF\n" <<flush; *P->inOut->logStdOut << timeMonthDayTime(rawTime) <<" ..... Processing annotations GTF\n" <<flush; ifstream sjdbStreamIn ( P->sjdbGTFfile.c_str() ); if (sjdbStreamIn.fail()) { ostringstream errOut; errOut << "FATAL error, could not open file sjdbGTFfile=" << P->sjdbGTFfile <<"\n"; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P); }; if (P->chrNameIndex.size()==0) { for (uint ii=0;ii<P->nChrReal;ii++) { P->chrNameIndex[P->chrName[ii]]=ii; }; }; std::map <string,uint> transcriptIDnumber, geneIDnumber; uint exonN=0; while (sjdbStreamIn.good()) {//count the number of exons string chr1,ddd2,featureType; sjdbStreamIn >> chr1 >> ddd2 >> featureType; if (chr1.substr(0,1)!="#" && featureType==P->sjdbGTFfeatureExon) { exonN++; }; sjdbStreamIn.ignore(1000000000,'\n'); //ignore the rest of the line }; if (exonN==0) { P->inOut->logMain << "WARNING: found no exons in sjdbGTFfile=" << P->sjdbGTFfile <<endl; return 0; }; uint* exonLoci=new uint [exonN*GTF_exonLoci_size]; char* transcriptStrand = new char [exonN]; vector <string> transcriptID, geneID; exonN=0;//re-calculate sjdbStreamIn.clear(); sjdbStreamIn.seekg(0,ios::beg); while (sjdbStreamIn.good()) { string oneLine,chr1,ddd2,featureType; getline(sjdbStreamIn,oneLine); istringstream oneLineStream (oneLine); oneLineStream >> chr1 >> ddd2 >> featureType; if (chr1.substr(0,1)!="#" && featureType==P->sjdbGTFfeatureExon) {//exonic line, process if (P->sjdbGTFchrPrefix!="-") chr1=P->sjdbGTFchrPrefix + chr1; if (P->chrNameIndex.count(chr1)==0) {//chr not in Genome P->inOut->logMain << "WARNING: while processing sjdbGTFfile=" << P->sjdbGTFfile <<": chromosome '"<<chr1<<"' not found in Genome fasta files for line:\n"; P->inOut->logMain << oneLine <<"\n"<<flush; continue; //do not process exons/transcripts on missing chromosomes }; uint ex1,ex2; char str1; oneLineStream >> ex1 >> ex2 >> ddd2 >> str1 >> ddd2; //read all fields except the last string oneLine1; getline(oneLineStream, oneLine1);//get the last field replace(oneLine1.begin(),oneLine1.end(),';',' ');//to separate attributes replace(oneLine1.begin(),oneLine1.end(),'=',' ');//for GFF3 processing oneLineStream.str(oneLine1); oneLineStream.clear(); string trID(""), gID(""), attr1(""); while (oneLineStream.good()) { oneLineStream >> attr1; if (attr1==P->sjdbGTFtagExonParentTranscript) { oneLineStream >> trID; trID.erase(remove(trID.begin(),trID.end(),'"'),trID.end()); trID.erase(remove(trID.begin(),trID.end(),';'),trID.end()); } else if (attr1==P->sjdbGTFtagExonParentGene) { oneLineStream >> gID; gID.erase(remove(gID.begin(),gID.end(),'"'),gID.end()); gID.erase(remove(gID.begin(),gID.end(),';'),gID.end()); }; };