void sjdbLoadFromFiles(Parameters *P, SjdbClass &sjdbLoci) {
if (P->sjdbFileChrStartEnd.at(0)!="-") {
for (uint ifile=0;ifile<P->sjdbFileChrStartEnd.size(); ifile++) {
ifstream sjdbStreamIn ( P->sjdbFileChrStartEnd.at(ifile).c_str() );
if (sjdbStreamIn.fail()) {
ostringstream errOut;
errOut << "FATAL INPUT error, could not open input file sjdbFileChrStartEnd=" << P->sjdbFileChrStartEnd.at(ifile) <<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
P->inOut->logMain << "Loaded database junctions from file: " << P->sjdbFileChrStartEnd.at(ifile) <<", total number of junctions: "<<sjdbLoci.chr.size()<<" junctions\n\n";
};
}; //if (P->sjdbFileChrStartEnd!="-")
};
void sjdbInsertJunctions(Parameters *P, Genome &genome) {
SjdbClass sjdbLoci;
time_t rawtime;
//load 1st pass junctions
if (P->twoPass.pass1sjFile.size()>0)
{
ifstream sjdbStreamIn ( P->twoPass.pass1sjFile.c_str() );
if (sjdbStreamIn.fail()) {
ostringstream errOut;
errOut << "FATAL INPUT error, could not open input file with junctions from the 1st pass="******"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the 1st pass file: " << P->twoPass.pass1sjFile <<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
//load from junction files
if (P->sjdbFileChrStartEnd.at(0)!="-")
{
sjdbLoadFromFiles(P,sjdbLoci);
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the sjdbFileChrStartEnd file(s), " << sjdbLoci.chr.size()<<" total junctions\n\n";
};
//load from GTF
if (P->sjdbGTFfile!="-")
{
loadGTF(sjdbLoci, P, P->genomeDirOut);
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the GTF file: " << P->sjdbGTFfile<<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
sjdbPrepare (sjdbLoci, P, genome.G, P->nGenome, P->twoPass.dir);//P->nGenome - change when replacing junctions
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Finished preparing junctions" <<endl;
//insert junctions into the genome and SA and SAi
sjdbBuildIndex (P, genome.G, genome.SA, genome.SA2, genome.SAi);
time ( &rawtime );
*P->inOut->logStdOut << timeMonthDayTime(rawtime) << " ..... Finished inserting 1st pass junctions into genome" <<endl;
//re-calculate genome-related parameters
P->winBinN = P->nGenome/(1LLU << P->winBinNbits)+1;
};
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());
};
};
void sjdbInsertJunctions(Parameters * P, Parameters * P1, Genome & genome, SjdbClass & sjdbLoci)
{
time_t rawtime;
if (P->sjdbN>0 && sjdbLoci.chr.size()==0)
{//load from the saved genome, only if the loading did not happen already (if sjdb insertion happens at the 1st pass, sjdbLoci will be populated
ifstream & sjdbStreamIn = ifstrOpen(P->genomeDir+"/sjdbList.out.tab", ERROR_OUT, "SOLUTION: re-generate the genome in genomeDir=" + P->genomeDir, P);
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),30);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the generated genome " << P->genomeDir+"/sjdbList.out.tab" <<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
if (P->twoPass.pass2)
{//load 1st pass new junctions
//sjdbLoci already contains the junctions from before 1st pass
ifstream sjdbStreamIn ( P->twoPass.pass1sjFile.c_str() );
if (sjdbStreamIn.fail()) {
ostringstream errOut;
errOut << "FATAL INPUT error, could not open input file with junctions from the 1st pass="******"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),0);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the 1st pass file: " << P->twoPass.pass1sjFile <<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
} else
{//loading junctions from GTF or tab or from the saved genome is only allowed at the 1st pass
//at the 2nd pass these are already in the sjdbLoci
if (P->sjdbFileChrStartEnd.at(0)!="-")
{//load from junction files
sjdbLoadFromFiles(P,sjdbLoci);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),10);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the sjdbFileChrStartEnd file(s), " << sjdbLoci.chr.size()<<" total junctions\n\n";
};
if (P->sjdbGTFfile!="-")
{//load from GTF
loadGTF(sjdbLoci, P, P->sjdbInsert.outDir);
sjdbLoci.priority.resize(sjdbLoci.chr.size(),20);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the GTF file: " << P->sjdbGTFfile<<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
};
char *Gsj=new char [2*P->sjdbLength*sjdbLoci.chr.size()+1];//array to store junction sequences, will be filled in sjdbPrepare
sjdbPrepare (sjdbLoci, P, P->chrStart[P->nChrReal], P->sjdbInsert.outDir, genome.G, Gsj);//P->nGenome - change when replacing junctions
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Finished preparing junctions" <<endl;
if (P->sjdbN>P->limitSjdbInsertNsj)
{
ostringstream errOut;
errOut << "Fatal LIMIT error: the number of junctions to be inserted on the fly ="<<P->sjdbN<<" is larger than the limitSjdbInsertNsj="<<P->limitSjdbInsertNsj<<"\n"; errOut << "Fatal LIMIT error: the number of junctions to be inserted on the fly ="<<P->sjdbN<<" is larger than the limitSjdbInsertNsj="<<P->limitSjdbInsertNsj<<"\n";
errOut << "SOLUTION: re-run with at least --limitSjdbInsertNsj "<<P->sjdbN<<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
//insert junctions into the genome and SA and SAi
sjdbBuildIndex (P, P1, Gsj, genome.G, genome.SA, (P->twoPass.pass2 ? genome.SApass2 : genome.SApass1), genome.SAi);
delete [] Gsj; //junction sequences have been added to G
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " ..... finished inserting junctions into genome" <<endl;
if (P->sjdbInsert.save=="All")
{//save and copy all genome files into sjdbInsert.outDir, except those created above
if (P->genomeDir != P->sjdbInsert.outDir)
{
copyFile(P->genomeDir+"/chrName.txt", P->sjdbInsert.outDir+"/chrName.txt");
copyFile(P->genomeDir+"/chrStart.txt", P->sjdbInsert.outDir+"/chrStart.txt");
copyFile(P->genomeDir+"/chrNameLength.txt", P->sjdbInsert.outDir+"/chrNameLength.txt");
copyFile(P->genomeDir+"/chrLength.txt", P->sjdbInsert.outDir+"/chrLength.txt");
};
genomeParametersWrite(P->sjdbInsert.outDir+("/genomeParameters.txt"), P, ERROR_OUT);
ofstream & genomeOut = ofstrOpen(P->sjdbInsert.outDir+"/Genome",ERROR_OUT, P);
fstreamWriteBig(genomeOut,genome.G,P->nGenome,P->sjdbInsert.outDir+"/Genome",ERROR_OUT,P);
genomeOut.close();
ofstream & saOut = ofstrOpen(P->sjdbInsert.outDir+"/SA",ERROR_OUT, P);
fstreamWriteBig(saOut,(char*) genome.SA.charArray, (streamsize) genome.SA.lengthByte, P->sjdbInsert.outDir+"/SA",ERROR_OUT,P);
saOut.close();
ofstream & saIndexOut = ofstrOpen(P->sjdbInsert.outDir+"/SAindex",ERROR_OUT, P);
fstreamWriteBig(saIndexOut, (char*) &P->genomeSAindexNbases, sizeof(P->genomeSAindexNbases),P->sjdbInsert.outDir+"/SAindex",ERROR_OUT,P);
fstreamWriteBig(saIndexOut, (char*) P->genomeSAindexStart, sizeof(P->genomeSAindexStart[0])*(P->genomeSAindexNbases+1),P->sjdbInsert.outDir+"/SAindex",ERROR_OUT,P);
fstreamWriteBig(saIndexOut, genome.SAi.charArray, genome.SAi.lengthByte,P->sjdbInsert.outDir+"/SAindex",ERROR_OUT,P);
saIndexOut.close();
};
//re-calculate genome-related parameters
P->winBinN = P->nGenome/(1LLU << P->winBinNbits)+1;
};
