if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
- fileAligned = true;
+ fileAligned = true; pairedOligos = false;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
length = 0;
- if(oligosfile != ""){ readOligos(); if (m->debug) { m->mothurOut("[DEBUG]: read oligos file. numprimers = " + toString(primers.size()) + ", revprimers = " + toString(revPrimer.size()) + ".\n"); } } if (m->control_pressed) { return 0; }
+ if(oligosfile != ""){ readOligos(); if (m->debug) { m->mothurOut("[DEBUG]: read oligos file. numprimers = " + toString(numFPrimers) + ", revprimers = " + toString(numRPrimers) + ".\n"); } } if (m->control_pressed) { return 0; }
if(ecolifile != "") { readEcoli(); } if (m->control_pressed) { return 0; }
vector<unsigned long long> positions;
//loop through and create all the processes you want
while (process != processors) {
- int pid = fork();
+ pid_t pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- string locationsFile = toString(getpid()) + ".temp";
- num = driverPcr(filename, goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", locationsFile, badSeqNames, lines[process], pstart, adjustNeeded);
+ string locationsFile = m->mothurGetpid(process) + ".temp";
+ num = driverPcr(filename, goodFileName + m->mothurGetpid(process) + ".temp", badFileName + m->mothurGetpid(process) + ".temp", locationsFile, badSeqNames, lines[process], pstart, adjustNeeded);
//pass numSeqs to parent
ofstream out;
- string tempFile = filename + toString(getpid()) + ".num.temp";
+ string tempFile = filename + m->mothurGetpid(process) + ".num.temp";
m->openOutputFile(tempFile, out);
out << pstart << '\t' << adjustNeeded << endl;
out << num << '\t' << badSeqNames.size() << endl;
}
}
- string locationsFile = toString(getpid()) + ".temp";
+ string locationsFile = m->mothurGetpid(process) + ".temp";
num = driverPcr(filename, goodFileName, badFileName, locationsFile, badSeqNames, lines[0], pstart, adjustNeeded);
//force parent to wait until all the processes are done
if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, locationsFile+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, keepdots, start, end, length, pdiffs, lines[i].start, lines[i].end);
+ pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, locationsFile+extension, m, oligosfile, ecolifile, nomatch, keepprimer, keepdots, start, end, length, pdiffs, lines[i].start, lines[i].end);
pDataArray.push_back(tempPcr);
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
string name = "";
int thisStart = -1; int thisEnd = -1;
- if (primers.size() != 0) { inLocations >> name >> thisStart; m->gobble(inLocations); }
- if (revPrimer.size() != 0) { inLocations >> name >> thisEnd; m->gobble(inLocations); }
+ if (numFPrimers != 0) { inLocations >> name >> thisStart; m->gobble(inLocations); }
+ if (numRPrimers != 0) { inLocations >> name >> thisEnd; m->gobble(inLocations); }
else { pend = -1; break; }
int myDiff = 0;
set<int> locations; //locations[0] = beginning locations,
//pdiffs, bdiffs, primers, barcodes, revPrimers
- map<string, int> faked;
- TrimOligos trim(pdiffs, 0, primers, faked, revPrimer);
+ map<string, int> primers;
+ map<string, int> barcodes; //not used
+ vector<string> revPrimer;
+ if (pairedOligos) {
+ map<int, oligosPair> primerPairs = oligos.getPairedPrimers();
+ for (map<int, oligosPair>::iterator it = primerPairs.begin(); it != primerPairs.end(); it++) {
+ primers[(it->second).forward] = it->first;
+ revPrimer.push_back((it->second).reverse);
+ }
+ if (pdiffs != 0) { m->mothurOut("[WARNING]: Pcr.seqs is only designed to allow diffs in forward primers. Reverse primers must be an exact match.\n"); }
+ }else{
+ primers = oligos.getPrimers();
+ revPrimer = oligos.getReversePrimers();
+ }
+
+ TrimOligos trim(pdiffs, 0, primers, barcodes, revPrimer);
while (!done) {
string name = "";
int thisStart = -1; int thisEnd = -1;
- if (primers.size() != 0) { inLocations >> name >> thisStart; m->gobble(inLocations); }
- if (revPrimer.size() != 0) { inLocations >> name >> thisEnd; m->gobble(inLocations); }
+ if (numFPrimers != 0) { inLocations >> name >> thisStart; m->gobble(inLocations); }
+ if (numRPrimers != 0) { inLocations >> name >> thisEnd; m->gobble(inLocations); }
//cout << seq.getName() << '\t' << thisStart << '\t' << thisEnd << '\t' << seq.getAligned().length() << endl;
exit(1);
}
}
-//********************************************************************/
-string PcrSeqsCommand::reverseOligo(string oligo){
- try {
- string reverse = "";
-
- for(int i=oligo.length()-1;i>=0;i--){
-
- if(oligo[i] == 'A') { reverse += 'T'; }
- else if(oligo[i] == 'T'){ reverse += 'A'; }
- else if(oligo[i] == 'U'){ reverse += 'A'; }
-
- else if(oligo[i] == 'G'){ reverse += 'C'; }
- else if(oligo[i] == 'C'){ reverse += 'G'; }
-
- else if(oligo[i] == 'R'){ reverse += 'Y'; }
- else if(oligo[i] == 'Y'){ reverse += 'R'; }
-
- else if(oligo[i] == 'M'){ reverse += 'K'; }
- else if(oligo[i] == 'K'){ reverse += 'M'; }
-
- else if(oligo[i] == 'W'){ reverse += 'W'; }
- else if(oligo[i] == 'S'){ reverse += 'S'; }
-
- else if(oligo[i] == 'B'){ reverse += 'V'; }
- else if(oligo[i] == 'V'){ reverse += 'B'; }
-
- else if(oligo[i] == 'D'){ reverse += 'H'; }
- else if(oligo[i] == 'H'){ reverse += 'D'; }
-
- else { reverse += 'N'; }
- }
-
-
- return reverse;
- }
- catch(exception& e) {
- m->errorOut(e, "PcrSeqsCommand", "reverseOligo");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-bool PcrSeqsCommand::readOligos(){
- try {
- ifstream inOligos;
- m->openInputFile(oligosfile, inOligos);
-
- string type, oligo, group;
- int primerCount = 0;
-
- while(!inOligos.eof()){
-
- inOligos >> type;
-
- if(type[0] == '#'){ //ignore
- while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- m->gobble(inOligos);
- }else{
- m->gobble(inOligos);
- //make type case insensitive
- for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
-
- inOligos >> oligo;
-
- for(int i=0;i<oligo.length();i++){
- oligo[i] = toupper(oligo[i]);
- if(oligo[i] == 'U') { oligo[i] = 'T'; }
- }
-
- if(type == "FORWARD"){
- // get rest of line in case there is a primer name
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- }
- primers[oligo] = primerCount; primerCount++;
- //cout << "for oligo = " << oligo << endl;
- }else if(type == "REVERSE"){
- string oligoRC = reverseOligo(oligo);
- revPrimer.push_back(oligoRC);
- //cout << "rev oligo = " << oligo << " reverse = " << oligoRC << endl;
- }else if(type == "BARCODE"){
- inOligos >> group;
- }else if(type == "PRIMER"){
- m->gobble(inOligos);
- primers[oligo] = primerCount; primerCount++;
-
- string roligo="";
- inOligos >> roligo;
-
- for(int i=0;i<roligo.length();i++){
- roligo[i] = toupper(roligo[i]);
- if(roligo[i] == 'U') { roligo[i] = 'T'; }
- }
- revPrimer.push_back(reverseOligo(roligo));
-
- // get rest of line in case there is a primer name
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- }
- //cout << "prim oligo = " << oligo << " reverse = " << roligo << endl;
- }else if((type == "LINKER")||(type == "SPACER")) {;}
- else{ m->mothurOut(type + " is not recognized as a valid type. Choices are primer, forward, reverse, linker, spacer and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- }
- m->gobble(inOligos);
- }
- inOligos.close();
-
- if ((primers.size() == 0) && (revPrimer.size() == 0)) {
- m->mothurOut("[ERROR]: your oligos file does not contain valid primers or reverse primers. Please correct."); m->mothurOutEndLine();
- m->control_pressed = true;
- return false;
- }
-
- return true;
-
- }catch(exception& e) {
- m->errorOut(e, "PcrSeqsCommand", "readOligos");
- exit(1);
- }
-}
//***************************************************************************************************************
bool PcrSeqsCommand::readEcoli(){
try {
exit(1);
}
}
+//***************************************************************************************************************
+
+int PcrSeqsCommand::readOligos(){
+ try {
+ oligos.read(oligosfile);
+
+ if (m->control_pressed) { return false; } //error in reading oligos
+
+ if (oligos.hasPairedBarcodes()) {
+ pairedOligos = true;
+ numFPrimers = oligos.getPairedPrimers().size();
+ }else {
+ pairedOligos = false;
+ numFPrimers = oligos.getPrimers().size();
+ }
+ numRPrimers = oligos.getReversePrimers().size();
+
+ if (oligos.getLinkers().size() != 0) { m->mothurOut("[WARNING]: pcr.seqs is not setup to remove linkers, ignoring.\n"); }
+ if (oligos.getSpacers().size() != 0) { m->mothurOut("[WARNING]: pcr.seqs is not setup to remove spacers, ignoring.\n"); }
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PcrSeqsCommand", "readOligos");
+ exit(1);
+ }
+}
+
/**************************************************************************************/
projects / mothur.git / blobdiff