if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
+ fileAligned = true;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
if (m->control_pressed) { return 0; }
set<string> badNames;
- if(processors == 1) { numFastaSeqs = driverPcr(fastafile, trimSeqFile, badSeqFile, badNames, lines[0]); }
- else { numFastaSeqs = createProcesses(fastafile, trimSeqFile, badSeqFile, badNames); }
+ numFastaSeqs = createProcesses(fastafile, trimSeqFile, badSeqFile, badNames);
if (m->control_pressed) { return 0; }
vector<int> processIDS;
int process = 1;
int num = 0;
+ int pstart = -1; int pend = -1;
+ bool adjustNeeded = false;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
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){
- num = driverPcr(filename, goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badSeqNames, lines[process]);
+ string locationsFile = toString(getpid()) + ".temp";
+ num = driverPcr(filename, goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", locationsFile, badSeqNames, lines[process], pstart, pend, adjustNeeded);
//pass numSeqs to parent
ofstream out;
string tempFile = filename + toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
+ out << pstart << '\t' << pend << '\t' << adjustNeeded << endl;
out << num << '\t' << badSeqNames.size() << endl;
for (set<string>::iterator it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
out << (*it) << endl;
}
}
- num = driverPcr(filename, goodFileName, badFileName, badSeqNames, lines[0]);
+ string locationsFile = toString(getpid()) + ".temp";
+ num = driverPcr(filename, goodFileName, badFileName, locationsFile, badSeqNames, lines[0], pstart, pend, adjustNeeded);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
string tempFile = filename + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
int numBadNames = 0; string name = "";
- if (!in.eof()) { int tempNum = 0; in >> tempNum >> numBadNames; num += tempNum; m->gobble(in); }
+ int tpstart = -1; int tpend = -1; bool tempAdjust = false;
+
+ if (!in.eof()) {
+ in >> tpstart >> tpend >> tempAdjust; m->gobble(in);
+
+ if (tempAdjust) { adjustNeeded = true; }
+ if (tpstart != -1) {
+ if (tpstart != pstart) { adjustNeeded = true; }
+ if (tpstart < pstart) { pstart = tpstart; } //smallest start
+ }
+ if (tpend != -1) {
+ if (tpend != pend) { adjustNeeded = true; }
+ if (tpend > pend) { pend = tpend; } //largest end
+ }
+ int tempNum = 0; in >> tempNum >> numBadNames; num += tempNum; m->gobble(in);
+ }
for (int j = 0; j < numBadNames; j++) {
in >> name; m->gobble(in);
badSeqNames.insert(name);
m->appendFiles((badFileName + toString(processIDS[i]) + ".temp"), badFileName);
m->mothurRemove((badFileName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((toString(processIDS[i]) + ".temp"), locationsFile);
+ m->mothurRemove((toString(processIDS[i]) + ".temp"));
}
#else
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
+ string locationsFile = "locationsFile.txt";
+ m->mothurRemove(locationsFile);
+ m->mothurRemove(goodFileName);
+ m->mothurRemove(badFileName);
+
//Create processor worker threads.
for( int i=0; i<processors-1; i++ ){
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, 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, primers, revPrimer, 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
}
//do your part
- num = driverPcr(filename, (goodFileName+toString(processors-1)+".temp"), (badFileName+toString(processors-1)+".temp"),badSeqNames, lines[processors-1]);
+ num = driverPcr(filename, (goodFileName+toString(processors-1)+".temp"), (badFileName+toString(processors-1)+".temp"), (locationsFile+toString(processors-1)+".temp"), badSeqNames, lines[processors-1], pstart, pend, adjustNeeded);
processIDS.push_back(processors-1);
//Wait until all threads have terminated.
if (pDataArray[i]->count != pDataArray[i]->fend) {
m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->fend) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
}
+ if (pDataArray[i]->adjustNeeded) { adjustNeeded = true; }
+ if (pDataArray[i]->pstart != -1) {
+ if (pDataArray[i]->pstart != pstart) { adjustNeeded = true; }
+ if (pDataArray[i]->pstart < pstart) { pstart = pDataArray[i]->pstart; }
+ } //smallest start
+ if (pDataArray[i]->pend != -1) {
+ if (pDataArray[i]->pend != pend) { adjustNeeded = true; }
+ if (pDataArray[i]->pend > pend) { pend = pDataArray[i]->pend; }
+ } //largest end
+
for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it); }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
m->appendFiles((badFileName + toString(processIDS[i]) + ".temp"), badFileName);
m->mothurRemove((badFileName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((locationsFile+toString(processIDS[i]) + ".temp"), locationsFile);
+ m->mothurRemove((locationsFile+toString(processIDS[i]) + ".temp"));
}
#endif
+ if (fileAligned && adjustNeeded) { adjustDots(goodFileName, locationsFile, pstart, pend); }
return num;
}
//**********************************************************************************************************************
-int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta, set<string>& badSeqNames, linePair filePos){
+int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta, string locationsName, set<string>& badSeqNames, linePair filePos, int& pstart, int& pend, bool& adjustNeeded){
try {
ofstream goodFile;
m->openOutputFile(goodFasta, goodFile);
ofstream badFile;
m->openOutputFile(badFasta, badFile);
+
+ ofstream locationsFile;
+ m->openOutputFile(locationsName, locationsFile);
ifstream inFASTA;
m->openInputFile(filename, inFASTA);
bool done = false;
int count = 0;
set<int> lengths;
+ vector< set<int> > locations; //locations[0] = beginning locations, locations[1] = ending locations
+ locations.resize(2);
//pdiffs, bdiffs, primers, barcodes, revPrimers
map<string, int> faked;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
+ if (fileAligned) { //assume aligned until proven otherwise
+ lengths.insert(currSeq.getAligned().length());
+ if (lengths.size() > 1) { fileAligned = false; }
+ }
+
string trashCode = "";
+ string locationsString = "";
+ int thisPStart = -1;
+ int thisPEnd = -1;
if (currSeq.getName() != "") {
if (m->debug) { m->mothurOut("[DEBUG]: seq name = " + currSeq.getName() + ".\n"); }
else{
//are you aligned
if (aligned) {
- if (!keepprimer) {
- if (keepdots) { currSeq.filterToPos(mapAligned[primerEnd]); }
- else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerEnd])); }
+ if (!keepprimer) {
+ if (keepdots) { currSeq.filterToPos(mapAligned[primerEnd-1]+1); } //mapAligned[primerEnd-1] is the location of the last base in the primer. we want to trim to the space just after that. The -1 & +1 ensures if the primer is followed by gaps they are not trimmed causing an aligned sequence dataset to become unaligned.
+ else {
+ currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerEnd-1]+1));
+ if (fileAligned) {
+ thisPStart = mapAligned[primerEnd-1]+1; //locations[0].insert(mapAligned[primerEnd-1]+1);
+ locationsString += currSeq.getName() + "\t" + toString(mapAligned[primerEnd-1]+1) + "\n";
+ }
+ }
}
else {
if (keepdots) { currSeq.filterToPos(mapAligned[primerStart]); }
- else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart])); }
+ else {
+ currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart]));
+ if (fileAligned) {
+ thisPStart = mapAligned[primerStart]; //locations[0].insert(mapAligned[primerStart]);
+ locationsString += currSeq.getName() + "\t" + toString(mapAligned[primerStart]) + "\n";
+ }
+ }
}
isAligned(currSeq.getAligned(), mapAligned);
}else {
int primerStart = 0; int primerEnd = 0;
bool good = trim.findReverse(currSeq, primerStart, primerEnd);
if(!good){ if (nomatch == "reject") { goodSeq = false; } trashCode += "r"; }
- else{
- //are you aligned
+ else{
+ //are you aligned
if (aligned) {
if (!keepprimer) {
if (keepdots) { currSeq.filterFromPos(mapAligned[primerStart]); }
- else { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerStart])); }
+ else {
+ currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerStart]));
+ if (fileAligned) {
+ thisPEnd = mapAligned[primerStart]; //locations[1].insert(mapAligned[primerStart]);
+ locationsString += currSeq.getName() + "\t" + toString(mapAligned[primerStart]) + "\n";
+ }
+ }
}
else {
- if (keepdots) { currSeq.filterFromPos(mapAligned[primerEnd]); }
- else { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerEnd])); }
+ if (keepdots) { currSeq.filterFromPos(mapAligned[primerEnd-1]+1); }
+ else {
+ currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerEnd-1]+1));
+ if (fileAligned) {
+ thisPEnd = mapAligned[primerEnd-1]+1; //locations[1].insert(mapAligned[primerEnd-1]+1);
+ locationsString += currSeq.getName() + "\t" + toString(mapAligned[primerEnd-1]+1) + "\n";
+ }
+ }
}
}
else {
}
}else if (ecolifile != "") {
//make sure the seqs are aligned
- lengths.insert(currSeq.getAligned().length());
- if (lengths.size() > 1) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
+ if (!fileAligned) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
else if (currSeq.getAligned().length() != length) {
m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); m->control_pressed = true; break;
}else {
}
}else{ //using start and end to trim
//make sure the seqs are aligned
- lengths.insert(currSeq.getAligned().length());
- if (lengths.size() > 1) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
+ if (!fileAligned) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
else {
if (end != -1) {
if (end > currSeq.getAligned().length()) { m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); m->control_pressed = true; break; }
//trimming removed all bases
if (currSeq.getUnaligned() == "") { goodSeq = false; }
- if(goodSeq == 1) { currSeq.printSequence(goodFile); }
+ if(goodSeq == 1) {
+ currSeq.printSequence(goodFile);
+ if (m->debug) { m->mothurOut("[DEBUG]: " + locationsString + "\n"); }
+ if (locationsString != "") { locationsFile << locationsString; }
+ if (thisPStart != -1) { locations[0].insert(thisPStart); }
+ if (thisPEnd != -1) { locations[1].insert(thisPEnd); }
+ }
else {
badSeqNames.insert(currSeq.getName());
currSeq.setName(currSeq.getName() + '|' + trashCode);
badFile.close();
goodFile.close();
inFASTA.close();
-
+ locationsFile.close();
+
+ if (m->debug) { m->mothurOut("[DEBUG]: fileAligned = " + toString(fileAligned) +'\n'); }
+
+ if (fileAligned && !keepdots) { //print out smallest start value and largest end value
+ if ((locations[0].size() > 1) || (locations[1].size() > 1)) { adjustNeeded = true; }
+ if (primers.size() != 0) { set<int>::iterator it = locations[0].begin(); pstart = *it; }
+ if (revPrimer.size() != 0) { set<int>::reverse_iterator it2 = locations[1].rbegin(); pend = *it2; }
+ }
+
return count;
}
catch(exception& e) {
exit(1);
}
}
+//**********************************************************************************************************************
+int PcrSeqsCommand::adjustDots(string goodFasta, string locations, int pstart, int pend){
+ try {
+ ifstream inFasta;
+ m->openInputFile(goodFasta, inFasta);
+
+ ifstream inLocations;
+ m->openInputFile(locations, inLocations);
+
+ ofstream out;
+ m->openOutputFile(goodFasta+".temp", out);
+
+ set<int> lengths;
+ //cout << pstart << '\t' << pend << endl;
+
+ while(!inFasta.eof()) {
+ if(m->control_pressed) { break; }
+
+ Sequence seq(inFasta); m->gobble(inFasta);
+
+ 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); }
+ //cout << seq.getName() << '\t' << thisStart << '\t' << thisEnd << '\t' << seq.getAligned().length() << endl;
+ //cout << seq.getName() << '\t' << pstart << '\t' << pend << endl;
+
+ if (name != seq.getName()) { m->mothurOut("[ERROR]: name mismatch in pcr.seqs.\n"); }
+ else {
+ if (pstart != -1) {
+ if (thisStart != -1) {
+ if (thisStart != pstart) {
+ string dots = "";
+ for (int i = pstart; i < thisStart; i++) { dots += "."; }
+ thisEnd += dots.length();
+ dots += seq.getAligned();
+ seq.setAligned(dots);
+ }
+ }
+ }
+
+ if (pend != -1) {
+ if (thisEnd != -1) {
+ if (thisEnd != pend) {
+ string dots = seq.getAligned();
+ for (int i = thisEnd; i < pend; i++) { dots += "."; }
+ seq.setAligned(dots);
+ }
+ }
+ }
+ lengths.insert(seq.getAligned().length());
+ }
+
+ seq.printSequence(out);
+ }
+ inFasta.close();
+ inLocations.close();
+ out.close();
+ m->mothurRemove(locations);
+ m->mothurRemove(goodFasta);
+ m->renameFile(goodFasta+".temp", goodFasta);
+
+ //cout << "final lengths = \n";
+ //for (set<int>::iterator it = lengths.begin(); it != lengths.end(); it++) {
+ // cout << *it << endl;
+ // }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PcrSeqsCommand", "adjustDots");
+ exit(1);
+ }
+}
//********************************************************************/
string PcrSeqsCommand::reverseOligo(string oligo){
try {
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 << "oligo = " << oligo << " reverse = " << oligoRC << endl;
+ //cout << "rev oligo = " << oligo << " reverse = " << oligoRC << endl;
}else if(type == "BARCODE"){
- inOligos >> group;
+ 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 forward, reverse, linker, spacer and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ 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);
}
//check for groups that have been eliminated
CountTable ct;
if (ct.testGroups(goodCountFile)) {
- ct.readTable(goodCountFile);
+ ct.readTable(goodCountFile, true);
ct.printTable(goodCountFile);
}
projects / mothur.git / blobdiff