//**********************************************************************************************************************
vector<string> PcrSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
- CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(pecoli);
- CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
- CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
- CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "",false,false); parameters.push_back(pnomatch);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
- CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptax);
+ CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false); parameters.push_back(pecoli);
+ CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pstart);
+ CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pend);
+ CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "","",false,false); parameters.push_back(pnomatch);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepprimer);
+ CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pkeepdots);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
helpString += "The pcr.seqs command reads a fasta file.\n";
- helpString += "The pcr.seqs command parameters are fasta, oligos, name, group, count, taxonomy, ecoli, start, end, nomatch, processors, keepprimer and keepdots.\n";
+ helpString += "The pcr.seqs command parameters are fasta, oligos, name, group, count, taxonomy, ecoli, start, end, nomatch, pdiffs, processors, keepprimer and keepdots.\n";
helpString += "The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence.\n";
helpString += "The start parameter allows you to provide a starting position to trim to.\n";
helpString += "The end parameter allows you to provide a ending position to trim from.\n";
helpString += "The processors parameter allows you to use multiple processors.\n";
helpString += "The keepprimer parameter allows you to keep the primer, default=false.\n";
helpString += "The keepdots parameter allows you to keep the leading and trailing .'s, default=true.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Pcr.seqs .\n";
return helpString;
exit(1);
}
}
-
//**********************************************************************************************************************
-string PcrSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PcrSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pcr.fasta"; }
- else if (type == "taxonomy") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "accnos") { outputFileName = "bad.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PcrSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pcr,[extension]-[filename],[tag],pcr,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "accnos") { pattern = "[filename],bad.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PcrSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
nomatch = validParameter.validFile(parameters, "nomatch", false); if (nomatch == "not found") { nomatch = "reject"; }
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string trimSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string trimSeqFile = getOutputFileName("fasta",variables);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
-
- string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "scrap." + getOutputFileNameTag("fasta");
+ variables["[tag]"] = "scrap";
+ string badSeqFile = getOutputFileName("fasta",variables);
length = 0;
- if(oligosfile != ""){ readOligos(); } if (m->control_pressed) { return 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(ecolifile != "") { readEcoli(); } if (m->control_pressed) { return 0; }
vector<unsigned long long> positions;
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, lines[i].start, lines[i].end);
+ 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);
pDataArray.push_back(tempPcr);
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ 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;
+ }
for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it); }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
int count = 0;
set<int> lengths;
+ //pdiffs, bdiffs, primers, barcodes, revPrimers
+ map<string, int> faked;
+ TrimOligos trim(pdiffs, 0, primers, faked, revPrimer);
+
while (!done) {
if (m->control_pressed) { break; }
string trashCode = "";
if (currSeq.getName() != "") {
+ if (m->debug) { m->mothurOut("[DEBUG]: seq name = " + currSeq.getName() + ".\n"); }
+
bool goodSeq = true;
if (oligosfile != "") {
map<int, int> mapAligned;
//process primers
if (primers.size() != 0) {
int primerStart = 0; int primerEnd = 0;
- bool good = findForward(currSeq, primerStart, primerEnd);
+ bool good = trim.findForward(currSeq, primerStart, primerEnd);
if(!good){ if (nomatch == "reject") { goodSeq = false; } trashCode += "f"; }
else{
}
else {
if (keepdots) { currSeq.filterToPos(mapAligned[primerStart]); }
- else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart])); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart])); }
}
+ isAligned(currSeq.getAligned(), mapAligned);
}else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(primerEnd)); }
else { currSeq.setAligned(currSeq.getUnaligned().substr(primerStart)); }
//process reverse primers
if (revPrimer.size() != 0) {
int primerStart = 0; int primerEnd = 0;
- bool good = findReverse(currSeq, primerStart, primerEnd);
+ bool good = trim.findReverse(currSeq, primerStart, primerEnd);
if(!good){ if (nomatch == "reject") { goodSeq = false; } trashCode += "r"; }
else{
- //are you aligned
+ //are you aligned
if (aligned) {
if (!keepprimer) {
if (keepdots) { currSeq.filterFromPos(mapAligned[primerStart]); }
}
}
//********************************************************************/
-bool PcrSeqsCommand::findForward(Sequence& seq, int& primerStart, int& primerEnd){
- try {
-
- string rawSequence = seq.getUnaligned();
-
- for(int j=0;j<primers.size();j++){
- string oligo = primers[j];
-
- if(rawSequence.length() < oligo.length()) { break; }
-
- //search for primer
- int olength = oligo.length();
- for (int j = 0; j < rawSequence.length()-olength; j++){
- if (m->control_pressed) { primerStart = 0; primerEnd = 0; return false; }
- string rawChunk = rawSequence.substr(j, olength);
- if(compareDNASeq(oligo, rawChunk)) {
- primerStart = j;
- primerEnd = primerStart + olength;
- return true;
- }
-
- }
- }
-
- primerStart = 0; primerEnd = 0;
- return false;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimOligos", "stripForward");
- exit(1);
- }
-}
-//******************************************************************/
-bool PcrSeqsCommand::findReverse(Sequence& seq, int& primerStart, int& primerEnd){
- try {
-
- string rawSequence = seq.getUnaligned();
-
- for(int i=0;i<revPrimer.size();i++){
- string oligo = revPrimer[i];
- if(rawSequence.length() < oligo.length()) { break; }
-
- //search for primer
- int olength = oligo.length();
- for (int j = rawSequence.length()-olength; j >= 0; j--){
- if (m->control_pressed) { primerStart = 0; primerEnd = 0; return false; }
- string rawChunk = rawSequence.substr(j, olength);
-
- if(compareDNASeq(oligo, rawChunk)) {
- primerStart = j;
- primerEnd = primerStart + olength;
- return true;
- }
-
- }
- }
-
- primerStart = 0; primerEnd = 0;
- return false;
- }
- catch(exception& e) {
- m->errorOut(e, "PcrSeqsCommand", "findReverse");
- exit(1);
- }
-}
-//********************************************************************/
bool PcrSeqsCommand::isAligned(string seq, map<int, int>& aligned){
try {
+ aligned.clear();
bool isAligned = false;
int countBases = 0;
m->openInputFile(oligosfile, inOligos);
string type, oligo, group;
+ int primerCount = 0;
while(!inOligos.eof()){
// get rest of line in case there is a primer name
while (!inOligos.eof()) {
char c = inOligos.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
}
- primers.push_back(oligo);
+ primers[oligo] = primerCount; primerCount++;
}else if(type == "REVERSE"){
string oligoRC = reverseOligo(oligo);
revPrimer.push_back(oligoRC);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("accnos",variables);
outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
ofstream out;
exit(1);
}
-}
-//******************************************************************/
-bool PcrSeqsCommand::compareDNASeq(string oligo, string seq){
- try {
- bool success = 1;
- int length = oligo.length();
-
- for(int i=0;i<length;i++){
-
- if(oligo[i] != seq[i]){
- if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
- else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
- else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
- else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
- else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
- else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
- else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
-
- if(success == 0) { break; }
- }
- else{
- success = 1;
- }
- }
-
- return success;
- }
- catch(exception& e) {
- m->errorOut(e, "PcrSeqsCommand", "compareDNASeq");
- exit(1);
- }
-
}
//***************************************************************************************************************
int PcrSeqsCommand::readName(set<string>& names){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
m->openInputFile(countfile, in);
set<string>::iterator it;
- string goodCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string goodCountFile = getOutputFileName("count", variables);
+
outputNames.push_back(goodCountFile); outputTypes["count"].push_back(goodCountFile);
ofstream goodCountOut; m->openOutputFile(goodCountFile, goodCountOut);
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