5 * Created by Pat Schloss on 6/6/09.
6 * Copyright 2009 Patrick D. Schloss. All rights reserved.
10 #include "trimseqscommand.h"
11 #include "needlemanoverlap.hpp"
13 //***************************************************************************************************************
15 TrimSeqsCommand::TrimSeqsCommand(string option) {
21 //allow user to run help
22 if(option == "help") { help(); abort = true; }
25 //valid paramters for this command
26 string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
27 "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
29 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
31 OptionParser parser(option);
32 map<string,string> parameters = parser.getParameters();
34 ValidParameters validParameter;
35 map<string,string>::iterator it;
37 //check to make sure all parameters are valid for command
38 for (it = parameters.begin(); it != parameters.end(); it++) {
39 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
42 //if the user changes the input directory command factory will send this info to us in the output parameter
43 string inputDir = validParameter.validFile(parameters, "inputdir", false);
44 if (inputDir == "not found"){ inputDir = ""; }
47 it = parameters.find("fasta");
48 //user has given a template file
49 if(it != parameters.end()){
50 path = m->hasPath(it->second);
51 //if the user has not given a path then, add inputdir. else leave path alone.
52 if (path == "") { parameters["fasta"] = inputDir + it->second; }
55 it = parameters.find("oligos");
56 //user has given a template file
57 if(it != parameters.end()){
58 path = m->hasPath(it->second);
59 //if the user has not given a path then, add inputdir. else leave path alone.
60 if (path == "") { parameters["oligos"] = inputDir + it->second; }
63 it = parameters.find("qfile");
64 //user has given a template file
65 if(it != parameters.end()){
66 path = m->hasPath(it->second);
67 //if the user has not given a path then, add inputdir. else leave path alone.
68 if (path == "") { parameters["qfile"] = inputDir + it->second; }
73 //check for required parameters
74 fastaFile = validParameter.validFile(parameters, "fasta", true);
75 if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
76 else if (fastaFile == "not open") { abort = true; }
78 //if the user changes the output directory command factory will send this info to us in the output parameter
79 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
81 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
85 //check for optional parameter and set defaults
86 // ...at some point should added some additional type checking...
88 temp = validParameter.validFile(parameters, "flip", false);
89 if (temp == "not found"){ flip = 0; }
90 else if(m->isTrue(temp)) { flip = 1; }
92 temp = validParameter.validFile(parameters, "oligos", true);
93 if (temp == "not found"){ oligoFile = ""; }
94 else if(temp == "not open"){ abort = true; }
95 else { oligoFile = temp; }
97 temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
98 convert(temp, maxAmbig);
100 temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
101 convert(temp, maxHomoP);
103 temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
104 convert(temp, minLength);
106 temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
107 convert(temp, maxLength);
109 temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
110 convert(temp, bdiffs);
112 temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
113 convert(temp, pdiffs);
115 temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
116 convert(temp, tdiffs);
118 if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; }
120 temp = validParameter.validFile(parameters, "qfile", true);
121 if (temp == "not found") { qFileName = ""; }
122 else if(temp == "not open") { abort = true; }
123 else { qFileName = temp; }
125 temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
126 convert(temp, qThreshold);
128 temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
129 qtrim = m->isTrue(temp);
131 temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
132 convert(temp, qRollAverage);
134 temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
135 convert(temp, qWindowAverage);
137 temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "100"; }
138 convert(temp, qWindowSize);
140 temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "10"; }
141 convert(temp, qWindowStep);
143 temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
144 convert(temp, qAverage);
146 temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
147 allFiles = m->isTrue(temp);
149 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
150 convert(temp, processors);
152 if(allFiles && oligoFile == ""){
153 m->mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); m->mothurOutEndLine();
155 if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
156 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
160 if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
161 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
167 catch(exception& e) {
168 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
172 //**********************************************************************************************************************
174 void TrimSeqsCommand::help(){
176 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
177 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
178 m->mothurOut("The fasta parameter is required.\n");
179 m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
180 m->mothurOut("The oligos parameter .... The default is "".\n");
181 m->mothurOut("The maxambig parameter .... The default is -1.\n");
182 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
183 m->mothurOut("The minlength parameter .... The default is 0.\n");
184 m->mothurOut("The maxlength parameter .... The default is 0.\n");
185 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
186 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
187 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
188 m->mothurOut("The qfile parameter .....\n");
189 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
190 m->mothurOut("The qaverage parameter .... The default is 0.\n");
191 m->mothurOut("The allfiles parameter .... The default is F.\n");
192 m->mothurOut("The qtrim parameter .... The default is F.\n");
193 m->mothurOut("The trim.seqs command should be in the following format: \n");
194 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
195 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
196 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
197 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
198 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
201 catch(exception& e) {
202 m->errorOut(e, "TrimSeqsCommand", "help");
208 //***************************************************************************************************************
210 TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ }
212 //***************************************************************************************************************
214 int TrimSeqsCommand::execute(){
217 if (abort == true) { return 0; }
219 numFPrimers = 0; //this needs to be initialized
222 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
223 outputNames.push_back(trimSeqFile);
224 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
225 outputNames.push_back(scrapSeqFile);
226 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
227 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
228 if (qFileName != "") { outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile); }
229 string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
231 vector<string> fastaFileNames;
232 vector<string> qualFileNames;
234 outputNames.push_back(groupFile);
235 getOligos(fastaFileNames, qualFileNames);
238 vector<unsigned long int> fastaFilePos;
239 vector<unsigned long int> qFilePos;
241 setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
243 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
244 lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
245 if (qFileName != "") { qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)])); }
247 if(qFileName == "") { qLines = lines; } //files with duds
249 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
252 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
254 for (int j = 0; j < fastaFileNames.size(); j++) {
255 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
258 for (int j = 0; j < qualFileNames.size(); j++) {
259 rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
264 createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
266 rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
267 rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
268 rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
271 rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str());
272 rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str());
276 for (int j = 0; j < fastaFileNames.size(); j++) {
277 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
280 for (int j = 0; j < qualFileNames.size(); j++) {
281 rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
286 for(int i=1;i<processors;i++){
287 m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
288 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
289 m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
290 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
292 m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
293 remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
294 m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
295 remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
297 m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
298 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
299 for (int j = 0; j < fastaFileNames.size(); j++) {
300 m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
301 remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
305 for (int j = 0; j < qualFileNames.size(); j++) {
306 m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
307 remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
315 if (m->control_pressed) { return 0; }
317 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
319 for (int j = 0; j < fastaFileNames.size(); j++) {
320 rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
323 for (int j = 0; j < qualFileNames.size(); j++) {
324 rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
328 if (m->control_pressed) { return 0; }
332 for(int i=0;i<fastaFileNames.size();i++){
333 if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
334 else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
338 m->openInputFile(fastaFileNames[i], inFASTA);
340 string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
341 m->openOutputFile(outGroupFilename, outGroups);
342 outputNames.push_back(outGroupFilename);
344 string thisGroup = "";
345 if (i > comboStarts) {
346 map<string, int>::iterator itCombo;
347 for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
348 if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
350 }else{ thisGroup = groupVector[i]; }
352 while(!inFASTA.eof()){
353 if(inFASTA.get() == '>'){
355 outGroups << seqName << '\t' << thisGroup << endl;
357 while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
365 for(int i=0;i<qualFileNames.size();i++){
366 if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
367 else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
371 m->openInputFile(qualFileNames[i], inQual);
372 // ofstream outGroups;
374 // string thisGroup = "";
375 // if (i > comboStarts) {
376 // map<string, int>::iterator itCombo;
377 // for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
378 // if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
381 // else{ thisGroup = groupVector[i]; }
389 if (m->control_pressed) {
390 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
394 m->mothurOutEndLine();
395 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
396 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
397 m->mothurOutEndLine();
402 catch(exception& e) {
403 m->errorOut(e, "TrimSeqsCommand", "execute");
408 /**************************************************************************************/
410 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames, linePair* line, linePair* qline) {
415 int able = m->openOutputFile(trimFile, outFASTA);
418 m->openOutputFile(scrapFile, scrapFASTA);
423 m->openOutputFile(trimQFile, outQual);
424 m->openOutputFile(scrapQFile, scrapQual);
428 vector<ofstream*> fastaFileNames;
429 vector<ofstream*> qualFileNames;
431 if (oligoFile != "") {
432 m->openOutputFile(groupFile, outGroups);
433 for (int i = 0; i < fastaNames.size(); i++) {
435 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
436 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
438 qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
441 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
443 qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
450 m->openInputFile(filename, inFASTA);
451 inFASTA.seekg(line->start);
454 if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
461 if (m->control_pressed) {
462 inFASTA.close(); outFASTA.close(); scrapFASTA.close();
463 if (oligoFile != "") { outGroups.close(); }
465 for(int i=0;i<fastaFileNames.size();i++){ fastaFileNames[i]->close(); delete fastaFileNames[i]; }
469 for(int i=0;i<qualFileNames.size();i++){ qualFileNames[i]->close(); delete qualFileNames[i]; }
471 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
479 Sequence currSeq(inFASTA); m->gobble(inFASTA);
481 QualityScores currQual;
483 currQual = QualityScores(qFile, currSeq.getNumBases()); m->gobble(qFile);
486 string origSeq = currSeq.getUnaligned();
488 int groupBar, groupPrime;
489 string trashCode = "";
490 int currentSeqsDiffs = 0;
493 if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
494 else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
495 else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
496 else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
498 if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
499 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
502 if(!success) { trashCode += 'q'; }
505 if(barcodes.size() != 0){
506 success = stripBarcode(currSeq, currQual, groupBar);
507 if(success > bdiffs) { trashCode += 'b'; }
508 else{ currentSeqsDiffs += success; }
511 if(numFPrimers != 0){
512 success = stripForward(currSeq, currQual, groupPrime);
513 if(success > pdiffs) { trashCode += 'f'; }
514 else{ currentSeqsDiffs += success; }
517 if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
519 if(numRPrimers != 0){
520 success = stripReverse(currSeq, currQual);
521 if(!success) { trashCode += 'r'; }
524 if(minLength > 0 || maxLength > 0){
525 success = cullLength(currSeq);
526 if(!success) { trashCode += 'l'; }
529 success = cullHomoP(currSeq);
530 if(!success) { trashCode += 'h'; }
533 success = cullAmbigs(currSeq);
534 if(!success) { trashCode += 'n'; }
537 if(flip){ currSeq.reverseComplement(); currQual.flipQScores(); } // should go last
539 if(trashCode.length() == 0){
540 currSeq.setAligned(currSeq.getUnaligned());
541 currSeq.printSequence(outFASTA);
542 currQual.printQScores(outQual);
544 if(barcodes.size() != 0){
545 string thisGroup = groupVector[groupBar];
546 int indexToFastaFile = groupBar;
547 if (primers.size() != 0){
548 //does this primer have a group
549 if (groupVector[groupPrime] != "") {
550 thisGroup += "." + groupVector[groupPrime];
551 indexToFastaFile = combos[thisGroup];
554 outGroups << currSeq.getName() << '\t' << thisGroup << endl;
556 currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
559 currQual.printQScores(*qualFileNames[indexToFastaFile]);
565 currSeq.setName(currSeq.getName() + '|' + trashCode);
566 currSeq.setUnaligned(origSeq);
567 currSeq.setAligned(origSeq);
568 currSeq.printSequence(scrapFASTA);
569 currQual.printQScores(scrapQual);
574 unsigned long int pos = inFASTA.tellg();
575 if ((pos == -1) || (pos >= line->end)) { break; }
578 if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
582 if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
588 if (oligoFile != "") { outGroups.close(); }
589 if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); }
591 for(int i=0;i<fastaFileNames.size();i++){
592 fastaFileNames[i]->close();
593 delete fastaFileNames[i];
597 for(int i=0;i<qualFileNames.size();i++){
598 qualFileNames[i]->close();
599 delete qualFileNames[i];
605 catch(exception& e) {
606 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
611 /**************************************************************************************************/
613 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
615 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
620 //loop through and create all the processes you want
621 while (process != processors) {
625 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
628 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]);
630 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
633 //force parent to wait until all the processes are done
634 for (int i=0;i<processors;i++) {
635 int temp = processIDS[i];
642 catch(exception& e) {
643 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
648 /**************************************************************************************************/
650 int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
653 //set file positions for fasta file
654 fastaFilePos = m->divideFile(filename, processors);
656 if (qfilename == "") { return processors; }
658 //get name of first sequence in each chunk
659 map<string, int> firstSeqNames;
660 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
662 m->openInputFile(filename, in);
663 in.seekg(fastaFilePos[i]);
666 firstSeqNames[temp.getName()] = i;
671 //seach for filePos of each first name in the qfile and save in qfileFilePos
673 m->openInputFile(qfilename, inQual);
676 while(!inQual.eof()){
677 input = m->getline(inQual);
679 if (input.length() != 0) {
680 if(input[0] == '>'){ //this is a sequence name line
681 istringstream nameStream(input);
683 string sname = ""; nameStream >> sname;
684 sname = sname.substr(1);
686 map<string, int>::iterator it = firstSeqNames.find(sname);
688 if(it != firstSeqNames.end()) { //this is the start of a new chunk
689 unsigned long int pos = inQual.tellg();
690 qfileFilePos.push_back(pos - input.length() - 1);
691 firstSeqNames.erase(it);
696 if (firstSeqNames.size() == 0) { break; }
700 if (firstSeqNames.size() != 0) {
701 for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
702 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
708 //get last file position of qfile
710 unsigned long int size;
712 //get num bytes in file
713 pFile = fopen (qfilename.c_str(),"rb");
714 if (pFile==NULL) perror ("Error opening file");
716 fseek (pFile, 0, SEEK_END);
721 qfileFilePos.push_back(size);
725 catch(exception& e) {
726 m->errorOut(e, "TrimSeqsCommand", "setLines");
730 //***************************************************************************************************************
732 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
735 m->openInputFile(oligoFile, inOligos);
739 string type, oligo, group;
741 //int indexPrimer = 0;
743 while(!inOligos.eof()){
747 while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
750 //make type case insensitive
751 for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
755 for(int i=0;i<oligo.length();i++){
756 oligo[i] = toupper(oligo[i]);
757 if(oligo[i] == 'U') { oligo[i] = 'T'; }
760 if(type == "FORWARD"){
763 // get rest of line in case there is a primer name
764 while (!inOligos.eof()) {
765 char c = inOligos.get();
766 if (c == 10 || c == 13){ break; }
767 else if (c == 32 || c == 9){;} //space or tab
771 //check for repeat barcodes
772 map<string, int>::iterator itPrime = primers.find(oligo);
773 if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
775 primers[oligo]=index; index++;
776 groupVector.push_back(group);
779 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
781 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
783 if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
784 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
786 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
789 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
791 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
797 else if(type == "REVERSE"){
798 Sequence oligoRC("reverse", oligo);
799 oligoRC.reverseComplement();
800 revPrimer.push_back(oligoRC.getUnaligned());
802 else if(type == "BARCODE"){
805 //check for repeat barcodes
806 map<string, int>::iterator itBar = barcodes.find(oligo);
807 if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
809 barcodes[oligo]=index; index++;
810 groupVector.push_back(group);
813 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
814 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
816 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
817 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
820 }else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
827 //add in potential combos
829 comboStarts = outFASTAVec.size()-1;
830 for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
831 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
832 if (groupVector[itPrime->second] != "") { //there is a group for this primer
833 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
834 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
835 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
838 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
839 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
846 numFPrimers = primers.size();
847 numRPrimers = revPrimer.size();
850 catch(exception& e) {
851 m->errorOut(e, "TrimSeqsCommand", "getOligos");
855 //***************************************************************************************************************
857 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
860 string rawSequence = seq.getUnaligned();
861 int success = bdiffs + 1; //guilty until proven innocent
863 //can you find the barcode
864 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
865 string oligo = it->first;
866 if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
867 success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
871 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
873 seq.setUnaligned(rawSequence.substr(oligo.length()));
875 if(qual.getName() != ""){
876 qual.trimQScores(oligo.length(), -1);
884 //if you found the barcode or if you don't want to allow for diffs
886 if ((bdiffs == 0) || (success == 0)) { return success; }
888 else { //try aligning and see if you can find it
893 Alignment* alignment;
894 if (barcodes.size() > 0) {
895 map<string,int>::iterator it=barcodes.begin();
897 for(it;it!=barcodes.end();it++){
898 if(it->first.length() > maxLength){
899 maxLength = it->first.length();
902 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
904 }else{ alignment = NULL; }
906 //can you find the barcode
912 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
913 string oligo = it->first;
914 // int length = oligo.length();
916 if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
917 success = bdiffs + 10;
921 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
922 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
923 oligo = alignment->getSeqAAln();
924 string temp = alignment->getSeqBAln();
926 int alnLength = oligo.length();
928 for(int i=oligo.length()-1;i>=0;i--){
929 if(oligo[i] != '-'){ alnLength = i+1; break; }
931 oligo = oligo.substr(0,alnLength);
932 temp = temp.substr(0,alnLength);
935 int numDiff = countDiffs(oligo, temp);
937 // cout << oligo << '\t' << temp << '\t' << numDiff << endl;
939 if(numDiff < minDiff){
942 minGroup = it->second;
944 for(int i=0;i<alnLength;i++){
950 else if(numDiff == minDiff){
956 if(minDiff > bdiffs) { success = minDiff; } //no good matches
957 else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
958 else{ //use the best match
960 seq.setUnaligned(rawSequence.substr(minPos));
962 if(qual.getName() != ""){
963 qual.trimQScores(minPos, -1);
968 if (alignment != NULL) { delete alignment; }
971 // cout << success << endl;
976 catch(exception& e) {
977 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
983 //***************************************************************************************************************
985 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
987 string rawSequence = seq.getUnaligned();
988 int success = pdiffs + 1; //guilty until proven innocent
990 //can you find the primer
991 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
992 string oligo = it->first;
993 if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
994 success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
998 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1000 seq.setUnaligned(rawSequence.substr(oligo.length()));
1001 if(qual.getName() != ""){
1002 qual.trimQScores(oligo.length(), -1);
1010 //if you found the barcode or if you don't want to allow for diffs
1012 if ((pdiffs == 0) || (success == 0)) { return success; }
1014 else { //try aligning and see if you can find it
1019 Alignment* alignment;
1020 if (primers.size() > 0) {
1021 map<string,int>::iterator it=primers.begin();
1023 for(it;it!=primers.end();it++){
1024 if(it->first.length() > maxLength){
1025 maxLength = it->first.length();
1028 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1030 }else{ alignment = NULL; }
1032 //can you find the barcode
1038 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1039 string oligo = it->first;
1040 // int length = oligo.length();
1042 if(rawSequence.length() < maxLength){
1043 success = pdiffs + 100;
1047 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1048 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1049 oligo = alignment->getSeqAAln();
1050 string temp = alignment->getSeqBAln();
1052 int alnLength = oligo.length();
1054 for(int i=oligo.length()-1;i>=0;i--){
1055 if(oligo[i] != '-'){ alnLength = i+1; break; }
1057 oligo = oligo.substr(0,alnLength);
1058 temp = temp.substr(0,alnLength);
1061 int numDiff = countDiffs(oligo, temp);
1063 // cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1065 if(numDiff < minDiff){
1068 minGroup = it->second;
1070 for(int i=0;i<alnLength;i++){
1076 else if(numDiff == minDiff){
1082 if(minDiff > pdiffs) { success = minDiff; } //no good matches
1083 else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
1084 else{ //use the best match
1086 seq.setUnaligned(rawSequence.substr(minPos));
1087 if(qual.getName() != ""){
1088 qual.trimQScores(minPos, -1);
1093 if (alignment != NULL) { delete alignment; }
1100 catch(exception& e) {
1101 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1106 //***************************************************************************************************************
1108 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1110 string rawSequence = seq.getUnaligned();
1111 bool success = 0; //guilty until proven innocent
1113 for(int i=0;i<numRPrimers;i++){
1114 string oligo = revPrimer[i];
1116 if(rawSequence.length() < oligo.length()){
1121 if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1122 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1123 if(qual.getName() != ""){
1124 qual.trimQScores(-1, rawSequence.length()-oligo.length());
1133 catch(exception& e) {
1134 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1139 //***************************************************************************************************************
1141 bool TrimSeqsCommand::cullLength(Sequence& seq){
1144 int length = seq.getNumBases();
1145 bool success = 0; //guilty until proven innocent
1147 if(length >= minLength && maxLength == 0) { success = 1; }
1148 else if(length >= minLength && length <= maxLength) { success = 1; }
1149 else { success = 0; }
1154 catch(exception& e) {
1155 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1161 //***************************************************************************************************************
1163 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1165 int longHomoP = seq.getLongHomoPolymer();
1166 bool success = 0; //guilty until proven innocent
1168 if(longHomoP <= maxHomoP){ success = 1; }
1169 else { success = 0; }
1173 catch(exception& e) {
1174 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1180 //***************************************************************************************************************
1182 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1184 int numNs = seq.getAmbigBases();
1185 bool success = 0; //guilty until proven innocent
1187 if(numNs <= maxAmbig) { success = 1; }
1188 else { success = 0; }
1192 catch(exception& e) {
1193 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1199 //***************************************************************************************************************
1201 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1204 int length = oligo.length();
1206 for(int i=0;i<length;i++){
1208 if(oligo[i] != seq[i]){
1209 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
1210 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
1211 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
1212 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
1213 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
1214 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
1215 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
1216 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
1217 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
1218 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
1219 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
1220 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
1222 if(success == 0) { break; }
1231 catch(exception& e) {
1232 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1237 //***************************************************************************************************************
1239 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1242 int length = oligo.length();
1245 for(int i=0;i<length;i++){
1247 if(oligo[i] != seq[i]){
1248 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.') { countDiffs++; }
1249 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
1250 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { countDiffs++; }
1251 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { countDiffs++; }
1252 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { countDiffs++; }
1253 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
1254 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { countDiffs++; }
1255 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
1256 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
1257 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
1258 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; }
1259 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
1266 catch(exception& e) {
1267 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1272 //***************************************************************************************************************
1274 //bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
1277 // string rawSequence = seq.getUnaligned();
1278 // int seqLength = seq.getNumBases();
1279 // bool success = 0; //guilty until proven innocent
1283 // if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
1285 // while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
1288 // int end = seqLength;
1290 // for(int i=0;i<seqLength;i++){
1293 // if(score < qThreshold){
1298 // for(int i=end+1;i<seqLength;i++){
1302 // seq.setUnaligned(rawSequence.substr(0,end));
1306 // catch(exception& e) {
1307 // m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1312 //***************************************************************************************************************
1314 //bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1316 // string rawSequence = seq.getUnaligned();
1317 // int seqLength = seq.getNumBases();
1318 // bool success = 0; //guilty until proven innocent
1322 // if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
1324 // while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
1327 // float average = 0;
1329 // for(int i=0;i<seqLength;i++){
1331 // average += score;
1333 // average /= seqLength;
1335 // if(average >= qAverage) { success = 1; }
1336 // else { success = 0; }
1340 // catch(exception& e) {
1341 // m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1346 //***************************************************************************************************************