5 * Created by Pat Schloss on 6/6/09.
6 * Copyright 2009 Patrick D. Schloss. All rights reserved.
10 #include "trimseqscommand.h"
12 //***************************************************************************************************************
14 TrimSeqsCommand::TrimSeqsCommand(string option){
19 //allow user to run help
20 if(option == "help") { help(); abort = true; }
23 //valid paramters for this command
24 string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles", "qtrim"};
26 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
28 OptionParser parser(option);
29 map<string,string> parameters = parser.getParameters();
31 ValidParameters validParameter;
33 //check to make sure all parameters are valid for command
34 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
35 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
38 //check for required parameters
39 fastaFile = validParameter.validFile(parameters, "fasta", true);
40 if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
41 else if (fastaFile == "not open") { abort = true; }
44 //check for optional parameter and set defaults
45 // ...at some point should added some additional type checking...
47 temp = validParameter.validFile(parameters, "flip", false);
48 if (temp == "not found"){ flip = 0; }
49 else if(isTrue(temp)) { flip = 1; }
51 temp = validParameter.validFile(parameters, "oligos", true);
52 if (temp == "not found"){ oligoFile = ""; }
53 else if(temp == "not open"){ abort = true; }
54 else { oligoFile = temp; }
56 temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
57 convert(temp, maxAmbig);
59 temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
60 convert(temp, maxHomoP);
62 temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
63 convert(temp, minLength);
65 temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
66 convert(temp, maxLength);
68 temp = validParameter.validFile(parameters, "qfile", true);
69 if (temp == "not found") { qFileName = ""; }
70 else if(temp == "not open") { abort = 0; }
71 else { qFileName = temp; }
73 temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
74 convert(temp, qThreshold);
76 temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
79 temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
80 convert(temp, qAverage);
82 temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
83 allFiles = isTrue(temp);
85 if(allFiles && oligoFile == ""){
86 mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); mothurOutEndLine();
88 if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
89 mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
93 if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
94 mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
100 catch(exception& e) {
101 errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
105 //**********************************************************************************************************************
107 void TrimSeqsCommand::help(){
109 mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
110 mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, qtrim and allfiles.\n");
111 mothurOut("The fasta parameter is required.\n");
112 mothurOut("The flip parameter .... The default is 0.\n");
113 mothurOut("The oligos parameter .... The default is "".\n");
114 mothurOut("The maxambig parameter .... The default is -1.\n");
115 mothurOut("The maxhomop parameter .... The default is 0.\n");
116 mothurOut("The minlength parameter .... The default is 0.\n");
117 mothurOut("The maxlength parameter .... The default is 0.\n");
118 mothurOut("The qfile parameter .....\n");
119 mothurOut("The qthreshold parameter .... The default is 0.\n");
120 mothurOut("The qaverage parameter .... The default is 0.\n");
121 mothurOut("The allfiles parameter .... The default is F.\n");
122 mothurOut("The qtrim parameter .... The default is F.\n");
123 mothurOut("The trim.seqs command should be in the following format: \n");
124 mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
125 mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
126 mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
127 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
128 mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
131 catch(exception& e) {
132 errorOut(e, "TrimSeqsCommand", "help");
138 //***************************************************************************************************************
140 TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ }
142 //***************************************************************************************************************
144 int TrimSeqsCommand::execute(){
147 if (abort == true) { return 0; }
150 openInputFile(fastaFile, inFASTA);
153 string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
154 openOutputFile(trimSeqFile, outFASTA);
157 vector<ofstream*> fastaFileNames;
159 string groupFile = getRootName(fastaFile) + "groups";
160 openOutputFile(groupFile, outGroups);
161 getOligos(fastaFileNames);
165 string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
166 openOutputFile(scrapSeqFile, scrapFASTA);
169 if(qFileName != "") { openInputFile(qFileName, qFile); }
173 while(!inFASTA.eof()){
174 Sequence currSeq(inFASTA);
175 string origSeq = currSeq.getUnaligned();
178 string trashCode = "";
181 if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
182 else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
183 if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
184 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
186 if(!success) { trashCode += 'q'; }
189 if(barcodes.size() != 0){
190 success = stripBarcode(currSeq, group);
191 if(!success){ trashCode += 'b'; }
194 if(numFPrimers != 0){
195 success = stripForward(currSeq);
196 if(!success){ trashCode += 'f'; }
199 if(numRPrimers != 0){
200 success = stripReverse(currSeq);
201 if(!success){ trashCode += 'r'; }
203 if(minLength > 0 || maxLength > 0){
204 success = cullLength(currSeq);
205 if(!success){ trashCode += 'l'; }
208 success = cullHomoP(currSeq);
209 if(!success){ trashCode += 'h'; }
212 success = cullAmbigs(currSeq);
213 if(!success){ trashCode += 'n'; }
216 if(flip){ currSeq.reverseComplement(); } // should go last
218 if(trashCode.length() == 0){
219 currSeq.setAligned(currSeq.getUnaligned()); //this is because of a modification we made to the sequence class to fix a bug. all seqs have an aligned version, which is the version that gets printed.
220 currSeq.printSequence(outFASTA);
221 if(barcodes.size() != 0){
222 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
225 currSeq.printSequence(*fastaFileNames[group]);
230 currSeq.setName(currSeq.getName() + '|' + trashCode);
231 currSeq.setUnaligned(origSeq);
232 currSeq.printSequence(scrapFASTA);
241 if(qFileName != "") { qFile.close(); }
243 for(int i=0;i<fastaFileNames.size();i++){
244 fastaFileNames[i]->close();
245 delete fastaFileNames[i];
248 for(int i=0;i<fastaFileNames.size();i++){
250 openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
252 openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
254 while(!inFASTA.eof()){
255 if(inFASTA.get() == '>'){
257 outGroups << seqName << '\t' << groupVector[i] << endl;
259 while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
268 catch(exception& e) {
269 errorOut(e, "TrimSeqsCommand", "execute");
274 //***************************************************************************************************************
276 void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
279 openInputFile(oligoFile, inOligos);
283 string type, oligo, group;
286 while(!inOligos.eof()){
290 while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
295 for(int i=0;i<oligo.length();i++){
296 oligo[i] = toupper(oligo[i]);
297 if(oligo[i] == 'U') { oligo[i] = 'T'; }
300 if(type == "forward"){
301 forPrimer.push_back(oligo);
303 else if(type == "reverse"){
304 revPrimer.push_back(oligo);
306 else if(type == "barcode"){
308 barcodes[oligo]=index++;
309 groupVector.push_back(group);
312 outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
320 numFPrimers = forPrimer.size();
321 numRPrimers = revPrimer.size();
324 catch(exception& e) {
325 errorOut(e, "TrimSeqsCommand", "getOligos");
331 //***************************************************************************************************************
333 bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
335 string rawSequence = seq.getUnaligned();
336 bool success = 0; //guilty until proven innocent
338 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
339 string oligo = it->first;
340 if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
345 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
347 seq.setUnaligned(rawSequence.substr(oligo.length()));
355 catch(exception& e) {
356 errorOut(e, "TrimSeqsCommand", "stripBarcode");
362 //***************************************************************************************************************
364 bool TrimSeqsCommand::stripForward(Sequence& seq){
366 string rawSequence = seq.getUnaligned();
367 bool success = 0; //guilty until proven innocent
369 for(int i=0;i<numFPrimers;i++){
370 string oligo = forPrimer[i];
372 if(rawSequence.length() < oligo.length()){
377 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
378 seq.setUnaligned(rawSequence.substr(oligo.length()));
387 catch(exception& e) {
388 errorOut(e, "TrimSeqsCommand", "stripForward");
393 //***************************************************************************************************************
395 bool TrimSeqsCommand::stripReverse(Sequence& seq){
397 string rawSequence = seq.getUnaligned();
398 bool success = 0; //guilty until proven innocent
400 for(int i=0;i<numRPrimers;i++){
401 string oligo = revPrimer[i];
403 if(rawSequence.length() < oligo.length()){
408 if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
409 seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
417 catch(exception& e) {
418 errorOut(e, "TrimSeqsCommand", "stripReverse");
423 //***************************************************************************************************************
425 bool TrimSeqsCommand::cullLength(Sequence& seq){
428 int length = seq.getNumBases();
429 bool success = 0; //guilty until proven innocent
431 if(length >= minLength && maxLength == 0) { success = 1; }
432 else if(length >= minLength && length <= maxLength) { success = 1; }
433 else { success = 0; }
438 catch(exception& e) {
439 errorOut(e, "TrimSeqsCommand", "cullLength");
445 //***************************************************************************************************************
447 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
449 int longHomoP = seq.getLongHomoPolymer();
450 bool success = 0; //guilty until proven innocent
452 if(longHomoP <= maxHomoP){ success = 1; }
453 else { success = 0; }
457 catch(exception& e) {
458 errorOut(e, "TrimSeqsCommand", "cullHomoP");
464 //***************************************************************************************************************
466 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
468 int numNs = seq.getAmbigBases();
469 bool success = 0; //guilty until proven innocent
471 if(numNs <= maxAmbig) { success = 1; }
472 else { success = 0; }
476 catch(exception& e) {
477 errorOut(e, "TrimSeqsCommand", "cullAmbigs");
483 //***************************************************************************************************************
485 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
488 int length = oligo.length();
490 for(int i=0;i<length;i++){
492 if(oligo[i] != seq[i]){
493 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
494 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
495 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
496 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
497 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
498 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
499 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
500 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
501 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
502 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
503 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
504 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
506 if(success == 0) { break; }
515 catch(exception& e) {
516 errorOut(e, "TrimSeqsCommand", "compareDNASeq");
522 //***************************************************************************************************************
524 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
526 string rawSequence = seq.getUnaligned();
527 int seqLength = rawSequence.length();
531 if (name.length() != 0) { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); } }
532 while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
537 for(int i=0;i<seqLength;i++){
540 if(score <= qThreshold){
545 for(int i=end+1;i<seqLength;i++){
549 seq.setUnaligned(rawSequence.substr(0,end));
553 catch(exception& e) {
554 errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
559 //***************************************************************************************************************
561 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
563 string rawSequence = seq.getUnaligned();
564 int seqLength = seq.getNumBases();
565 bool success = 0; //guilty until proven innocent
569 if (name[0] == '>') { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine(); } }
571 while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
576 for(int i=0;i<seqLength;i++){
580 average /= seqLength;
582 if(average >= qAverage) { success = 1; }
583 else { success = 0; }
587 catch(exception& e) {
588 errorOut(e, "TrimSeqsCommand", "cullQualAverage");
593 //***************************************************************************************************************