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"};
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") { cout << "fasta is a required parameter for the screen.seqs command." << endl; 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, "qaverage", false); if (temp == "not found") { temp = "0"; }
77 convert(temp, qAverage);
79 temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
80 allFiles = isTrue(temp);
82 if(allFiles && oligoFile == ""){
83 cout << "You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request." << endl;
85 if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
86 cout << "You didn't provide a quality file name, quality criteria will be ignored." << endl;
90 if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
91 cout << "You didn't set any options... quiting command." << endl;
98 cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
102 cout << "An unknown error has occurred in the TrimSeqsCommand class function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
106 //**********************************************************************************************************************
108 void TrimSeqsCommand::help(){
110 cout << "The trim.seqs command reads a fastaFile and creates ....." << "\n";
111 cout << "The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength." << "\n";
112 cout << "The fasta parameter is required." << "\n";
113 cout << "The flip parameter .... The default is 0." << "\n";
114 cout << "The oligos parameter .... The default is ""." << "\n";
115 cout << "The maxambig parameter .... The default is -1." << "\n";
116 cout << "The maxhomop parameter .... The default is 0." << "\n";
117 cout << "The minlength parameter .... The default is 0." << "\n";
118 cout << "The maxlength parameter .... The default is 0." << "\n";
119 cout << "The trim.seqs command should be in the following format: " << "\n";
120 cout << "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, " << "\n";
121 cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) " << "\n";
122 cout << "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...)." << "\n";
123 cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
126 catch(exception& e) {
127 cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
131 cout << "An unknown error has occurred in the TrimSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
137 //***************************************************************************************************************
139 TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ }
141 //***************************************************************************************************************
143 int TrimSeqsCommand::execute(){
146 if (abort == true) { return 0; }
149 openInputFile(fastaFile, inFASTA);
152 string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
153 openOutputFile(trimSeqFile, outFASTA);
156 vector<ofstream*> fastaFileNames;
158 string groupFile = getRootName(fastaFile) + "groups";
159 openOutputFile(groupFile, outGroups);
160 getOligos(fastaFileNames);
164 string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
165 openOutputFile(scrapSeqFile, scrapFASTA);
168 if(qFileName != "") { openInputFile(qFileName, qFile); }
172 while(!inFASTA.eof()){
173 Sequence currSeq(inFASTA);
174 string origSeq = currSeq.getUnaligned();
176 string trashCode = "";
179 if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
180 else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
181 if(!success) { trashCode += 'q'; }
184 if(barcodes.size() != 0){
185 success = stripBarcode(currSeq, group);
186 if(!success){ trashCode += 'b'; }
188 if(numFPrimers != 0){
189 success = stripForward(currSeq);
190 if(!success){ trashCode += 'f'; }
192 if(numRPrimers != 0){
193 success = stripReverse(currSeq);
194 if(!success){ trashCode += 'r'; }
196 if(minLength > 0 || maxLength > 0){
197 success = cullLength(currSeq);
198 if(!success){ trashCode += 'l'; }
201 success = cullHomoP(currSeq);
202 if(!success){ trashCode += 'h'; }
205 success = cullAmbigs(currSeq);
206 if(!success){ trashCode += 'n'; }
209 if(flip){ currSeq.reverseComplement(); } // should go last
211 if(trashCode.length() == 0){
212 currSeq.printSequence(outFASTA);
213 if(barcodes.size() != 0){
214 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
217 currSeq.printSequence(*fastaFileNames[group]);
222 currSeq.setName(currSeq.getName() + '|' + trashCode);
223 currSeq.setUnaligned(origSeq);
224 currSeq.printSequence(scrapFASTA);
233 for(int i=0;i<fastaFileNames.size();i++){
234 fastaFileNames[i]->close();
235 delete fastaFileNames[i];
238 for(int i=0;i<fastaFileNames.size();i++){
240 openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
242 openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
244 while(!inFASTA.eof()){
245 if(inFASTA.get() == '>'){
247 outGroups << seqName << '\t' << groupVector[i] << endl;
249 while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
258 catch(exception& e) {
259 cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
263 cout << "An unknown error has occurred in the TrimSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
268 //***************************************************************************************************************
270 void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
273 openInputFile(oligoFile, inOligos);
277 string type, oligo, group;
280 while(!inOligos.eof()){
284 while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
289 for(int i=0;i<oligo.length();i++){
290 oligo[i] = toupper(oligo[i]);
291 if(oligo[i] == 'U') { oligo[i] = 'T'; }
294 if(type == "forward"){
295 forPrimer.push_back(oligo);
297 else if(type == "reverse"){
298 revPrimer.push_back(oligo);
300 else if(type == "barcode"){
302 barcodes[oligo]=index++;
303 groupVector.push_back(group);
306 outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
314 numFPrimers = forPrimer.size();
315 numRPrimers = revPrimer.size();
318 //***************************************************************************************************************
320 bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
322 string rawSequence = seq.getUnaligned();
323 bool success = 0; //guilty until proven innocent
325 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
326 string oligo = it->first;
327 if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
332 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
334 seq.setUnaligned(rawSequence.substr(oligo.length()));
343 //***************************************************************************************************************
345 bool TrimSeqsCommand::stripForward(Sequence& seq){
347 string rawSequence = seq.getUnaligned();
348 bool success = 0; //guilty until proven innocent
350 for(int i=0;i<numFPrimers;i++){
351 string oligo = forPrimer[i];
353 if(rawSequence.length() < oligo.length()){
358 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
359 seq.setUnaligned(rawSequence.substr(oligo.length()));
369 //***************************************************************************************************************
371 bool TrimSeqsCommand::stripReverse(Sequence& seq){
373 string rawSequence = seq.getUnaligned();
374 bool success = 0; //guilty until proven innocent
376 for(int i=0;i<numRPrimers;i++){
377 string oligo = revPrimer[i];
379 if(rawSequence.length() < oligo.length()){
384 if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
385 seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
394 //***************************************************************************************************************
396 bool TrimSeqsCommand::cullLength(Sequence& seq){
398 int length = seq.getNumBases();
399 bool success = 0; //guilty until proven innocent
401 if(length >= minLength && maxLength == 0) { success = 1; }
402 else if(length >= minLength && length <= maxLength) { success = 1; }
403 else { success = 0; }
409 //***************************************************************************************************************
411 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
413 int longHomoP = seq.getLongHomoPolymer();
414 bool success = 0; //guilty until proven innocent
416 if(longHomoP <= maxHomoP){ success = 1; }
417 else { success = 0; }
423 //***************************************************************************************************************
425 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
427 int numNs = seq.getAmbigBases();
428 bool success = 0; //guilty until proven innocent
430 if(numNs <= maxAmbig) { success = 1; }
431 else { success = 0; }
437 //***************************************************************************************************************
439 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
442 int length = oligo.length();
444 for(int i=0;i<length;i++){
446 if(oligo[i] != seq[i]){
447 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
448 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
449 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
450 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
451 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
452 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
453 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
454 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
455 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
456 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
457 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
458 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
460 if(success == 0) { break; }
470 //***************************************************************************************************************
472 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
474 string rawSequence = seq.getUnaligned();
475 int seqLength = rawSequence.length();
479 if(name.substr(1) != seq.getName()) { cout << "sequence name mismatch btwn fasta and qual file" << endl; }
480 while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
485 for(int i=0;i<seqLength;i++){
488 if(score <= qThreshold){
493 for(int i=end+1;i<seqLength;i++){
497 seq.setUnaligned(rawSequence.substr(0,end));
502 //***************************************************************************************************************
504 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
506 string rawSequence = seq.getUnaligned();
507 int seqLength = seq.getNumBases();
508 bool success = 0; //guilty until proven innocent
512 if(name.substr(1) != seq.getName()) { cout << "sequence name mismatch btwn fasta and qual file" << endl; }
513 while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
518 for(int i=0;i<seqLength;i++){
522 average /= seqLength;
524 if(average >= qAverage) { success = 1; }
525 else { success = 0; }
530 //***************************************************************************************************************