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"
12 #include "trimoligos.h"
14 //**********************************************************************************************************************
15 vector<string> TrimSeqsCommand::setParameters(){
17 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
18 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
19 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
20 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
21 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
22 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
23 CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxhomop);
24 CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
25 CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
26 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
27 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
28 CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
29 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
30 CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
31 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
32 CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
33 CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepforward);
34 CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqtrim);
35 CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqthreshold);
36 CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqaverage);
37 CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(prollaverage);
38 CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqwindowaverage);
39 CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "",false,false); parameters.push_back(pqstepsize);
40 CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "",false,false); parameters.push_back(pqwindowsize);
41 CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
42 CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
43 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
44 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
46 vector<string> myArray;
47 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
51 m->errorOut(e, "TrimSeqsCommand", "setParameters");
55 //**********************************************************************************************************************
56 string TrimSeqsCommand::getHelpString(){
58 string helpString = "";
59 helpString += "The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n";
60 helpString += "The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n";
61 helpString += "The trim.seqs command parameters are fasta, name, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
62 helpString += "The fasta parameter is required.\n";
63 helpString += "The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n";
64 helpString += "The oligos parameter allows you to provide an oligos file.\n";
65 helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
66 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
67 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
68 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
69 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
70 helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
71 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
72 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
73 helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
74 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
75 helpString += "The qfile parameter allows you to provide a quality file.\n";
76 helpString += "The qthreshold parameter allows you to set a minimum quality score allowed. \n";
77 helpString += "The qaverage parameter allows you to set a minimum average quality score allowed. \n";
78 helpString += "The qwindowsize parameter allows you to set a number of bases in a window. Default=50.\n";
79 helpString += "The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. \n";
80 helpString += "The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n";
81 helpString += "The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n";
82 helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
83 helpString += "The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.\n";
84 helpString += "The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n";
85 helpString += "The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n";
86 helpString += "The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n";
87 helpString += "The trim.seqs command should be in the following format: \n";
88 helpString += "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n";
89 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n";
90 helpString += "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
91 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
92 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n";
96 m->errorOut(e, "TrimSeqsCommand", "getHelpString");
100 //**********************************************************************************************************************
101 string TrimSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
103 string outputFileName = "";
104 map<string, vector<string> >::iterator it;
106 //is this a type this command creates
107 it = outputTypes.find(type);
108 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
110 if (type == "qfile") { outputFileName = "qual"; }
111 else if (type == "fasta") { outputFileName = "fasta"; }
112 else if (type == "group") { outputFileName = "groups"; }
113 else if (type == "name") { outputFileName = "names"; }
114 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
116 return outputFileName;
118 catch(exception& e) {
119 m->errorOut(e, "TrimSeqsCommand", "getOutputFileNameTag");
125 //**********************************************************************************************************************
127 TrimSeqsCommand::TrimSeqsCommand(){
129 abort = true; calledHelp = true;
131 vector<string> tempOutNames;
132 outputTypes["fasta"] = tempOutNames;
133 outputTypes["qfile"] = tempOutNames;
134 outputTypes["group"] = tempOutNames;
135 outputTypes["name"] = tempOutNames;
137 catch(exception& e) {
138 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
142 //***************************************************************************************************************
144 TrimSeqsCommand::TrimSeqsCommand(string option) {
147 abort = false; calledHelp = false;
150 //allow user to run help
151 if(option == "help") { help(); abort = true; calledHelp = true; }
152 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
155 vector<string> myArray = setParameters();
157 OptionParser parser(option);
158 map<string,string> parameters = parser.getParameters();
160 ValidParameters validParameter;
161 map<string,string>::iterator it;
163 //check to make sure all parameters are valid for command
164 for (it = parameters.begin(); it != parameters.end(); it++) {
165 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
168 //initialize outputTypes
169 vector<string> tempOutNames;
170 outputTypes["fasta"] = tempOutNames;
171 outputTypes["qfile"] = tempOutNames;
172 outputTypes["group"] = tempOutNames;
173 outputTypes["name"] = tempOutNames;
175 //if the user changes the input directory command factory will send this info to us in the output parameter
176 string inputDir = validParameter.validFile(parameters, "inputdir", false);
177 if (inputDir == "not found"){ inputDir = ""; }
180 it = parameters.find("fasta");
181 //user has given a template file
182 if(it != parameters.end()){
183 path = m->hasPath(it->second);
184 //if the user has not given a path then, add inputdir. else leave path alone.
185 if (path == "") { parameters["fasta"] = inputDir + it->second; }
188 it = parameters.find("oligos");
189 //user has given a template file
190 if(it != parameters.end()){
191 path = m->hasPath(it->second);
192 //if the user has not given a path then, add inputdir. else leave path alone.
193 if (path == "") { parameters["oligos"] = inputDir + it->second; }
196 it = parameters.find("qfile");
197 //user has given a template file
198 if(it != parameters.end()){
199 path = m->hasPath(it->second);
200 //if the user has not given a path then, add inputdir. else leave path alone.
201 if (path == "") { parameters["qfile"] = inputDir + it->second; }
204 it = parameters.find("name");
205 //user has given a template file
206 if(it != parameters.end()){
207 path = m->hasPath(it->second);
208 //if the user has not given a path then, add inputdir. else leave path alone.
209 if (path == "") { parameters["name"] = inputDir + it->second; }
215 //check for required parameters
216 fastaFile = validParameter.validFile(parameters, "fasta", true);
217 if (fastaFile == "not found") {
218 fastaFile = m->getFastaFile();
219 if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
220 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
221 }else if (fastaFile == "not open") { abort = true; }
222 else { m->setFastaFile(fastaFile); }
224 //if the user changes the output directory command factory will send this info to us in the output parameter
225 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
227 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
231 //check for optional parameter and set defaults
232 // ...at some point should added some additional type checking...
234 temp = validParameter.validFile(parameters, "flip", false);
235 if (temp == "not found") { flip = 0; }
236 else { flip = m->isTrue(temp); }
238 temp = validParameter.validFile(parameters, "oligos", true);
239 if (temp == "not found"){ oligoFile = ""; }
240 else if(temp == "not open"){ abort = true; }
241 else { oligoFile = temp; m->setOligosFile(oligoFile); }
244 temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
245 m->mothurConvert(temp, maxAmbig);
247 temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
248 m->mothurConvert(temp, maxHomoP);
250 temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
251 m->mothurConvert(temp, minLength);
253 temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
254 m->mothurConvert(temp, maxLength);
256 temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
257 m->mothurConvert(temp, bdiffs);
259 temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
260 m->mothurConvert(temp, pdiffs);
262 temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
263 m->mothurConvert(temp, ldiffs);
265 temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
266 m->mothurConvert(temp, sdiffs);
268 temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
269 m->mothurConvert(temp, tdiffs);
271 if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
273 temp = validParameter.validFile(parameters, "qfile", true);
274 if (temp == "not found") { qFileName = ""; }
275 else if(temp == "not open") { abort = true; }
276 else { qFileName = temp; m->setQualFile(qFileName); }
278 temp = validParameter.validFile(parameters, "name", true);
279 if (temp == "not found") { nameFile = ""; }
280 else if(temp == "not open") { nameFile = ""; abort = true; }
281 else { nameFile = temp; m->setNameFile(nameFile); }
283 temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
284 m->mothurConvert(temp, qThreshold);
286 temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "t"; }
287 qtrim = m->isTrue(temp);
289 temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
290 convert(temp, qRollAverage);
292 temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
293 convert(temp, qWindowAverage);
295 temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "50"; }
296 convert(temp, qWindowSize);
298 temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "1"; }
299 convert(temp, qWindowStep);
301 temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
302 convert(temp, qAverage);
304 temp = validParameter.validFile(parameters, "keepfirst", false); if (temp == "not found") { temp = "0"; }
305 convert(temp, keepFirst);
307 temp = validParameter.validFile(parameters, "removelast", false); if (temp == "not found") { temp = "0"; }
308 convert(temp, removeLast);
310 temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
311 allFiles = m->isTrue(temp);
313 temp = validParameter.validFile(parameters, "keepforward", false); if (temp == "not found") { temp = "F"; }
314 keepforward = m->isTrue(temp);
316 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
317 m->setProcessors(temp);
318 m->mothurConvert(temp, processors);
321 if(allFiles && (oligoFile == "")){
322 m->mothurOut("You selected allfiles, but didn't enter an oligos. Ignoring the allfiles request."); m->mothurOutEndLine();
324 if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
325 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
329 if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
330 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
334 if (nameFile == "") {
335 vector<string> files; files.push_back(fastaFile);
336 parser.getNameFile(files);
341 catch(exception& e) {
342 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
346 //***************************************************************************************************************
348 int TrimSeqsCommand::execute(){
351 if (abort == true) { if (calledHelp) { return 0; } return 2; }
353 numFPrimers = 0; //this needs to be initialized
358 vector<vector<string> > fastaFileNames;
359 vector<vector<string> > qualFileNames;
360 vector<vector<string> > nameFileNames;
362 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("fasta");
363 outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
365 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("fasta");
366 outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
368 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("qfile");
369 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("qfile");
371 if (qFileName != "") {
372 outputNames.push_back(trimQualFile);
373 outputNames.push_back(scrapQualFile);
374 outputTypes["qfile"].push_back(trimQualFile);
375 outputTypes["qfile"].push_back(scrapQualFile);
378 string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim." + getOutputFileNameTag("name");
379 string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap." + getOutputFileNameTag("name");
381 if (nameFile != "") {
382 m->readNames(nameFile, nameMap);
383 outputNames.push_back(trimNameFile);
384 outputNames.push_back(scrapNameFile);
385 outputTypes["name"].push_back(trimNameFile);
386 outputTypes["name"].push_back(scrapNameFile);
389 if (m->control_pressed) { return 0; }
391 string outputGroupFileName;
393 createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
395 outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");
396 outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
400 //fills lines and qlines
401 setLines(fastaFile, qFileName);
404 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
406 createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
410 if (m->control_pressed) { return 0; }
413 map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
414 map<string, string>::iterator it;
415 set<string> namesToRemove;
416 for(int i=0;i<fastaFileNames.size();i++){
417 for(int j=0;j<fastaFileNames[0].size();j++){
418 if (fastaFileNames[i][j] != "") {
419 if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
420 if(m->isBlank(fastaFileNames[i][j])){
421 m->mothurRemove(fastaFileNames[i][j]);
422 namesToRemove.insert(fastaFileNames[i][j]);
425 m->mothurRemove(qualFileNames[i][j]);
426 namesToRemove.insert(qualFileNames[i][j]);
430 m->mothurRemove(nameFileNames[i][j]);
431 namesToRemove.insert(nameFileNames[i][j]);
434 it = uniqueFastaNames.find(fastaFileNames[i][j]);
435 if (it == uniqueFastaNames.end()) {
436 uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
444 //remove names for outputFileNames, just cleans up the output
445 vector<string> outputNames2;
446 for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
447 outputNames = outputNames2;
449 for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
451 m->openInputFile(it->first, in);
454 string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + getOutputFileNameTag("group");
455 outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
456 m->openOutputFile(thisGroupName, out);
459 if (m->control_pressed) { break; }
461 Sequence currSeq(in); m->gobble(in);
462 out << currSeq.getName() << '\t' << it->second << endl;
464 if (nameFile != "") {
465 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
466 if (itName != nameMap.end()) {
467 vector<string> thisSeqsNames;
468 m->splitAtChar(itName->second, thisSeqsNames, ',');
469 for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
470 out << thisSeqsNames[k] << '\t' << it->second << endl;
472 }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
480 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
482 //output group counts
483 m->mothurOutEndLine();
485 if (groupCounts.size() != 0) { m->mothurOut("Group count: \n"); }
486 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
487 total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
489 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
491 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
493 //set fasta file as new current fastafile
495 itTypes = outputTypes.find("fasta");
496 if (itTypes != outputTypes.end()) {
497 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
500 itTypes = outputTypes.find("name");
501 if (itTypes != outputTypes.end()) {
502 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
505 itTypes = outputTypes.find("qfile");
506 if (itTypes != outputTypes.end()) {
507 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
510 itTypes = outputTypes.find("group");
511 if (itTypes != outputTypes.end()) {
512 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
515 m->mothurOutEndLine();
516 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
517 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
518 m->mothurOutEndLine();
523 catch(exception& e) {
524 m->errorOut(e, "TrimSeqsCommand", "execute");
529 /**************************************************************************************/
531 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline) {
535 ofstream trimFASTAFile;
536 m->openOutputFile(trimFileName, trimFASTAFile);
538 ofstream scrapFASTAFile;
539 m->openOutputFile(scrapFileName, scrapFASTAFile);
541 ofstream trimQualFile;
542 ofstream scrapQualFile;
544 m->openOutputFile(trimQFileName, trimQualFile);
545 m->openOutputFile(scrapQFileName, scrapQualFile);
548 ofstream trimNameFile;
549 ofstream scrapNameFile;
551 m->openOutputFile(trimNFileName, trimNameFile);
552 m->openOutputFile(scrapNFileName, scrapNameFile);
556 ofstream outGroupsFile;
557 if (createGroup){ m->openOutputFile(groupFileName, outGroupsFile); }
559 for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
560 for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
561 if (fastaFileNames[i][j] != "") {
563 m->openOutputFile(fastaFileNames[i][j], temp); temp.close();
565 m->openOutputFile(qualFileNames[i][j], temp); temp.close();
569 m->openOutputFile(nameFileNames[i][j], temp); temp.close();
577 m->openInputFile(filename, inFASTA);
578 inFASTA.seekg(line.start);
581 if(qFileName != "") {
582 m->openInputFile(qFileName, qFile);
583 qFile.seekg(qline.start);
588 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer);
592 if (m->control_pressed) {
593 inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
594 if (createGroup) { outGroupsFile.close(); }
599 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
605 string trashCode = "";
606 int currentSeqsDiffs = 0;
608 Sequence currSeq(inFASTA); m->gobble(inFASTA);
609 //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
611 QualityScores currQual;
613 currQual = QualityScores(qFile); m->gobble(qFile);
614 //cout << currQual.getName() << endl;
617 string origSeq = currSeq.getUnaligned();
620 int barcodeIndex = 0;
624 success = trimOligos.stripLinker(currSeq, currQual);
625 if(success > ldiffs) { trashCode += 'k'; }
626 else{ currentSeqsDiffs += success; }
630 if(barcodes.size() != 0){
631 success = trimOligos.stripBarcode(currSeq, currQual, barcodeIndex);
632 if(success > bdiffs) { trashCode += 'b'; }
633 else{ currentSeqsDiffs += success; }
636 if(rbarcodes.size() != 0){
637 success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
638 if(success > bdiffs) { trashCode += 'b'; }
639 else{ currentSeqsDiffs += success; }
643 success = trimOligos.stripSpacer(currSeq, currQual);
644 if(success > sdiffs) { trashCode += 's'; }
645 else{ currentSeqsDiffs += success; }
649 if(numFPrimers != 0){
650 success = trimOligos.stripForward(currSeq, currQual, primerIndex, keepforward);
651 if(success > pdiffs) { trashCode += 'f'; }
652 else{ currentSeqsDiffs += success; }
655 if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
657 if(numRPrimers != 0){
658 success = trimOligos.stripReverse(currSeq, currQual);
659 if(!success) { trashCode += 'r'; }
663 success = keepFirstTrim(currSeq, currQual);
667 success = removeLastTrim(currSeq, currQual);
668 if(!success) { trashCode += 'l'; }
673 int origLength = currSeq.getNumBases();
675 if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
676 else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
677 else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
678 else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
679 else { success = 1; }
681 //you don't want to trim, if it fails above then scrap it
682 if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
684 if(!success) { trashCode += 'q'; }
687 if(minLength > 0 || maxLength > 0){
688 success = cullLength(currSeq);
689 if(!success) { trashCode += 'l'; }
692 success = cullHomoP(currSeq);
693 if(!success) { trashCode += 'h'; }
696 success = cullAmbigs(currSeq);
697 if(!success) { trashCode += 'n'; }
700 if(flip){ // should go last
701 currSeq.reverseComplement();
703 currQual.flipQScores();
707 if(trashCode.length() == 0){
708 currSeq.setAligned(currSeq.getUnaligned());
709 currSeq.printSequence(trimFASTAFile);
712 currQual.printQScores(trimQualFile);
717 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
718 if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
719 else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
723 if(barcodes.size() != 0){
724 string thisGroup = barcodeNameVector[barcodeIndex];
725 if (primers.size() != 0) {
726 if (primerNameVector[primerIndex] != "") {
727 if(thisGroup != "") {
728 thisGroup += "." + primerNameVector[primerIndex];
730 thisGroup = primerNameVector[primerIndex];
735 outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
737 int numRedundants = 0;
738 if (nameFile != "") {
739 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
740 if (itName != nameMap.end()) {
741 vector<string> thisSeqsNames;
742 m->splitAtChar(itName->second, thisSeqsNames, ',');
743 numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
744 for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
745 outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
747 }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
750 map<string, int>::iterator it = groupCounts.find(thisGroup);
751 if (it == groupCounts.end()) { groupCounts[thisGroup] = 1 + numRedundants; }
752 else { groupCounts[it->first] += (1 + numRedundants); }
759 m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
760 currSeq.printSequence(output);
764 m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
765 currQual.printQScores(output);
770 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
771 if (itName != nameMap.end()) {
772 m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
773 output << itName->first << '\t' << itName->second << endl;
775 }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
780 if(nameFile != ""){ //needs to be before the currSeq name is changed
781 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
782 if (itName != nameMap.end()) { scrapNameFile << itName->first << '\t' << itName->second << endl; }
783 else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
785 currSeq.setName(currSeq.getName() + '|' + trashCode);
786 currSeq.setUnaligned(origSeq);
787 currSeq.setAligned(origSeq);
788 currSeq.printSequence(scrapFASTAFile);
790 currQual.printQScores(scrapQualFile);
796 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
797 unsigned long long pos = inFASTA.tellg();
798 if ((pos == -1) || (pos >= line.end)) { break; }
801 if (inFASTA.eof()) { break; }
805 if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
809 if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
813 trimFASTAFile.close();
814 scrapFASTAFile.close();
815 if (createGroup) { outGroupsFile.close(); }
816 if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
817 if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
821 catch(exception& e) {
822 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
827 /**************************************************************************************************/
829 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
836 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
837 //loop through and create all the processes you want
838 while (process != processors) {
842 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
846 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
847 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
848 vector<vector<string> > tempNameFileNames = nameFileNames;
853 for(int i=0;i<tempFASTAFileNames.size();i++){
854 for(int j=0;j<tempFASTAFileNames[i].size();j++){
855 if (tempFASTAFileNames[i][j] != "") {
856 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
857 m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
860 tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
861 m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
864 tempNameFileNames[i][j] += toString(getpid()) + ".temp";
865 m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
872 driverCreateTrim(filename,
874 (trimFASTAFileName + toString(getpid()) + ".temp"),
875 (scrapFASTAFileName + toString(getpid()) + ".temp"),
876 (trimQualFileName + toString(getpid()) + ".temp"),
877 (scrapQualFileName + toString(getpid()) + ".temp"),
878 (trimNameFileName + toString(getpid()) + ".temp"),
879 (scrapNameFileName + toString(getpid()) + ".temp"),
880 (groupFile + toString(getpid()) + ".temp"),
882 tempPrimerQualFileNames,
887 if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
889 //pass groupCounts to parent
892 string tempFile = filename + toString(getpid()) + ".num.temp";
893 m->openOutputFile(tempFile, out);
895 out << groupCounts.size() << endl;
897 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
898 out << it->first << '\t' << it->second << endl;
904 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
905 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
912 m->openOutputFile(trimFASTAFileName, temp); temp.close();
913 m->openOutputFile(scrapFASTAFileName, temp); temp.close();
915 m->openOutputFile(trimQualFileName, temp); temp.close();
916 m->openOutputFile(scrapQualFileName, temp); temp.close();
918 if (nameFile != "") {
919 m->openOutputFile(trimNameFileName, temp); temp.close();
920 m->openOutputFile(scrapNameFileName, temp); temp.close();
923 driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
925 //force parent to wait until all the processes are done
926 for (int i=0;i<processIDS.size();i++) {
927 int temp = processIDS[i];
931 //////////////////////////////////////////////////////////////////////////////////////////////////////
932 //Windows version shared memory, so be careful when passing variables through the trimData struct.
933 //Above fork() will clone, so memory is separate, but that's not the case with windows,
934 //////////////////////////////////////////////////////////////////////////////////////////////////////
936 vector<trimData*> pDataArray;
937 DWORD dwThreadIdArray[processors-1];
938 HANDLE hThreadArray[processors-1];
940 //Create processor worker threads.
941 for( int i=0; i<processors-1; i++){
943 string extension = "";
944 if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
945 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
946 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
947 vector<vector<string> > tempNameFileNames = nameFileNames;
952 for(int i=0;i<tempFASTAFileNames.size();i++){
953 for(int j=0;j<tempFASTAFileNames[i].size();j++){
954 if (tempFASTAFileNames[i][j] != "") {
955 tempFASTAFileNames[i][j] += extension;
956 m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
959 tempPrimerQualFileNames[i][j] += extension;
960 m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
963 tempNameFileNames[i][j] += extension;
964 m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
972 trimData* tempTrim = new trimData(filename,
974 (trimFASTAFileName+extension),
975 (scrapFASTAFileName+extension),
976 (trimQualFileName+extension),
977 (scrapQualFileName+extension),
978 (trimNameFileName+extension),
979 (scrapNameFileName+extension),
980 (groupFile+extension),
982 tempPrimerQualFileNames,
984 lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
985 pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer,
986 primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
987 qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
988 minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap);
989 pDataArray.push_back(tempTrim);
991 hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
996 m->openOutputFile(trimFASTAFileName, temp); temp.close();
997 m->openOutputFile(scrapFASTAFileName, temp); temp.close();
999 m->openOutputFile(trimQualFileName, temp); temp.close();
1000 m->openOutputFile(scrapQualFileName, temp); temp.close();
1002 if (nameFile != "") {
1003 m->openOutputFile(trimNameFileName, temp); temp.close();
1004 m->openOutputFile(scrapNameFileName, temp); temp.close();
1007 driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
1008 processIDS.push_back(processors-1);
1011 //Wait until all threads have terminated.
1012 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1014 //Close all thread handles and free memory allocations.
1015 for(int i=0; i < pDataArray.size(); i++){
1016 for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
1017 map<string, int>::iterator it2 = groupCounts.find(it->first);
1018 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
1019 else { groupCounts[it->first] += it->second; }
1021 CloseHandle(hThreadArray[i]);
1022 delete pDataArray[i];
1029 for(int i=0;i<processIDS.size();i++){
1031 m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1033 m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
1034 m->mothurRemove((trimFASTAFileName + toString(processIDS[i]) + ".temp"));
1035 m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
1036 m->mothurRemove((scrapFASTAFileName + toString(processIDS[i]) + ".temp"));
1038 if(qFileName != ""){
1039 m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
1040 m->mothurRemove((trimQualFileName + toString(processIDS[i]) + ".temp"));
1041 m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
1042 m->mothurRemove((scrapQualFileName + toString(processIDS[i]) + ".temp"));
1046 m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
1047 m->mothurRemove((trimNameFileName + toString(processIDS[i]) + ".temp"));
1048 m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
1049 m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
1053 m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
1054 m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
1059 for(int j=0;j<fastaFileNames.size();j++){
1060 for(int k=0;k<fastaFileNames[j].size();k++){
1061 if (fastaFileNames[j][k] != "") {
1062 m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
1063 m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1065 if(qFileName != ""){
1066 m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
1067 m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1071 m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
1072 m->mothurRemove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1079 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1082 string tempFile = filename + toString(processIDS[i]) + ".num.temp";
1083 m->openInputFile(tempFile, in);
1087 in >> tempNum; m->gobble(in);
1091 in >> group >> tempNum; m->gobble(in);
1093 map<string, int>::iterator it = groupCounts.find(group);
1094 if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
1095 else { groupCounts[it->first] += tempNum; }
1098 in.close(); m->mothurRemove(tempFile);
1105 catch(exception& e) {
1106 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
1111 /**************************************************************************************************/
1113 int TrimSeqsCommand::setLines(string filename, string qfilename) {
1116 vector<unsigned long long> fastaFilePos;
1117 vector<unsigned long long> qfileFilePos;
1119 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1120 //set file positions for fasta file
1121 fastaFilePos = m->divideFile(filename, processors);
1123 //get name of first sequence in each chunk
1124 map<string, int> firstSeqNames;
1125 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1127 m->openInputFile(filename, in);
1128 in.seekg(fastaFilePos[i]);
1131 firstSeqNames[temp.getName()] = i;
1136 if(qfilename != "") {
1137 //seach for filePos of each first name in the qfile and save in qfileFilePos
1139 m->openInputFile(qfilename, inQual);
1142 while(!inQual.eof()){
1143 input = m->getline(inQual);
1145 if (input.length() != 0) {
1146 if(input[0] == '>'){ //this is a sequence name line
1147 istringstream nameStream(input);
1149 string sname = ""; nameStream >> sname;
1150 sname = sname.substr(1);
1152 map<string, int>::iterator it = firstSeqNames.find(sname);
1154 if(it != firstSeqNames.end()) { //this is the start of a new chunk
1155 unsigned long long pos = inQual.tellg();
1156 qfileFilePos.push_back(pos - input.length() - 1);
1157 firstSeqNames.erase(it);
1162 if (firstSeqNames.size() == 0) { break; }
1167 if (firstSeqNames.size() != 0) {
1168 for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
1169 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
1175 //get last file position of qfile
1177 unsigned long long size;
1179 //get num bytes in file
1180 pFile = fopen (qfilename.c_str(),"rb");
1181 if (pFile==NULL) perror ("Error opening file");
1183 fseek (pFile, 0, SEEK_END);
1188 qfileFilePos.push_back(size);
1191 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1192 if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); }
1193 lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
1194 if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)])); }
1196 if(qfilename == "") { qLines = lines; } //files with duds
1202 if (processors == 1) { //save time
1203 //fastaFilePos.push_back(0); qfileFilePos.push_back(0);
1204 //fastaFilePos.push_back(1000); qfileFilePos.push_back(1000);
1205 lines.push_back(linePair(0, 1000));
1206 if (qfilename != "") { qLines.push_back(linePair(0, 1000)); }
1208 int numFastaSeqs = 0;
1209 fastaFilePos = m->setFilePosFasta(filename, numFastaSeqs);
1210 if (fastaFilePos.size() < processors) { processors = fastaFilePos.size(); }
1212 if (qfilename != "") {
1213 int numQualSeqs = 0;
1214 qfileFilePos = m->setFilePosFasta(qfilename, numQualSeqs);
1216 if (numFastaSeqs != numQualSeqs) {
1217 m->mothurOut("[ERROR]: You have " + toString(numFastaSeqs) + " sequences in your fasta file, but " + toString(numQualSeqs) + " sequences in your quality file."); m->mothurOutEndLine(); m->control_pressed = true;
1221 //figure out how many sequences you have to process
1222 int numSeqsPerProcessor = numFastaSeqs / processors;
1223 for (int i = 0; i < processors; i++) {
1224 int startIndex = i * numSeqsPerProcessor;
1225 if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
1226 lines.push_back(linePair(fastaFilePos[startIndex], numSeqsPerProcessor));
1227 if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
1230 if(qfilename == "") { qLines = lines; } //files with duds
1235 catch(exception& e) {
1236 m->errorOut(e, "TrimSeqsCommand", "setLines");
1241 //***************************************************************************************************************
1243 bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
1246 m->openInputFile(oligoFile, inOligos);
1250 string type, oligo, group;
1252 int indexPrimer = 0;
1253 int indexBarcode = 0;
1255 while(!inOligos.eof()){
1259 if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1262 while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
1263 m->gobble(inOligos);
1266 m->gobble(inOligos);
1267 //make type case insensitive
1268 for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
1272 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
1274 for(int i=0;i<oligo.length();i++){
1275 oligo[i] = toupper(oligo[i]);
1276 if(oligo[i] == 'U') { oligo[i] = 'T'; }
1279 if(type == "FORWARD"){
1282 // get rest of line in case there is a primer name
1283 while (!inOligos.eof()) {
1284 char c = inOligos.get();
1285 if (c == 10 || c == 13){ break; }
1286 else if (c == 32 || c == 9){;} //space or tab
1287 else { group += c; }
1290 //check for repeat barcodes
1291 map<string, int>::iterator itPrime = primers.find(oligo);
1292 if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
1294 if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
1296 primers[oligo]=indexPrimer; indexPrimer++;
1297 primerNameVector.push_back(group);
1299 else if(type == "REVERSE"){
1300 //Sequence oligoRC("reverse", oligo);
1301 //oligoRC.reverseComplement();
1302 string oligoRC = reverseOligo(oligo);
1303 revPrimer.push_back(oligoRC);
1305 else if(type == "BARCODE"){
1308 //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
1309 //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
1311 while (!inOligos.eof()) {
1312 char c = inOligos.get();
1313 if (c == 10 || c == 13){ break; }
1314 else if (c == 32 || c == 9){;} //space or tab
1318 //then this is illumina data with 4 columns
1321 for(int i=0;i<group.length();i++){
1322 group[i] = toupper(group[i]);
1323 if(group[i] == 'U') { group[i] = 'T'; }
1326 if (m->debug) { m->mothurOut("[DEBUG]: reading reverse " + group + ", and group = " + temp + ".\n"); }
1328 string reverseBarcode = reverseOligo(group); //reverse barcode
1329 //check for repeat barcodes
1330 map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
1331 if (itBar != rbarcodes.end()) { m->mothurOut("reverse barcode " + group + " is in your oligos file already."); m->mothurOutEndLine(); }
1334 rbarcodes[reverseBarcode]=indexBarcode;
1335 }else { if (m->debug) { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); } }
1337 //check for repeat barcodes
1338 map<string, int>::iterator itBar = barcodes.find(oligo);
1339 if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
1341 barcodes[oligo]=indexBarcode; indexBarcode++;
1342 barcodeNameVector.push_back(group);
1343 }else if(type == "LINKER"){
1344 linker.push_back(oligo);
1345 }else if(type == "SPACER"){
1346 spacer.push_back(oligo);
1348 else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
1350 m->gobble(inOligos);
1354 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
1356 //add in potential combos
1357 if(barcodeNameVector.size() == 0){
1359 barcodeNameVector.push_back("");
1362 if(primerNameVector.size() == 0){
1364 primerNameVector.push_back("");
1367 fastaFileNames.resize(barcodeNameVector.size());
1368 for(int i=0;i<fastaFileNames.size();i++){
1369 fastaFileNames[i].assign(primerNameVector.size(), "");
1371 if(qFileName != "") { qualFileNames = fastaFileNames; }
1372 if(nameFile != "") { nameFileNames = fastaFileNames; }
1375 set<string> uniqueNames; //used to cleanup outputFileNames
1376 for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1377 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1379 string primerName = primerNameVector[itPrimer->second];
1380 string barcodeName = barcodeNameVector[itBar->second];
1382 string comboGroupName = "";
1383 string fastaFileName = "";
1384 string qualFileName = "";
1385 string nameFileName = "";
1387 if(primerName == ""){
1388 comboGroupName = barcodeNameVector[itBar->second];
1391 if(barcodeName == ""){
1392 comboGroupName = primerNameVector[itPrimer->second];
1395 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
1401 fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
1402 if (uniqueNames.count(fastaFileName) == 0) {
1403 outputNames.push_back(fastaFileName);
1404 outputTypes["fasta"].push_back(fastaFileName);
1405 uniqueNames.insert(fastaFileName);
1408 fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
1409 m->openOutputFile(fastaFileName, temp); temp.close();
1411 if(qFileName != ""){
1412 qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
1413 if (uniqueNames.count(qualFileName) == 0) {
1414 outputNames.push_back(qualFileName);
1415 outputTypes["qfile"].push_back(qualFileName);
1418 qualFileNames[itBar->second][itPrimer->second] = qualFileName;
1419 m->openOutputFile(qualFileName, temp); temp.close();
1423 nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
1424 if (uniqueNames.count(nameFileName) == 0) {
1425 outputNames.push_back(nameFileName);
1426 outputTypes["name"].push_back(nameFileName);
1429 nameFileNames[itBar->second][itPrimer->second] = nameFileName;
1430 m->openOutputFile(nameFileName, temp); temp.close();
1436 numFPrimers = primers.size();
1437 numRPrimers = revPrimer.size();
1438 numLinkers = linker.size();
1439 numSpacers = spacer.size();
1441 bool allBlank = true;
1442 for (int i = 0; i < barcodeNameVector.size(); i++) {
1443 if (barcodeNameVector[i] != "") {
1448 for (int i = 0; i < primerNameVector.size(); i++) {
1449 if (primerNameVector[i] != "") {
1456 m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
1464 catch(exception& e) {
1465 m->errorOut(e, "TrimSeqsCommand", "getOligos");
1469 //***************************************************************************************************************
1471 bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
1474 if(qscores.getName() != ""){
1475 qscores.trimQScores(-1, keepFirst);
1477 sequence.trim(keepFirst);
1480 catch(exception& e) {
1481 m->errorOut(e, "keepFirstTrim", "countDiffs");
1487 //***************************************************************************************************************
1489 bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
1493 int length = sequence.getNumBases() - removeLast;
1496 if(qscores.getName() != ""){
1497 qscores.trimQScores(-1, length);
1499 sequence.trim(length);
1508 catch(exception& e) {
1509 m->errorOut(e, "removeLastTrim", "countDiffs");
1515 //***************************************************************************************************************
1517 bool TrimSeqsCommand::cullLength(Sequence& seq){
1520 int length = seq.getNumBases();
1521 bool success = 0; //guilty until proven innocent
1523 if(length >= minLength && maxLength == 0) { success = 1; }
1524 else if(length >= minLength && length <= maxLength) { success = 1; }
1525 else { success = 0; }
1530 catch(exception& e) {
1531 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1537 //***************************************************************************************************************
1539 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1541 int longHomoP = seq.getLongHomoPolymer();
1542 bool success = 0; //guilty until proven innocent
1544 if(longHomoP <= maxHomoP){ success = 1; }
1545 else { success = 0; }
1549 catch(exception& e) {
1550 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1555 //********************************************************************/
1556 string TrimSeqsCommand::reverseOligo(string oligo){
1558 string reverse = "";
1560 for(int i=oligo.length()-1;i>=0;i--){
1562 if(oligo[i] == 'A') { reverse += 'T'; }
1563 else if(oligo[i] == 'T'){ reverse += 'A'; }
1564 else if(oligo[i] == 'U'){ reverse += 'A'; }
1566 else if(oligo[i] == 'G'){ reverse += 'C'; }
1567 else if(oligo[i] == 'C'){ reverse += 'G'; }
1569 else if(oligo[i] == 'R'){ reverse += 'Y'; }
1570 else if(oligo[i] == 'Y'){ reverse += 'R'; }
1572 else if(oligo[i] == 'M'){ reverse += 'K'; }
1573 else if(oligo[i] == 'K'){ reverse += 'M'; }
1575 else if(oligo[i] == 'W'){ reverse += 'W'; }
1576 else if(oligo[i] == 'S'){ reverse += 'S'; }
1578 else if(oligo[i] == 'B'){ reverse += 'V'; }
1579 else if(oligo[i] == 'V'){ reverse += 'B'; }
1581 else if(oligo[i] == 'D'){ reverse += 'H'; }
1582 else if(oligo[i] == 'H'){ reverse += 'D'; }
1584 else { reverse += 'N'; }
1590 catch(exception& e) {
1591 m->errorOut(e, "TrimSeqsCommand", "reverseOligo");
1596 //***************************************************************************************************************
1598 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1600 int numNs = seq.getAmbigBases();
1601 bool success = 0; //guilty until proven innocent
1603 if(numNs <= maxAmbig) { success = 1; }
1604 else { success = 0; }
1608 catch(exception& e) {
1609 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1614 //***************************************************************************************************************