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;
610 QualityScores currQual;
612 currQual = QualityScores(qFile); m->gobble(qFile);
615 string origSeq = currSeq.getUnaligned();
618 int barcodeIndex = 0;
622 success = trimOligos.stripLinker(currSeq, currQual);
623 if(success > ldiffs) { trashCode += 'k'; }
624 else{ currentSeqsDiffs += success; }
628 if(barcodes.size() != 0){
629 success = trimOligos.stripBarcode(currSeq, currQual, barcodeIndex);
630 if(success > bdiffs) { trashCode += 'b'; }
631 else{ currentSeqsDiffs += success; }
634 if(rbarcodes.size() != 0){
635 success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
636 if(success > bdiffs) { trashCode += 'b'; }
637 else{ currentSeqsDiffs += success; }
641 success = trimOligos.stripSpacer(currSeq, currQual);
642 if(success > sdiffs) { trashCode += 's'; }
643 else{ currentSeqsDiffs += success; }
647 if(numFPrimers != 0){
648 success = trimOligos.stripForward(currSeq, currQual, primerIndex, keepforward);
649 if(success > pdiffs) { trashCode += 'f'; }
650 else{ currentSeqsDiffs += success; }
653 if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
655 if(numRPrimers != 0){
656 success = trimOligos.stripReverse(currSeq, currQual);
657 if(!success) { trashCode += 'r'; }
661 success = keepFirstTrim(currSeq, currQual);
665 success = removeLastTrim(currSeq, currQual);
666 if(!success) { trashCode += 'l'; }
671 int origLength = currSeq.getNumBases();
673 if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
674 else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
675 else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
676 else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
677 else { success = 1; }
679 //you don't want to trim, if it fails above then scrap it
680 if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
682 if(!success) { trashCode += 'q'; }
685 if(minLength > 0 || maxLength > 0){
686 success = cullLength(currSeq);
687 if(!success) { trashCode += 'l'; }
690 success = cullHomoP(currSeq);
691 if(!success) { trashCode += 'h'; }
694 success = cullAmbigs(currSeq);
695 if(!success) { trashCode += 'n'; }
698 if(flip){ // should go last
699 currSeq.reverseComplement();
701 currQual.flipQScores();
705 if(trashCode.length() == 0){
706 currSeq.setAligned(currSeq.getUnaligned());
707 currSeq.printSequence(trimFASTAFile);
710 currQual.printQScores(trimQualFile);
715 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
716 if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
717 else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
721 if(barcodes.size() != 0){
722 string thisGroup = barcodeNameVector[barcodeIndex];
723 if (primers.size() != 0) {
724 if (primerNameVector[primerIndex] != "") {
725 if(thisGroup != "") {
726 thisGroup += "." + primerNameVector[primerIndex];
728 thisGroup = primerNameVector[primerIndex];
733 outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
735 int numRedundants = 0;
736 if (nameFile != "") {
737 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
738 if (itName != nameMap.end()) {
739 vector<string> thisSeqsNames;
740 m->splitAtChar(itName->second, thisSeqsNames, ',');
741 numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
742 for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
743 outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
745 }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
748 map<string, int>::iterator it = groupCounts.find(thisGroup);
749 if (it == groupCounts.end()) { groupCounts[thisGroup] = 1 + numRedundants; }
750 else { groupCounts[it->first] += (1 + numRedundants); }
757 m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
758 currSeq.printSequence(output);
762 m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
763 currQual.printQScores(output);
768 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
769 if (itName != nameMap.end()) {
770 m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
771 output << itName->first << '\t' << itName->second << endl;
773 }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
778 if(nameFile != ""){ //needs to be before the currSeq name is changed
779 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
780 if (itName != nameMap.end()) { scrapNameFile << itName->first << '\t' << itName->second << endl; }
781 else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
783 currSeq.setName(currSeq.getName() + '|' + trashCode);
784 currSeq.setUnaligned(origSeq);
785 currSeq.setAligned(origSeq);
786 currSeq.printSequence(scrapFASTAFile);
788 currQual.printQScores(scrapQualFile);
794 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
795 unsigned long long pos = inFASTA.tellg();
796 if ((pos == -1) || (pos >= line.end)) { break; }
799 if (inFASTA.eof()) { break; }
803 if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
807 if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
811 trimFASTAFile.close();
812 scrapFASTAFile.close();
813 if (createGroup) { outGroupsFile.close(); }
814 if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
815 if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
819 catch(exception& e) {
820 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
825 /**************************************************************************************************/
827 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) {
834 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
835 //loop through and create all the processes you want
836 while (process != processors) {
840 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
844 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
845 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
846 vector<vector<string> > tempNameFileNames = nameFileNames;
851 for(int i=0;i<tempFASTAFileNames.size();i++){
852 for(int j=0;j<tempFASTAFileNames[i].size();j++){
853 if (tempFASTAFileNames[i][j] != "") {
854 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
855 m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
858 tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
859 m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
862 tempNameFileNames[i][j] += toString(getpid()) + ".temp";
863 m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
870 driverCreateTrim(filename,
872 (trimFASTAFileName + toString(getpid()) + ".temp"),
873 (scrapFASTAFileName + toString(getpid()) + ".temp"),
874 (trimQualFileName + toString(getpid()) + ".temp"),
875 (scrapQualFileName + toString(getpid()) + ".temp"),
876 (trimNameFileName + toString(getpid()) + ".temp"),
877 (scrapNameFileName + toString(getpid()) + ".temp"),
878 (groupFile + toString(getpid()) + ".temp"),
880 tempPrimerQualFileNames,
885 //pass groupCounts to parent
888 string tempFile = filename + toString(getpid()) + ".num.temp";
889 m->openOutputFile(tempFile, out);
891 out << groupCounts.size() << endl;
893 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
894 out << it->first << '\t' << it->second << endl;
900 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
901 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
908 m->openOutputFile(trimFASTAFileName, temp); temp.close();
909 m->openOutputFile(scrapFASTAFileName, temp); temp.close();
911 m->openOutputFile(trimQualFileName, temp); temp.close();
912 m->openOutputFile(scrapQualFileName, temp); temp.close();
914 if (nameFile != "") {
915 m->openOutputFile(trimNameFileName, temp); temp.close();
916 m->openOutputFile(scrapNameFileName, temp); temp.close();
919 driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
921 //force parent to wait until all the processes are done
922 for (int i=0;i<processIDS.size();i++) {
923 int temp = processIDS[i];
927 //////////////////////////////////////////////////////////////////////////////////////////////////////
928 //Windows version shared memory, so be careful when passing variables through the trimData struct.
929 //Above fork() will clone, so memory is separate, but that's not the case with windows,
930 //////////////////////////////////////////////////////////////////////////////////////////////////////
932 vector<trimData*> pDataArray;
933 DWORD dwThreadIdArray[processors-1];
934 HANDLE hThreadArray[processors-1];
936 //Create processor worker threads.
937 for( int i=0; i<processors-1; i++){
939 string extension = "";
940 if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
941 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
942 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
943 vector<vector<string> > tempNameFileNames = nameFileNames;
948 for(int i=0;i<tempFASTAFileNames.size();i++){
949 for(int j=0;j<tempFASTAFileNames[i].size();j++){
950 if (tempFASTAFileNames[i][j] != "") {
951 tempFASTAFileNames[i][j] += extension;
952 m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
955 tempPrimerQualFileNames[i][j] += extension;
956 m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
959 tempNameFileNames[i][j] += extension;
960 m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
968 trimData* tempTrim = new trimData(filename,
970 (trimFASTAFileName+extension),
971 (scrapFASTAFileName+extension),
972 (trimQualFileName+extension),
973 (scrapQualFileName+extension),
974 (trimNameFileName+extension),
975 (scrapNameFileName+extension),
976 (groupFile+extension),
978 tempPrimerQualFileNames,
980 lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
981 pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer,
982 primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
983 qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
984 minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap);
985 pDataArray.push_back(tempTrim);
987 hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
992 m->openOutputFile(trimFASTAFileName, temp); temp.close();
993 m->openOutputFile(scrapFASTAFileName, temp); temp.close();
995 m->openOutputFile(trimQualFileName, temp); temp.close();
996 m->openOutputFile(scrapQualFileName, temp); temp.close();
998 if (nameFile != "") {
999 m->openOutputFile(trimNameFileName, temp); temp.close();
1000 m->openOutputFile(scrapNameFileName, temp); temp.close();
1003 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]);
1004 processIDS.push_back(processors-1);
1007 //Wait until all threads have terminated.
1008 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1010 //Close all thread handles and free memory allocations.
1011 for(int i=0; i < pDataArray.size(); i++){
1012 for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
1013 map<string, int>::iterator it2 = groupCounts.find(it->first);
1014 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
1015 else { groupCounts[it->first] += it->second; }
1017 CloseHandle(hThreadArray[i]);
1018 delete pDataArray[i];
1025 for(int i=0;i<processIDS.size();i++){
1027 m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1029 m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
1030 m->mothurRemove((trimFASTAFileName + toString(processIDS[i]) + ".temp"));
1031 m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
1032 m->mothurRemove((scrapFASTAFileName + toString(processIDS[i]) + ".temp"));
1034 if(qFileName != ""){
1035 m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
1036 m->mothurRemove((trimQualFileName + toString(processIDS[i]) + ".temp"));
1037 m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
1038 m->mothurRemove((scrapQualFileName + toString(processIDS[i]) + ".temp"));
1042 m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
1043 m->mothurRemove((trimNameFileName + toString(processIDS[i]) + ".temp"));
1044 m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
1045 m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
1049 m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
1050 m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
1055 for(int j=0;j<fastaFileNames.size();j++){
1056 for(int k=0;k<fastaFileNames[j].size();k++){
1057 if (fastaFileNames[j][k] != "") {
1058 m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
1059 m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1061 if(qFileName != ""){
1062 m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
1063 m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1067 m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
1068 m->mothurRemove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1075 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1078 string tempFile = filename + toString(processIDS[i]) + ".num.temp";
1079 m->openInputFile(tempFile, in);
1083 in >> tempNum; m->gobble(in);
1087 in >> group >> tempNum; m->gobble(in);
1089 map<string, int>::iterator it = groupCounts.find(group);
1090 if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
1091 else { groupCounts[it->first] += tempNum; }
1094 in.close(); m->mothurRemove(tempFile);
1101 catch(exception& e) {
1102 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
1107 /**************************************************************************************************/
1109 int TrimSeqsCommand::setLines(string filename, string qfilename) {
1112 vector<unsigned long long> fastaFilePos;
1113 vector<unsigned long long> qfileFilePos;
1115 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1116 //set file positions for fasta file
1117 fastaFilePos = m->divideFile(filename, processors);
1119 //get name of first sequence in each chunk
1120 map<string, int> firstSeqNames;
1121 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1123 m->openInputFile(filename, in);
1124 in.seekg(fastaFilePos[i]);
1127 firstSeqNames[temp.getName()] = i;
1132 if(qfilename != "") {
1133 //seach for filePos of each first name in the qfile and save in qfileFilePos
1135 m->openInputFile(qfilename, inQual);
1138 while(!inQual.eof()){
1139 input = m->getline(inQual);
1141 if (input.length() != 0) {
1142 if(input[0] == '>'){ //this is a sequence name line
1143 istringstream nameStream(input);
1145 string sname = ""; nameStream >> sname;
1146 sname = sname.substr(1);
1148 map<string, int>::iterator it = firstSeqNames.find(sname);
1150 if(it != firstSeqNames.end()) { //this is the start of a new chunk
1151 unsigned long long pos = inQual.tellg();
1152 qfileFilePos.push_back(pos - input.length() - 1);
1153 firstSeqNames.erase(it);
1158 if (firstSeqNames.size() == 0) { break; }
1163 if (firstSeqNames.size() != 0) {
1164 for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
1165 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
1171 //get last file position of qfile
1173 unsigned long long size;
1175 //get num bytes in file
1176 pFile = fopen (qfilename.c_str(),"rb");
1177 if (pFile==NULL) perror ("Error opening file");
1179 fseek (pFile, 0, SEEK_END);
1184 qfileFilePos.push_back(size);
1187 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1188 lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
1189 if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)])); }
1191 if(qfilename == "") { qLines = lines; } //files with duds
1197 if (processors == 1) { //save time
1198 //fastaFilePos.push_back(0); qfileFilePos.push_back(0);
1199 //fastaFilePos.push_back(1000); qfileFilePos.push_back(1000);
1200 lines.push_back(linePair(0, 1000));
1201 if (qfilename != "") { qLines.push_back(linePair(0, 1000)); }
1203 int numFastaSeqs = 0;
1204 fastaFilePos = m->setFilePosFasta(filename, numFastaSeqs);
1205 if (fastaFilePos.size() < processors) { processors = fastaFilePos.size(); }
1207 if (qfilename != "") {
1208 int numQualSeqs = 0;
1209 qfileFilePos = m->setFilePosFasta(qfilename, numQualSeqs);
1211 if (numFastaSeqs != numQualSeqs) {
1212 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;
1216 //figure out how many sequences you have to process
1217 int numSeqsPerProcessor = numFastaSeqs / processors;
1218 for (int i = 0; i < processors; i++) {
1219 int startIndex = i * numSeqsPerProcessor;
1220 if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
1221 lines.push_back(linePair(fastaFilePos[startIndex], numSeqsPerProcessor));
1222 if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
1225 if(qfilename == "") { qLines = lines; } //files with duds
1230 catch(exception& e) {
1231 m->errorOut(e, "TrimSeqsCommand", "setLines");
1236 //***************************************************************************************************************
1238 bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
1241 m->openInputFile(oligoFile, inOligos);
1245 string type, oligo, group;
1247 int indexPrimer = 0;
1248 int indexBarcode = 0;
1250 while(!inOligos.eof()){
1255 while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
1256 m->gobble(inOligos);
1259 m->gobble(inOligos);
1260 //make type case insensitive
1261 for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
1265 for(int i=0;i<oligo.length();i++){
1266 oligo[i] = toupper(oligo[i]);
1267 if(oligo[i] == 'U') { oligo[i] = 'T'; }
1270 if(type == "FORWARD"){
1273 // get rest of line in case there is a primer name
1274 while (!inOligos.eof()) {
1275 char c = inOligos.get();
1276 if (c == 10 || c == 13){ break; }
1277 else if (c == 32 || c == 9){;} //space or tab
1278 else { group += c; }
1281 //check for repeat barcodes
1282 map<string, int>::iterator itPrime = primers.find(oligo);
1283 if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
1285 primers[oligo]=indexPrimer; indexPrimer++;
1286 primerNameVector.push_back(group);
1288 else if(type == "REVERSE"){
1289 //Sequence oligoRC("reverse", oligo);
1290 //oligoRC.reverseComplement();
1291 string oligoRC = reverseOligo(oligo);
1292 revPrimer.push_back(oligoRC);
1294 else if(type == "BARCODE"){
1297 //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
1298 //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
1300 while (!inOligos.eof()) {
1301 char c = inOligos.get();
1302 if (c == 10 || c == 13){ break; }
1303 else if (c == 32 || c == 9){;} //space or tab
1307 //then this is illumina data with 4 columns
1309 string reverseBarcode = reverseOligo(group); //reverse barcode
1312 //check for repeat barcodes
1313 map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
1314 if (itBar != rbarcodes.end()) { m->mothurOut("barcode " + reverseBarcode + " is in your oligos file already."); m->mothurOutEndLine(); }
1316 rbarcodes[reverseBarcode]=indexBarcode;
1319 //check for repeat barcodes
1320 map<string, int>::iterator itBar = barcodes.find(oligo);
1321 if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
1323 barcodes[oligo]=indexBarcode; indexBarcode++;
1324 barcodeNameVector.push_back(group);
1325 }else if(type == "LINKER"){
1326 linker.push_back(oligo);
1327 }else if(type == "SPACER"){
1328 spacer.push_back(oligo);
1330 else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
1332 m->gobble(inOligos);
1336 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
1338 //add in potential combos
1339 if(barcodeNameVector.size() == 0){
1341 barcodeNameVector.push_back("");
1344 if(primerNameVector.size() == 0){
1346 primerNameVector.push_back("");
1349 fastaFileNames.resize(barcodeNameVector.size());
1350 for(int i=0;i<fastaFileNames.size();i++){
1351 fastaFileNames[i].assign(primerNameVector.size(), "");
1353 if(qFileName != "") { qualFileNames = fastaFileNames; }
1354 if(nameFile != "") { nameFileNames = fastaFileNames; }
1357 set<string> uniqueNames; //used to cleanup outputFileNames
1358 for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1359 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1361 string primerName = primerNameVector[itPrimer->second];
1362 string barcodeName = barcodeNameVector[itBar->second];
1364 string comboGroupName = "";
1365 string fastaFileName = "";
1366 string qualFileName = "";
1367 string nameFileName = "";
1369 if(primerName == ""){
1370 comboGroupName = barcodeNameVector[itBar->second];
1373 if(barcodeName == ""){
1374 comboGroupName = primerNameVector[itPrimer->second];
1377 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
1383 fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
1384 if (uniqueNames.count(fastaFileName) == 0) {
1385 outputNames.push_back(fastaFileName);
1386 outputTypes["fasta"].push_back(fastaFileName);
1387 uniqueNames.insert(fastaFileName);
1390 fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
1391 m->openOutputFile(fastaFileName, temp); temp.close();
1393 if(qFileName != ""){
1394 qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
1395 if (uniqueNames.count(qualFileName) == 0) {
1396 outputNames.push_back(qualFileName);
1397 outputTypes["qfile"].push_back(qualFileName);
1400 qualFileNames[itBar->second][itPrimer->second] = qualFileName;
1401 m->openOutputFile(qualFileName, temp); temp.close();
1405 nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
1406 if (uniqueNames.count(nameFileName) == 0) {
1407 outputNames.push_back(nameFileName);
1408 outputTypes["name"].push_back(nameFileName);
1411 nameFileNames[itBar->second][itPrimer->second] = nameFileName;
1412 m->openOutputFile(nameFileName, temp); temp.close();
1418 numFPrimers = primers.size();
1419 numRPrimers = revPrimer.size();
1420 numLinkers = linker.size();
1421 numSpacers = spacer.size();
1423 bool allBlank = true;
1424 for (int i = 0; i < barcodeNameVector.size(); i++) {
1425 if (barcodeNameVector[i] != "") {
1430 for (int i = 0; i < primerNameVector.size(); i++) {
1431 if (primerNameVector[i] != "") {
1438 m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
1446 catch(exception& e) {
1447 m->errorOut(e, "TrimSeqsCommand", "getOligos");
1451 //***************************************************************************************************************
1453 bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
1456 if(qscores.getName() != ""){
1457 qscores.trimQScores(-1, keepFirst);
1459 sequence.trim(keepFirst);
1462 catch(exception& e) {
1463 m->errorOut(e, "keepFirstTrim", "countDiffs");
1469 //***************************************************************************************************************
1471 bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
1475 int length = sequence.getNumBases() - removeLast;
1478 if(qscores.getName() != ""){
1479 qscores.trimQScores(-1, length);
1481 sequence.trim(length);
1490 catch(exception& e) {
1491 m->errorOut(e, "removeLastTrim", "countDiffs");
1497 //***************************************************************************************************************
1499 bool TrimSeqsCommand::cullLength(Sequence& seq){
1502 int length = seq.getNumBases();
1503 bool success = 0; //guilty until proven innocent
1505 if(length >= minLength && maxLength == 0) { success = 1; }
1506 else if(length >= minLength && length <= maxLength) { success = 1; }
1507 else { success = 0; }
1512 catch(exception& e) {
1513 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1519 //***************************************************************************************************************
1521 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1523 int longHomoP = seq.getLongHomoPolymer();
1524 bool success = 0; //guilty until proven innocent
1526 if(longHomoP <= maxHomoP){ success = 1; }
1527 else { success = 0; }
1531 catch(exception& e) {
1532 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1537 //********************************************************************/
1538 string TrimSeqsCommand::reverseOligo(string oligo){
1540 string reverse = "";
1542 for(int i=oligo.length()-1;i>=0;i--){
1544 if(oligo[i] == 'A') { reverse += 'T'; }
1545 else if(oligo[i] == 'T'){ reverse += 'A'; }
1546 else if(oligo[i] == 'U'){ reverse += 'A'; }
1548 else if(oligo[i] == 'G'){ reverse += 'C'; }
1549 else if(oligo[i] == 'C'){ reverse += 'G'; }
1551 else if(oligo[i] == 'R'){ reverse += 'Y'; }
1552 else if(oligo[i] == 'Y'){ reverse += 'R'; }
1554 else if(oligo[i] == 'M'){ reverse += 'K'; }
1555 else if(oligo[i] == 'K'){ reverse += 'M'; }
1557 else if(oligo[i] == 'W'){ reverse += 'W'; }
1558 else if(oligo[i] == 'S'){ reverse += 'S'; }
1560 else if(oligo[i] == 'B'){ reverse += 'V'; }
1561 else if(oligo[i] == 'V'){ reverse += 'B'; }
1563 else if(oligo[i] == 'D'){ reverse += 'H'; }
1564 else if(oligo[i] == 'H'){ reverse += 'D'; }
1566 else { reverse += 'N'; }
1572 catch(exception& e) {
1573 m->errorOut(e, "TrimSeqsCommand", "reverseOligo");
1578 //***************************************************************************************************************
1580 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1582 int numNs = seq.getAmbigBases();
1583 bool success = 0; //guilty until proven innocent
1585 if(numNs <= maxAmbig) { success = 1; }
1586 else { success = 0; }
1590 catch(exception& e) {
1591 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1596 //***************************************************************************************************************