2 * removelineagecommand.cpp
5 * Created by westcott on 9/24/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "removelineagecommand.h"
11 #include "sequence.hpp"
12 #include "listvector.hpp"
14 //**********************************************************************************************************************
15 vector<string> RemoveLineageCommand::setParameters(){
17 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
18 CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
19 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
20 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
21 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
22 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
23 CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
24 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
25 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
26 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
28 vector<string> myArray;
29 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
33 m->errorOut(e, "RemoveLineageCommand", "setParameters");
37 //**********************************************************************************************************************
38 string RemoveLineageCommand::getHelpString(){
40 string helpString = "";
41 helpString += "The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n";
42 helpString += "It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n";
43 helpString += "The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy unless you have a valid current taxonomy file.\n";
44 helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
45 helpString += "The taxon parameter allows you to select the taxons you would like to remove, and is required.\n";
46 helpString += "You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n";
47 helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
48 helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
49 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
50 helpString += "Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n";
51 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
52 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
56 m->errorOut(e, "RemoveLineageCommand", "getHelpString");
62 //**********************************************************************************************************************
63 RemoveLineageCommand::RemoveLineageCommand(){
65 abort = true; calledHelp = true;
67 vector<string> tempOutNames;
68 outputTypes["fasta"] = tempOutNames;
69 outputTypes["taxonomy"] = tempOutNames;
70 outputTypes["name"] = tempOutNames;
71 outputTypes["group"] = tempOutNames;
72 outputTypes["alignreport"] = tempOutNames;
73 outputTypes["list"] = tempOutNames;
76 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
80 //**********************************************************************************************************************
81 RemoveLineageCommand::RemoveLineageCommand(string option) {
83 abort = false; calledHelp = false;
85 //allow user to run help
86 if(option == "help") { help(); abort = true; calledHelp = true; }
89 //valid paramters for this command
90 string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
91 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
93 OptionParser parser(option);
94 map<string,string> parameters = parser.getParameters();
96 ValidParameters validParameter;
97 map<string,string>::iterator it;
99 //check to make sure all parameters are valid for command
100 for (it = parameters.begin(); it != parameters.end(); it++) {
101 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
104 //initialize outputTypes
105 vector<string> tempOutNames;
106 outputTypes["fasta"] = tempOutNames;
107 outputTypes["taxonomy"] = tempOutNames;
108 outputTypes["name"] = tempOutNames;
109 outputTypes["group"] = tempOutNames;
110 outputTypes["alignreport"] = tempOutNames;
111 outputTypes["list"] = tempOutNames;
113 //if the user changes the output directory command factory will send this info to us in the output parameter
114 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
116 //if the user changes the input directory command factory will send this info to us in the output parameter
117 string inputDir = validParameter.validFile(parameters, "inputdir", false);
118 if (inputDir == "not found"){ inputDir = ""; }
121 it = parameters.find("alignreport");
122 //user has given a template file
123 if(it != parameters.end()){
124 path = m->hasPath(it->second);
125 //if the user has not given a path then, add inputdir. else leave path alone.
126 if (path == "") { parameters["alignreport"] = inputDir + it->second; }
129 it = parameters.find("fasta");
130 //user has given a template file
131 if(it != parameters.end()){
132 path = m->hasPath(it->second);
133 //if the user has not given a path then, add inputdir. else leave path alone.
134 if (path == "") { parameters["fasta"] = inputDir + it->second; }
137 it = parameters.find("list");
138 //user has given a template file
139 if(it != parameters.end()){
140 path = m->hasPath(it->second);
141 //if the user has not given a path then, add inputdir. else leave path alone.
142 if (path == "") { parameters["list"] = inputDir + it->second; }
145 it = parameters.find("name");
146 //user has given a template file
147 if(it != parameters.end()){
148 path = m->hasPath(it->second);
149 //if the user has not given a path then, add inputdir. else leave path alone.
150 if (path == "") { parameters["name"] = inputDir + it->second; }
153 it = parameters.find("group");
154 //user has given a template file
155 if(it != parameters.end()){
156 path = m->hasPath(it->second);
157 //if the user has not given a path then, add inputdir. else leave path alone.
158 if (path == "") { parameters["group"] = inputDir + it->second; }
161 it = parameters.find("taxonomy");
162 //user has given a template file
163 if(it != parameters.end()){
164 path = m->hasPath(it->second);
165 //if the user has not given a path then, add inputdir. else leave path alone.
166 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
171 //check for required parameters
172 fastafile = validParameter.validFile(parameters, "fasta", true);
173 if (fastafile == "not open") { abort = true; }
174 else if (fastafile == "not found") { fastafile = ""; }
176 namefile = validParameter.validFile(parameters, "name", true);
177 if (namefile == "not open") { abort = true; }
178 else if (namefile == "not found") { namefile = ""; }
180 groupfile = validParameter.validFile(parameters, "group", true);
181 if (groupfile == "not open") { abort = true; }
182 else if (groupfile == "not found") { groupfile = ""; }
184 alignfile = validParameter.validFile(parameters, "alignreport", true);
185 if (alignfile == "not open") { abort = true; }
186 else if (alignfile == "not found") { alignfile = ""; }
188 listfile = validParameter.validFile(parameters, "list", true);
189 if (listfile == "not open") { abort = true; }
190 else if (listfile == "not found") { listfile = ""; }
192 taxfile = validParameter.validFile(parameters, "taxonomy", true);
193 if (taxfile == "not open") { abort = true; }
194 else if (taxfile == "not found") {
195 taxfile = m->getTaxonomyFile();
196 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
197 else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
200 string usedDups = "true";
201 string temp = validParameter.validFile(parameters, "dups", false);
202 if (temp == "not found") {
203 if (namefile != "") { temp = "true"; }
204 else { temp = "false"; usedDups = ""; }
206 dups = m->isTrue(temp);
208 taxons = validParameter.validFile(parameters, "taxon", false);
209 if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
212 if (taxons[0] == '\'') { taxons = taxons.substr(1); }
213 if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
217 if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
219 if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
224 catch(exception& e) {
225 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
229 //**********************************************************************************************************************
231 int RemoveLineageCommand::execute(){
234 if (abort == true) { if (calledHelp) { return 0; } return 2; }
236 if (m->control_pressed) { return 0; }
238 //read through the correct file and output lines you want to keep
239 if (taxfile != "") { readTax(); } //fills the set of names to remove
240 if (namefile != "") { readName(); }
241 if (fastafile != "") { readFasta(); }
242 if (groupfile != "") { readGroup(); }
243 if (alignfile != "") { readAlign(); }
244 if (listfile != "") { readList(); }
247 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
249 if (outputNames.size() != 0) {
250 m->mothurOutEndLine();
251 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
252 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
253 m->mothurOutEndLine();
255 //set fasta file as new current fastafile
257 itTypes = outputTypes.find("fasta");
258 if (itTypes != outputTypes.end()) {
259 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
262 itTypes = outputTypes.find("name");
263 if (itTypes != outputTypes.end()) {
264 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
267 itTypes = outputTypes.find("group");
268 if (itTypes != outputTypes.end()) {
269 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
272 itTypes = outputTypes.find("list");
273 if (itTypes != outputTypes.end()) {
274 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
277 itTypes = outputTypes.find("taxonomy");
278 if (itTypes != outputTypes.end()) {
279 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
286 catch(exception& e) {
287 m->errorOut(e, "RemoveLineageCommand", "execute");
292 //**********************************************************************************************************************
293 int RemoveLineageCommand::readFasta(){
295 string thisOutputDir = outputDir;
296 if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
297 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
300 m->openOutputFile(outputFileName, out);
303 m->openInputFile(fastafile, in);
306 bool wroteSomething = false;
309 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
311 Sequence currSeq(in);
312 name = currSeq.getName();
315 //if this name is in the accnos file
316 if (names.count(name) == 0) {
317 wroteSomething = true;
319 currSeq.printSequence(out);
327 if (wroteSomething == false) { m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
328 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
333 catch(exception& e) {
334 m->errorOut(e, "RemoveLineageCommand", "readFasta");
338 //**********************************************************************************************************************
339 int RemoveLineageCommand::readList(){
341 string thisOutputDir = outputDir;
342 if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
343 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
346 m->openOutputFile(outputFileName, out);
349 m->openInputFile(listfile, in);
351 bool wroteSomething = false;
354 //read in list vector
357 //make a new list vector
359 newList.setLabel(list.getLabel());
362 for (int i = 0; i < list.getNumBins(); i++) {
363 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
365 //parse out names that are in accnos file
366 string binnames = list.get(i);
368 string newNames = "";
369 while (binnames.find_first_of(',') != -1) {
370 string name = binnames.substr(0,binnames.find_first_of(','));
371 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
373 //if that name is in the .accnos file, add it
374 if (names.count(name) == 0) { newNames += name + ","; }
378 if (names.count(binnames) == 0) { newNames += binnames + ","; }
380 //if there are names in this bin add to new list
381 if (newNames != "") {
382 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
383 newList.push_back(newNames);
387 //print new listvector
388 if (newList.getNumBins() != 0) {
389 wroteSomething = true;
398 if (wroteSomething == false) { m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
399 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
404 catch(exception& e) {
405 m->errorOut(e, "RemoveLineageCommand", "readList");
409 //**********************************************************************************************************************
410 int RemoveLineageCommand::readName(){
412 string thisOutputDir = outputDir;
413 if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
414 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
417 m->openOutputFile(outputFileName, out);
420 m->openInputFile(namefile, in);
421 string name, firstCol, secondCol;
423 bool wroteSomething = false;
426 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
431 vector<string> parsedNames;
432 m->splitAtComma(secondCol, parsedNames);
434 vector<string> validSecond; validSecond.clear();
435 for (int i = 0; i < parsedNames.size(); i++) {
436 if (names.count(parsedNames[i]) == 0) {
437 validSecond.push_back(parsedNames[i]);
441 if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone
442 for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
444 //if the name in the first column is in the set then print it and any other names in second column also in set
445 if (names.count(firstCol) == 0) {
447 wroteSomething = true;
449 out << firstCol << '\t';
451 //you know you have at least one valid second since first column is valid
452 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
453 out << validSecond[validSecond.size()-1] << endl;
455 //make first name in set you come to first column and then add the remaining names to second column
458 //you want part of this row
459 if (validSecond.size() != 0) {
461 wroteSomething = true;
463 out << validSecond[0] << '\t';
465 //you know you have at least one valid second since first column is valid
466 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
467 out << validSecond[validSecond.size()-1] << endl;
476 if (wroteSomething == false) { m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
477 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
481 catch(exception& e) {
482 m->errorOut(e, "RemoveLineageCommand", "readName");
487 //**********************************************************************************************************************
488 int RemoveLineageCommand::readGroup(){
490 string thisOutputDir = outputDir;
491 if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
492 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
495 m->openOutputFile(outputFileName, out);
498 m->openInputFile(groupfile, in);
501 bool wroteSomething = false;
504 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
506 in >> name; //read from first column
507 in >> group; //read from second column
509 //if this name is in the accnos file
510 if (names.count(name) == 0) {
511 wroteSomething = true;
512 out << name << '\t' << group << endl;
520 if (wroteSomething == false) { m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
521 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
525 catch(exception& e) {
526 m->errorOut(e, "RemoveLineageCommand", "readGroup");
530 //**********************************************************************************************************************
531 int RemoveLineageCommand::readTax(){
533 string thisOutputDir = outputDir;
534 if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
535 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
537 m->openOutputFile(outputFileName, out);
540 m->openInputFile(taxfile, in);
543 bool wroteSomething = false;
545 bool taxonsHasConfidence = false;
546 vector< map<string, float> > searchTaxons;
547 string noConfidenceTaxons = taxons;
548 int hasConPos = taxons.find_first_of('(');
549 if (hasConPos != string::npos) {
550 taxonsHasConfidence = true;
551 searchTaxons = getTaxons(taxons);
552 noConfidenceTaxons = removeConfidences(taxons);
558 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
560 in >> name; //read from first column
561 in >> tax; //read from second column
565 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
566 if (!taxonsHasConfidence) {
568 int hasConfidences = tax.find_first_of('(');
569 if (hasConfidences != string::npos) {
570 newtax = removeConfidences(tax);
573 int pos = newtax.find(taxons);
575 if (pos == string::npos) {
576 wroteSomething = true;
577 out << name << '\t' << tax << endl;
578 }else{ //this sequence contains the taxon the user wants to remove
582 }else{//if taxons has them and you don't them remove taxons
583 int hasConfidences = tax.find_first_of('(');
584 if (hasConfidences == string::npos) {
586 int pos = newtax.find(noConfidenceTaxons);
588 if (pos == string::npos) {
589 wroteSomething = true;
590 out << name << '\t' << tax << endl;
591 }else{ //this sequence contains the taxon the user wants to remove
594 }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
595 //first remove confidences from both and see if the taxonomy exists
597 string noNewTax = tax;
598 int hasConfidences = tax.find_first_of('(');
599 if (hasConfidences != string::npos) {
600 noNewTax = removeConfidences(tax);
603 int pos = noNewTax.find(noConfidenceTaxons);
605 if (pos != string::npos) { //if yes, then are the confidences okay
608 vector< map<string, float> > usersTaxon = getTaxons(newtax);
610 //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
611 //we want to "line them up", so we will find the the index where the searchstring starts
613 for (int i = 0; i < usersTaxon.size(); i++) {
615 if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) {
618 bool goodspot = true;
619 //is this really the start, or are we dealing with a taxon of the same name?
620 while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) {
621 if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
625 if (goodspot) { break; }
629 for (int i = 0; i < searchTaxons.size(); i++) {
631 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
632 if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
642 //passed the test so remove you
646 wroteSomething = true;
647 out << name << '\t' << tax << endl;
650 wroteSomething = true;
651 out << name << '\t' << tax << endl;
664 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
665 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
670 catch(exception& e) {
671 m->errorOut(e, "RemoveLineageCommand", "readTax");
675 /**************************************************************************************************/
676 vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
679 vector< map<string, float> > t;
681 int taxLength = tax.length();
682 for(int i=0;i<taxLength;i++){
685 int openParen = taxon.find_first_of('(');
686 int closeParen = taxon.find_last_of(')');
688 string newtaxon, confidence;
689 if ((openParen != string::npos) && (closeParen != string::npos)) {
690 newtaxon = taxon.substr(0, openParen); //rip off confidence
691 confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
697 convert(confidence, con);
699 map<string, float> temp;
700 temp[newtaxon] = con;
712 catch(exception& e) {
713 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
717 /**************************************************************************************************/
718 string RemoveLineageCommand::removeConfidences(string tax) {
722 int taxLength = tax.length();
723 for(int i=0;i<taxLength;i++){
725 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
735 catch(exception& e) {
736 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
740 //**********************************************************************************************************************
741 //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
742 int RemoveLineageCommand::readAlign(){
744 string thisOutputDir = outputDir;
745 if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
746 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
749 m->openOutputFile(outputFileName, out);
752 m->openInputFile(alignfile, in);
755 bool wroteSomething = false;
757 //read column headers
758 for (int i = 0; i < 16; i++) {
759 if (!in.eof()) { in >> junk; out << junk << '\t'; }
765 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
767 in >> name; //read from first column
769 //if this name is in the accnos file
770 if (names.count(name) == 0) {
771 wroteSomething = true;
776 for (int i = 0; i < 15; i++) {
777 if (!in.eof()) { in >> junk; out << junk << '\t'; }
782 }else {//still read just don't do anything with it
785 for (int i = 0; i < 15; i++) {
786 if (!in.eof()) { in >> junk; }
796 if (wroteSomething == false) { m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
797 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
802 catch(exception& e) {
803 m->errorOut(e, "RemoveLineageCommand", "readAlign");
807 //**********************************************************************************************************************