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; }
87 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
90 vector<string> myArray = setParameters();
92 OptionParser parser(option);
93 map<string,string> parameters = parser.getParameters();
95 ValidParameters validParameter;
96 map<string,string>::iterator it;
98 //check to make sure all parameters are valid for command
99 for (it = parameters.begin(); it != parameters.end(); it++) {
100 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
103 //initialize outputTypes
104 vector<string> tempOutNames;
105 outputTypes["fasta"] = tempOutNames;
106 outputTypes["taxonomy"] = tempOutNames;
107 outputTypes["name"] = tempOutNames;
108 outputTypes["group"] = tempOutNames;
109 outputTypes["alignreport"] = tempOutNames;
110 outputTypes["list"] = tempOutNames;
112 //if the user changes the output directory command factory will send this info to us in the output parameter
113 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
115 //if the user changes the input directory command factory will send this info to us in the output parameter
116 string inputDir = validParameter.validFile(parameters, "inputdir", false);
117 if (inputDir == "not found"){ inputDir = ""; }
120 it = parameters.find("alignreport");
121 //user has given a template file
122 if(it != parameters.end()){
123 path = m->hasPath(it->second);
124 //if the user has not given a path then, add inputdir. else leave path alone.
125 if (path == "") { parameters["alignreport"] = inputDir + it->second; }
128 it = parameters.find("fasta");
129 //user has given a template file
130 if(it != parameters.end()){
131 path = m->hasPath(it->second);
132 //if the user has not given a path then, add inputdir. else leave path alone.
133 if (path == "") { parameters["fasta"] = inputDir + it->second; }
136 it = parameters.find("list");
137 //user has given a template file
138 if(it != parameters.end()){
139 path = m->hasPath(it->second);
140 //if the user has not given a path then, add inputdir. else leave path alone.
141 if (path == "") { parameters["list"] = inputDir + it->second; }
144 it = parameters.find("name");
145 //user has given a template file
146 if(it != parameters.end()){
147 path = m->hasPath(it->second);
148 //if the user has not given a path then, add inputdir. else leave path alone.
149 if (path == "") { parameters["name"] = inputDir + it->second; }
152 it = parameters.find("group");
153 //user has given a template file
154 if(it != parameters.end()){
155 path = m->hasPath(it->second);
156 //if the user has not given a path then, add inputdir. else leave path alone.
157 if (path == "") { parameters["group"] = inputDir + it->second; }
160 it = parameters.find("taxonomy");
161 //user has given a template file
162 if(it != parameters.end()){
163 path = m->hasPath(it->second);
164 //if the user has not given a path then, add inputdir. else leave path alone.
165 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
170 //check for required parameters
171 fastafile = validParameter.validFile(parameters, "fasta", true);
172 if (fastafile == "not open") { abort = true; }
173 else if (fastafile == "not found") { fastafile = ""; }
175 namefile = validParameter.validFile(parameters, "name", true);
176 if (namefile == "not open") { abort = true; }
177 else if (namefile == "not found") { namefile = ""; }
179 groupfile = validParameter.validFile(parameters, "group", true);
180 if (groupfile == "not open") { abort = true; }
181 else if (groupfile == "not found") { groupfile = ""; }
183 alignfile = validParameter.validFile(parameters, "alignreport", true);
184 if (alignfile == "not open") { abort = true; }
185 else if (alignfile == "not found") { alignfile = ""; }
187 listfile = validParameter.validFile(parameters, "list", true);
188 if (listfile == "not open") { abort = true; }
189 else if (listfile == "not found") { listfile = ""; }
191 taxfile = validParameter.validFile(parameters, "taxonomy", true);
192 if (taxfile == "not open") { abort = true; }
193 else if (taxfile == "not found") {
194 taxfile = m->getTaxonomyFile();
195 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
196 else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
199 string usedDups = "true";
200 string temp = validParameter.validFile(parameters, "dups", false);
201 if (temp == "not found") {
202 if (namefile != "") { temp = "true"; }
203 else { temp = "false"; usedDups = ""; }
205 dups = m->isTrue(temp);
207 taxons = validParameter.validFile(parameters, "taxon", false);
208 if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
211 if (taxons[0] == '\'') { taxons = taxons.substr(1); }
212 if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
214 m->splitAtChar(taxons, listOfTaxons, '-');
216 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; }
218 if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
223 catch(exception& e) {
224 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
228 //**********************************************************************************************************************
230 int RemoveLineageCommand::execute(){
233 if (abort == true) { if (calledHelp) { return 0; } return 2; }
235 if (m->control_pressed) { return 0; }
237 //read through the correct file and output lines you want to keep
238 if (taxfile != "") { readTax(); } //fills the set of names to remove
239 if (namefile != "") { readName(); }
240 if (fastafile != "") { readFasta(); }
241 if (groupfile != "") { readGroup(); }
242 if (alignfile != "") { readAlign(); }
243 if (listfile != "") { readList(); }
246 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
248 if (outputNames.size() != 0) {
249 m->mothurOutEndLine();
250 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
251 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
252 m->mothurOutEndLine();
254 //set fasta file as new current fastafile
256 itTypes = outputTypes.find("fasta");
257 if (itTypes != outputTypes.end()) {
258 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
261 itTypes = outputTypes.find("name");
262 if (itTypes != outputTypes.end()) {
263 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
266 itTypes = outputTypes.find("group");
267 if (itTypes != outputTypes.end()) {
268 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
271 itTypes = outputTypes.find("list");
272 if (itTypes != outputTypes.end()) {
273 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
276 itTypes = outputTypes.find("taxonomy");
277 if (itTypes != outputTypes.end()) {
278 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
285 catch(exception& e) {
286 m->errorOut(e, "RemoveLineageCommand", "execute");
291 //**********************************************************************************************************************
292 int RemoveLineageCommand::readFasta(){
294 string thisOutputDir = outputDir;
295 if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
296 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
299 m->openOutputFile(outputFileName, out);
302 m->openInputFile(fastafile, in);
305 bool wroteSomething = false;
308 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
310 Sequence currSeq(in);
311 name = currSeq.getName();
314 //if this name is in the accnos file
315 if (names.count(name) == 0) {
316 wroteSomething = true;
318 currSeq.printSequence(out);
326 if (wroteSomething == false) { m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
327 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
332 catch(exception& e) {
333 m->errorOut(e, "RemoveLineageCommand", "readFasta");
337 //**********************************************************************************************************************
338 int RemoveLineageCommand::readList(){
340 string thisOutputDir = outputDir;
341 if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
342 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
345 m->openOutputFile(outputFileName, out);
348 m->openInputFile(listfile, in);
350 bool wroteSomething = false;
353 //read in list vector
356 //make a new list vector
358 newList.setLabel(list.getLabel());
361 for (int i = 0; i < list.getNumBins(); i++) {
362 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
364 //parse out names that are in accnos file
365 string binnames = list.get(i);
367 string newNames = "";
368 while (binnames.find_first_of(',') != -1) {
369 string name = binnames.substr(0,binnames.find_first_of(','));
370 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
372 //if that name is in the .accnos file, add it
373 if (names.count(name) == 0) { newNames += name + ","; }
377 if (names.count(binnames) == 0) { newNames += binnames + ","; }
379 //if there are names in this bin add to new list
380 if (newNames != "") {
381 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
382 newList.push_back(newNames);
386 //print new listvector
387 if (newList.getNumBins() != 0) {
388 wroteSomething = true;
397 if (wroteSomething == false) { m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
398 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
403 catch(exception& e) {
404 m->errorOut(e, "RemoveLineageCommand", "readList");
408 //**********************************************************************************************************************
409 int RemoveLineageCommand::readName(){
411 string thisOutputDir = outputDir;
412 if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
413 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
416 m->openOutputFile(outputFileName, out);
419 m->openInputFile(namefile, in);
420 string name, firstCol, secondCol;
422 bool wroteSomething = false;
425 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
430 vector<string> parsedNames;
431 m->splitAtComma(secondCol, parsedNames);
433 vector<string> validSecond; validSecond.clear();
434 for (int i = 0; i < parsedNames.size(); i++) {
435 if (names.count(parsedNames[i]) == 0) {
436 validSecond.push_back(parsedNames[i]);
440 if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone
441 for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
443 //if the name in the first column is in the set then print it and any other names in second column also in set
444 if (names.count(firstCol) == 0) {
446 wroteSomething = true;
448 out << firstCol << '\t';
450 //you know you have at least one valid second since first column is valid
451 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
452 out << validSecond[validSecond.size()-1] << endl;
454 //make first name in set you come to first column and then add the remaining names to second column
457 //you want part of this row
458 if (validSecond.size() != 0) {
460 wroteSomething = true;
462 out << validSecond[0] << '\t';
464 //you know you have at least one valid second since first column is valid
465 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
466 out << validSecond[validSecond.size()-1] << endl;
475 if (wroteSomething == false) { m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
476 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
480 catch(exception& e) {
481 m->errorOut(e, "RemoveLineageCommand", "readName");
486 //**********************************************************************************************************************
487 int RemoveLineageCommand::readGroup(){
489 string thisOutputDir = outputDir;
490 if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
491 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
494 m->openOutputFile(outputFileName, out);
497 m->openInputFile(groupfile, in);
500 bool wroteSomething = false;
503 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
505 in >> name; //read from first column
506 in >> group; //read from second column
508 //if this name is in the accnos file
509 if (names.count(name) == 0) {
510 wroteSomething = true;
511 out << name << '\t' << group << endl;
519 if (wroteSomething == false) { m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
520 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
524 catch(exception& e) {
525 m->errorOut(e, "RemoveLineageCommand", "readGroup");
529 //**********************************************************************************************************************
530 int RemoveLineageCommand::readTax(){
532 string thisOutputDir = outputDir;
533 if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
534 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
536 m->openOutputFile(outputFileName, out);
539 m->openInputFile(taxfile, in);
542 bool wroteSomething = false;
544 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
545 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
546 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
548 for (int i = 0; i < listOfTaxons.size(); i++) {
549 noConfidenceTaxons[i] = listOfTaxons[i];
550 int hasConPos = listOfTaxons[i].find_first_of('(');
551 if (hasConPos != string::npos) {
552 taxonsHasConfidence[i] = true;
553 searchTaxons[i] = getTaxons(listOfTaxons[i]);
554 noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]);
561 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
563 in >> name; //read from first column
564 in >> tax; //read from second column
568 for (int j = 0; j < listOfTaxons.size(); j++) {
571 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
572 if (!taxonsHasConfidence[j]) {
574 int hasConfidences = tax.find_first_of('(');
575 if (hasConfidences != string::npos) {
576 newtax = removeConfidences(tax);
579 int pos = newtax.find(noConfidenceTaxons[j]);
581 if (pos == string::npos) {
582 //wroteSomething = true;
583 //out << name << '\t' << tax << endl;
584 }else{ //this sequence contains the taxon the user wants to remove
589 }else{//if taxons has them and you don't them remove taxons
590 int hasConfidences = tax.find_first_of('(');
591 if (hasConfidences == string::npos) {
593 int pos = newtax.find(noConfidenceTaxons[j]);
595 if (pos == string::npos) {
596 //wroteSomething = true;
597 //out << name << '\t' << tax << endl;
598 }else{ //this sequence contains the taxon the user wants to remove
602 }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
603 //first remove confidences from both and see if the taxonomy exists
605 string noNewTax = tax;
606 int hasConfidences = tax.find_first_of('(');
607 if (hasConfidences != string::npos) {
608 noNewTax = removeConfidences(tax);
611 int pos = noNewTax.find(noConfidenceTaxons[j]);
613 if (pos != string::npos) { //if yes, then are the confidences okay
615 vector< map<string, float> > usersTaxon = getTaxons(newtax);
617 //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
618 //we want to "line them up", so we will find the the index where the searchstring starts
620 for (int i = 0; i < usersTaxon.size(); i++) {
622 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
625 bool goodspot = true;
626 //is this really the start, or are we dealing with a taxon of the same name?
627 while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
628 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
632 if (goodspot) { break; }
636 for (int i = 0; i < searchTaxons[j].size(); i++) {
638 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
639 if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
649 //passed the test so remove you
654 //wroteSomething = true;
655 //out << name << '\t' << tax << endl;
658 //wroteSomething = true;
659 //out << name << '\t' << tax << endl;
666 if (!remove) { wroteSomething = true; out << name << '\t' << tax << endl; }
672 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
673 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
678 catch(exception& e) {
679 m->errorOut(e, "RemoveLineageCommand", "readTax");
683 /**************************************************************************************************/
684 vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
687 vector< map<string, float> > t;
689 int taxLength = tax.length();
690 for(int i=0;i<taxLength;i++){
693 int openParen = taxon.find_first_of('(');
694 int closeParen = taxon.find_last_of(')');
696 string newtaxon, confidence;
697 if ((openParen != string::npos) && (closeParen != string::npos)) {
698 newtaxon = taxon.substr(0, openParen); //rip off confidence
699 confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
705 convert(confidence, con);
707 map<string, float> temp;
708 temp[newtaxon] = con;
720 catch(exception& e) {
721 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
725 /**************************************************************************************************/
726 string RemoveLineageCommand::removeConfidences(string tax) {
730 int taxLength = tax.length();
731 for(int i=0;i<taxLength;i++){
733 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
743 catch(exception& e) {
744 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
748 //**********************************************************************************************************************
749 //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
750 int RemoveLineageCommand::readAlign(){
752 string thisOutputDir = outputDir;
753 if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
754 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
757 m->openOutputFile(outputFileName, out);
760 m->openInputFile(alignfile, in);
763 bool wroteSomething = false;
765 //read column headers
766 for (int i = 0; i < 16; i++) {
767 if (!in.eof()) { in >> junk; out << junk << '\t'; }
773 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
775 in >> name; //read from first column
777 //if this name is in the accnos file
778 if (names.count(name) == 0) {
779 wroteSomething = true;
784 for (int i = 0; i < 15; i++) {
785 if (!in.eof()) { in >> junk; out << junk << '\t'; }
790 }else {//still read just don't do anything with it
793 for (int i = 0; i < 15; i++) {
794 if (!in.eof()) { in >> junk; }
804 if (wroteSomething == false) { m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
805 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
810 catch(exception& e) {
811 m->errorOut(e, "RemoveLineageCommand", "readAlign");
815 //**********************************************************************************************************************