5 * Created by Sarah Westcott on 7/8/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "getseqscommand.h"
11 #include "sequence.hpp"
12 #include "listvector.hpp"
14 //**********************************************************************************************************************
15 vector<string> GetSeqsCommand::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,false); parameters.push_back(ptaxonomy);
22 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
23 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
24 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
25 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
26 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
27 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
28 CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
30 vector<string> myArray;
31 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
35 m->errorOut(e, "GetSeqsCommand", "setParameters");
39 //**********************************************************************************************************************
40 string GetSeqsCommand::getHelpString(){
42 string helpString = "";
43 helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n";
44 helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
45 helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
46 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";
47 helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
48 helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
49 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
53 m->errorOut(e, "GetSeqsCommand", "getHelpString");
58 //**********************************************************************************************************************
59 GetSeqsCommand::GetSeqsCommand(){
61 abort = true; calledHelp = true;
63 vector<string> tempOutNames;
64 outputTypes["fasta"] = tempOutNames;
65 outputTypes["taxonomy"] = tempOutNames;
66 outputTypes["name"] = tempOutNames;
67 outputTypes["group"] = tempOutNames;
68 outputTypes["alignreport"] = tempOutNames;
69 outputTypes["list"] = tempOutNames;
70 outputTypes["qfile"] = tempOutNames;
71 outputTypes["accnosreport"] = tempOutNames;
74 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
78 //**********************************************************************************************************************
79 GetSeqsCommand::GetSeqsCommand(string option) {
81 abort = false; calledHelp = false;
83 //allow user to run help
84 if(option == "help") { help(); abort = true; calledHelp = true; }
85 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
88 vector<string> myArray = setParameters();
90 OptionParser parser(option);
91 map<string,string> parameters = parser.getParameters();
93 ValidParameters validParameter;
94 map<string,string>::iterator it;
96 //check to make sure all parameters are valid for command
97 for (it = parameters.begin(); it != parameters.end(); it++) {
98 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
101 //initialize outputTypes
102 vector<string> tempOutNames;
103 outputTypes["fasta"] = tempOutNames;
104 outputTypes["taxonomy"] = tempOutNames;
105 outputTypes["name"] = tempOutNames;
106 outputTypes["group"] = tempOutNames;
107 outputTypes["alignreport"] = tempOutNames;
108 outputTypes["list"] = tempOutNames;
109 outputTypes["qfile"] = tempOutNames;
110 outputTypes["accnosreport"] = 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("accnos");
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["accnos"] = inputDir + it->second; }
144 it = parameters.find("accnos2");
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["accnos2"] = inputDir + it->second; }
152 it = parameters.find("list");
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["list"] = inputDir + it->second; }
160 it = parameters.find("name");
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["name"] = inputDir + it->second; }
168 it = parameters.find("group");
169 //user has given a template file
170 if(it != parameters.end()){
171 path = m->hasPath(it->second);
172 //if the user has not given a path then, add inputdir. else leave path alone.
173 if (path == "") { parameters["group"] = inputDir + it->second; }
176 it = parameters.find("taxonomy");
177 //user has given a template file
178 if(it != parameters.end()){
179 path = m->hasPath(it->second);
180 //if the user has not given a path then, add inputdir. else leave path alone.
181 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
184 it = parameters.find("qfile");
185 //user has given a template file
186 if(it != parameters.end()){
187 path = m->hasPath(it->second);
188 //if the user has not given a path then, add inputdir. else leave path alone.
189 if (path == "") { parameters["qfile"] = inputDir + it->second; }
194 //check for required parameters
195 accnosfile = validParameter.validFile(parameters, "accnos", true);
196 if (accnosfile == "not open") { abort = true; }
197 else if (accnosfile == "not found") {
198 accnosfile = m->getAccnosFile();
199 if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
201 m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
204 }else { m->setAccnosFile(accnosfile); }
206 if (accnosfile2 == "not found") { accnosfile2 = ""; }
208 fastafile = validParameter.validFile(parameters, "fasta", true);
209 if (fastafile == "not open") { abort = true; }
210 else if (fastafile == "not found") { fastafile = ""; }
211 else { m->setFastaFile(fastafile); }
213 namefile = validParameter.validFile(parameters, "name", true);
214 if (namefile == "not open") { abort = true; }
215 else if (namefile == "not found") { namefile = ""; }
216 else { m->setNameFile(namefile); }
218 groupfile = validParameter.validFile(parameters, "group", true);
219 if (groupfile == "not open") { abort = true; }
220 else if (groupfile == "not found") { groupfile = ""; }
221 else { m->setGroupFile(groupfile); }
223 alignfile = validParameter.validFile(parameters, "alignreport", true);
224 if (alignfile == "not open") { abort = true; }
225 else if (alignfile == "not found") { alignfile = ""; }
227 listfile = validParameter.validFile(parameters, "list", true);
228 if (listfile == "not open") { abort = true; }
229 else if (listfile == "not found") { listfile = ""; }
230 else { m->setListFile(listfile); }
232 taxfile = validParameter.validFile(parameters, "taxonomy", true);
233 if (taxfile == "not open") { abort = true; }
234 else if (taxfile == "not found") { taxfile = ""; }
235 else { m->setTaxonomyFile(taxfile); }
237 qualfile = validParameter.validFile(parameters, "qfile", true);
238 if (qualfile == "not open") { abort = true; }
239 else if (qualfile == "not found") { qualfile = ""; }
240 else { m->setQualFile(qualfile); }
242 accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
243 if (accnosfile2 == "not open") { abort = true; }
244 else if (accnosfile2 == "not found") { accnosfile2 = ""; }
247 string usedDups = "true";
248 string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "true"; usedDups = ""; }
249 dups = m->isTrue(temp);
251 if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
255 catch(exception& e) {
256 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
260 //**********************************************************************************************************************
262 int GetSeqsCommand::execute(){
265 if (abort == true) { if (calledHelp) { return 0; } return 2; }
267 //get names you want to keep
270 if (m->control_pressed) { return 0; }
272 //read through the correct file and output lines you want to keep
273 if (namefile != "") { readName(); }
274 if (fastafile != "") { readFasta(); }
275 if (groupfile != "") { readGroup(); }
276 if (alignfile != "") { readAlign(); }
277 if (listfile != "") { readList(); }
278 if (taxfile != "") { readTax(); }
279 if (qualfile != "") { readQual(); }
280 if (accnosfile2 != "") { compareAccnos(); }
282 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
285 if (outputNames.size() != 0) {
286 m->mothurOutEndLine();
287 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
288 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
289 m->mothurOutEndLine();
291 //set fasta file as new current fastafile
293 itTypes = outputTypes.find("fasta");
294 if (itTypes != outputTypes.end()) {
295 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
298 itTypes = outputTypes.find("name");
299 if (itTypes != outputTypes.end()) {
300 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
303 itTypes = outputTypes.find("group");
304 if (itTypes != outputTypes.end()) {
305 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
308 itTypes = outputTypes.find("list");
309 if (itTypes != outputTypes.end()) {
310 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
313 itTypes = outputTypes.find("taxonomy");
314 if (itTypes != outputTypes.end()) {
315 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
318 itTypes = outputTypes.find("qfile");
319 if (itTypes != outputTypes.end()) {
320 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
328 catch(exception& e) {
329 m->errorOut(e, "GetSeqsCommand", "execute");
334 //**********************************************************************************************************************
335 int GetSeqsCommand::readFasta(){
337 string thisOutputDir = outputDir;
338 if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
339 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
341 m->openOutputFile(outputFileName, out);
345 m->openInputFile(fastafile, in);
348 bool wroteSomething = false;
349 int selectedCount = 0;
353 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
355 Sequence currSeq(in);
356 name = currSeq.getName();
359 //if this name is in the accnos file
360 if (names.count(name) != 0) {
361 wroteSomething = true;
363 currSeq.printSequence(out);
373 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
374 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
376 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
381 catch(exception& e) {
382 m->errorOut(e, "GetSeqsCommand", "readFasta");
386 //**********************************************************************************************************************
387 int GetSeqsCommand::readQual(){
389 string thisOutputDir = outputDir;
390 if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
391 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" + m->getExtension(qualfile);
393 m->openOutputFile(outputFileName, out);
397 m->openInputFile(qualfile, in);
400 bool wroteSomething = false;
401 int selectedCount = 0;
405 string saveName = "";
411 if (name.length() != 0) {
412 saveName = name.substr(1);
415 if (c == 10 || c == 13){ break; }
422 char letter= in.get();
423 if(letter == '>'){ in.putback(letter); break; }
424 else{ scores += letter; }
429 if (names.count(saveName) != 0) {
430 wroteSomething = true;
432 out << name << endl << scores;
442 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
443 outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName);
445 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
451 catch(exception& e) {
452 m->errorOut(e, "GetSeqsCommand", "readQual");
456 //**********************************************************************************************************************
457 int GetSeqsCommand::readList(){
459 string thisOutputDir = outputDir;
460 if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
461 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
463 m->openOutputFile(outputFileName, out);
466 m->openInputFile(listfile, in);
468 bool wroteSomething = false;
469 int selectedCount = 0;
475 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
477 //read in list vector
480 //make a new list vector
482 newList.setLabel(list.getLabel());
485 for (int i = 0; i < list.getNumBins(); i++) {
487 //parse out names that are in accnos file
488 string binnames = list.get(i);
490 string newNames = "";
491 while (binnames.find_first_of(',') != -1) {
492 string name = binnames.substr(0,binnames.find_first_of(','));
493 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
495 //if that name is in the .accnos file, add it
496 if (names.count(name) != 0) { newNames += name + ","; selectedCount++; }
500 if (names.count(binnames) != 0) { newNames += binnames + ","; selectedCount++; }
502 //if there are names in this bin add to new list
503 if (newNames != "") {
504 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
505 newList.push_back(newNames);
509 //print new listvector
510 if (newList.getNumBins() != 0) {
511 wroteSomething = true;
520 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
521 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
523 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
528 catch(exception& e) {
529 m->errorOut(e, "GetSeqsCommand", "readList");
533 //**********************************************************************************************************************
534 int GetSeqsCommand::readName(){
536 string thisOutputDir = outputDir;
537 if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
538 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
540 m->openOutputFile(outputFileName, out);
544 m->openInputFile(namefile, in);
545 string name, firstCol, secondCol;
547 bool wroteSomething = false;
548 int selectedCount = 0;
552 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
558 if (dups) { hold = secondCol; }
560 vector<string> parsedNames;
561 m->splitAtComma(secondCol, parsedNames);
563 vector<string> validSecond;
564 for (int i = 0; i < parsedNames.size(); i++) {
565 if (names.count(parsedNames[i]) != 0) {
566 validSecond.push_back(parsedNames[i]);
570 if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
571 for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
572 out << firstCol << '\t' << hold << endl;
573 wroteSomething = true;
574 selectedCount += parsedNames.size();
576 selectedCount += validSecond.size();
578 //if the name in the first column is in the set then print it and any other names in second column also in set
579 if (names.count(firstCol) != 0) {
581 wroteSomething = true;
583 out << firstCol << '\t';
585 //you know you have at least one valid second since first column is valid
586 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
587 out << validSecond[validSecond.size()-1] << endl;
590 //make first name in set you come to first column and then add the remaining names to second column
592 //you want part of this row
593 if (validSecond.size() != 0) {
595 wroteSomething = true;
597 out << validSecond[0] << '\t';
599 //you know you have at least one valid second since first column is valid
600 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
601 out << validSecond[validSecond.size()-1] << endl;
610 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
611 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
613 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
618 catch(exception& e) {
619 m->errorOut(e, "GetSeqsCommand", "readName");
624 //**********************************************************************************************************************
625 int GetSeqsCommand::readGroup(){
627 string thisOutputDir = outputDir;
628 if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
629 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
631 m->openOutputFile(outputFileName, out);
635 m->openInputFile(groupfile, in);
638 bool wroteSomething = false;
639 int selectedCount = 0;
643 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
646 in >> name; //read from first column
647 in >> group; //read from second column
649 //if this name is in the accnos file
650 if (names.count(name) != 0) {
651 wroteSomething = true;
653 out << name << '\t' << group << endl;
662 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
663 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
665 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
671 catch(exception& e) {
672 m->errorOut(e, "GetSeqsCommand", "readGroup");
676 //**********************************************************************************************************************
677 int GetSeqsCommand::readTax(){
679 string thisOutputDir = outputDir;
680 if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
681 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
683 m->openOutputFile(outputFileName, out);
686 m->openInputFile(taxfile, in);
689 bool wroteSomething = false;
690 int selectedCount = 0;
694 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
696 in >> name; //read from first column
697 in >> tax; //read from second column
699 //if this name is in the accnos file
700 if (names.count(name) != 0) {
701 wroteSomething = true;
703 out << name << '\t' << tax << endl;
712 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
713 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
715 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
720 catch(exception& e) {
721 m->errorOut(e, "GetSeqsCommand", "readTax");
725 //**********************************************************************************************************************
726 //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
727 int GetSeqsCommand::readAlign(){
729 string thisOutputDir = outputDir;
730 if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
731 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
733 m->openOutputFile(outputFileName, out);
737 m->openInputFile(alignfile, in);
740 bool wroteSomething = false;
741 int selectedCount = 0;
743 //read column headers
744 for (int i = 0; i < 16; i++) {
745 if (!in.eof()) { in >> junk; out << junk << '\t'; }
752 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
755 in >> name; //read from first column
757 //if this name is in the accnos file
758 if (names.count(name) != 0) {
759 wroteSomething = true;
765 for (int i = 0; i < 15; i++) {
766 if (!in.eof()) { in >> junk; out << junk << '\t'; }
771 }else {//still read just don't do anything with it
773 for (int i = 0; i < 15; i++) {
774 if (!in.eof()) { in >> junk; }
784 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
785 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
787 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
792 catch(exception& e) {
793 m->errorOut(e, "GetSeqsCommand", "readAlign");
797 //**********************************************************************************************************************
799 int GetSeqsCommand::readAccnos(){
803 m->openInputFile(accnosfile, in);
818 catch(exception& e) {
819 m->errorOut(e, "GetSeqsCommand", "readAccnos");
823 //**********************************************************************************************************************
825 int GetSeqsCommand::compareAccnos(){
828 string thisOutputDir = outputDir;
829 if (outputDir == "") { thisOutputDir += m->hasPath(accnosfile); }
830 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
832 m->openOutputFile(outputFileName, out);
835 m->openInputFile(accnosfile2, in);
838 set<string> namesAccnos2;
839 set<string> namesDups;
840 set<string> namesAccnos = names;
842 map<string, int> nameCount;
844 if (namefile != "") {
846 m->openInputFile(namefile, inName);
849 while(!inName.eof()){
851 if (m->control_pressed) { inName.close(); return 0; }
853 string thisname, repnames;
855 inName >> thisname; m->gobble(inName); //read from first column
856 inName >> repnames; //read from second column
858 int num = m->getNumNames(repnames);
859 nameCount[thisname] = num;
869 if (namesAccnos.count(name) == 0){ //name unique to accnos2
870 int pos = name.find_last_of('_');
871 string tempName = name;
872 if (pos != string::npos) { tempName = tempName.substr(pos+1); cout << tempName << endl; }
873 if (namesAccnos.count(tempName) == 0){
874 namesAccnos2.insert(name);
875 }else { //you are in both so erase
876 namesAccnos.erase(name);
877 namesDups.insert(name);
879 }else { //you are in both so erase
880 namesAccnos.erase(name);
881 namesDups.insert(name);
888 out << "Names in both files : " + toString(namesDups.size()) << endl;
889 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
891 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
893 if (namefile != "") { out << '\t' << nameCount[(*it)]; }
897 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
898 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
900 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
902 if (namefile != "") { out << '\t' << nameCount[(*it)]; }
906 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
907 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
909 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
911 if (namefile != "") { out << '\t' << nameCount[(*it)]; }
917 outputNames.push_back(outputFileName); outputTypes["accnosreport"].push_back(outputFileName);
922 catch(exception& e) {
923 m->errorOut(e, "GetSeqsCommand", "readAccnos");
929 //**********************************************************************************************************************