--- /dev/null
+//
+// sortseqscommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 2/3/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "sortseqscommand.h"
+#include "sequence.hpp"
+#include "qualityscores.h"
+
+//**********************************************************************************************************************
+vector<string> SortSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SortSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The sort.seqs command puts the sequences in the same order for the following file types: accnos fasta, name, group, taxonomy or quality file.\n";
+ helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, qfile and large.\n";
+ helpString += "The accnos file allows you to specify the order you want the files in. If none is provided, mothur will use the order of the first file it reads.\n";
+ helpString += "The large parameters is used to indicate your files are too large to fit in RAM.\n";
+ helpString += "The sort.seqs command should be in the following format: sort.seqs(fasta=yourFasta).\n";
+ helpString += "Example sort.seqs(fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+SortSeqsCommand::SortSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SortSeqsCommand::SortSeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("qfile");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["qfile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("accnos");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["accnos"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for parameters
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { accnosfile = ""; abort = true; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+ else { m->setAccnosFile(accnosfile); }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+ else { m->setFastaFile(fastafile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ taxfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxfile == "not open") { abort = true; }
+ else if (taxfile == "not found") { taxfile = ""; }
+ else { m->setTaxonomyFile(taxfile); }
+
+ qualfile = validParameter.validFile(parameters, "qfile", true);
+ if (qualfile == "not open") { abort = true; }
+ else if (qualfile == "not found") { qualfile = ""; }
+ else { m->setQualFile(qualfile); }
+
+ string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "f"; }
+ large = m->isTrue(temp);
+
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy or quality."); m->mothurOutEndLine(); abort = true; }
+
+ if ((fastafile != "") && (namefile == "")) {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int SortSeqsCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //read through the correct file and output lines you want to keep
+ if (accnosfile != "") { readAccnos(); }
+ if (fastafile != "") { readFasta(); }
+ if (qualfile != "") { readQual(); }
+ if (namefile != "") { readName(); }
+ if (groupfile != "") { readGroup(); }
+ if (taxfile != "") { readTax(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ if (outputNames.size() != 0) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
+
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
+ }
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SortSeqsCommand::readFasta(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "sorted" + m->getExtension(fastafile);
+ outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ string name;
+
+ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
+
+ if (large) { //if the file is too large to fit in memory we can still process it, but the io will be very time consuming.
+ //read through the file looking for 1000 seqs at a time. Once we find them output them and start looking for the next 1000.
+ //this way we only store 1000 seqs in memory at a time.
+
+ int numNames = names.size();
+ int numNamesInFile = 0;
+
+ //to make sure we dont miss any seqs, add any seqs that are not in names but in the file to the end of names
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ numNamesInFile++;
+ map<string, int>::iterator it = names.find(name);
+ if (it == names.end()) {
+ names[name] = numNames; numNames++;
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ int numLeft = names.size();
+ if (numNamesInFile < numLeft) { numLeft = numNamesInFile; }
+
+ int size = 1000; //assume that user can hold 1000 seqs in memory
+ if (numLeft < size) { size = numLeft; }
+ int times = 0;
+
+ vector<Sequence> seqs; seqs.resize(size);
+
+ while (numLeft > 0) {
+
+ ifstream in2;
+ m->openInputFile(fastafile, in2);
+
+ if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; }
+
+ int found = 0;
+ int needToFind = size;
+ if (numLeft < size) { needToFind = numLeft; }
+
+ while(!in2.eof()){
+ if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //stop reading if we already found the seqs we are looking for
+ if (found >= needToFind) { break; }
+
+ Sequence currSeq(in2);
+ name = currSeq.getName();
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ //is it in the set of seqs we are looking for this time around
+ int thisSeqsPlace = it->second;
+ thisSeqsPlace -= (times * size);
+ if ((thisSeqsPlace < size) && (thisSeqsPlace >= 0)) {
+ seqs[thisSeqsPlace] = currSeq;
+ found++;
+ }
+ }else { m->mothurOut("[ERROR]: in logic of readFasta function.\n"); m->control_pressed = true; }
+ }
+ m->gobble(in2);
+ }
+ in2.close();
+
+ ofstream out2;
+ m->openOutputFileAppend(outputFileName, out2);
+
+ int output = seqs.size();
+ if (numLeft < seqs.size()) { output = numLeft; }
+
+ for (int i = 0; i < output; i++) {
+ seqs[i].printSequence(out2);
+ }
+ out2.close();
+
+ times++;
+ numLeft -= output;
+ }
+
+ m->mothurOut("Ordered " + toString(numNamesInFile) + " sequences from " + fastafile + ".\n");
+ }else {
+
+ vector<Sequence> seqs; seqs.resize(names.size());
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = currSeq;
+ }else { //if we cant find it then add it to the end
+ names[name] = seqs.size();
+ seqs.push_back(currSeq);
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+
+ for (int i = 0; i < seqs.size(); i++) {
+ seqs[i].printSequence(out);
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + fastafile + ".\n");
+ }
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ //if this name is in the accnos file
+ names[name] = count;
+ count++;
+ currSeq.printSequence(out);
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + fastafile + " to determine the order. It contains " + toString(count) + " sequences.\n");
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readFasta");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SortSeqsCommand::readQual(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "sorted" + m->getExtension(qualfile);
+ outputTypes["qfile"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(qualfile, in);
+ string name;
+
+ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
+
+ if (large) { //if the file is too large to fit in memory we can still process it, but the io will be very time consuming.
+ //read through the file looking for 1000 seqs at a time. Once we find them output them and start looking for the next 1000.
+ //this way we only store 1000 seqs in memory at a time.
+
+ int numNames = names.size();
+ int numNamesInFile = 0;
+
+ //to make sure we dont miss any seqs, add any seqs that are not in names but in the file to the end of names
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ QualityScores currQual;
+ currQual = QualityScores(in);
+ name = currQual.getName();
+
+ if (name != "") {
+ numNamesInFile++;
+ map<string, int>::iterator it = names.find(name);
+ if (it == names.end()) {
+ names[name] = numNames; numNames++;
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ int numLeft = names.size();
+ if (numNamesInFile < numLeft) { numLeft = numNamesInFile; }
+
+ int size = 1000; //assume that user can hold 1000 seqs in memory
+ if (numLeft < size) { size = numLeft; }
+ int times = 0;
+
+
+ vector<QualityScores> seqs; seqs.resize(size);
+
+ while (numLeft > 0) {
+
+ ifstream in2;
+ m->openInputFile(qualfile, in2);
+
+ if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; }
+
+ int found = 0;
+ int needToFind = size;
+ if (numLeft < size) { needToFind = numLeft; }
+
+ while(!in2.eof()){
+ if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //stop reading if we already found the seqs we are looking for
+ if (found >= needToFind) { break; }
+
+ QualityScores currQual;
+ currQual = QualityScores(in2);
+ name = currQual.getName();
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ //is it in the set of seqs we are looking for this time around
+ int thisSeqsPlace = it->second;
+ thisSeqsPlace -= (times * size);
+ if ((thisSeqsPlace < size) && (thisSeqsPlace >= 0)) {
+ seqs[thisSeqsPlace] = currQual;
+ found++;
+ }
+ }else { m->mothurOut("[ERROR]: in logic of readQual function.\n"); m->control_pressed = true; }
+ }
+ m->gobble(in2);
+ }
+ in2.close();
+
+ ofstream out2;
+ m->openOutputFileAppend(outputFileName, out2);
+
+ int output = seqs.size();
+ if (numLeft < seqs.size()) { output = numLeft; }
+
+ for (int i = 0; i < output; i++) {
+ seqs[i].printQScores(out2);
+ }
+ out2.close();
+
+ times++;
+ numLeft -= output;
+ }
+
+ m->mothurOut("Ordered " + toString(numNamesInFile) + " sequences from " + qualfile + ".\n");
+
+ }else {
+
+ vector<QualityScores> seqs; seqs.resize(names.size());
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ QualityScores currQual;
+ currQual = QualityScores(in);
+ name = currQual.getName();
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = currQual;
+ }else { //if we cant find it then add it to the end
+ names[name] = seqs.size();
+ seqs.push_back(currQual);
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+
+ for (int i = 0; i < seqs.size(); i++) {
+ seqs[i].printQScores(out);
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + qualfile + ".\n");
+ }
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ QualityScores currQual;
+ currQual = QualityScores(in);
+
+ m->gobble(in);
+
+ if (currQual.getName() != "") {
+ //if this name is in the accnos file
+ names[currQual.getName()] = count;
+ count++;
+ currQual.printQScores(out);
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + qualfile + " to determine the order. It contains " + toString(count) + " sequences.\n");
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readQual");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SortSeqsCommand::readName(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "sorted" + m->getExtension(namefile);
+ outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string name, firstCol, secondCol;
+
+ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
+
+ vector<string> seqs; seqs.resize(names.size());
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> firstCol; m->gobble(in);
+ in >> secondCol; m->gobble(in);
+
+ if (firstCol != "") {
+ map<string, int>::iterator it = names.find(firstCol);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = firstCol + '\t' + secondCol;
+ }else { //if we cant find it then add it to the end
+ names[firstCol] = seqs.size();
+ seqs.push_back((firstCol + '\t' + secondCol));
+ m->mothurOut(firstCol + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ }
+ in.close();
+
+ for (int i = 0; i < seqs.size(); i++) {
+ out << seqs[i] << endl;
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + namefile + ".\n");
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> firstCol; m->gobble(in);
+ in >> secondCol; m->gobble(in);
+
+ if (firstCol != "") {
+ //if this name is in the accnos file
+ names[firstCol] = count;
+ count++;
+ out << firstCol << '\t' << secondCol << endl;
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + namefile + " to determine the order. It contains " + toString(count) + " representative sequences.\n");
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SortSeqsCommand::readGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+ outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
+
+ vector<string> seqs; seqs.resize(names.size());
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; m->gobble(in);
+ in >> group; m->gobble(in);
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = name + '\t' + group;
+ }else { //if we cant find it then add it to the end
+ names[name] = seqs.size();
+ seqs.push_back((name + '\t' + group));
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ }
+ in.close();
+
+ for (int i = 0; i < seqs.size(); i++) {
+ out << seqs[i] << endl;
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + groupfile + ".\n");
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; m->gobble(in);
+ in >> group; m->gobble(in);
+
+ if (name != "") {
+ //if this name is in the accnos file
+ names[name] = count;
+ count++;
+ out << name << '\t' << group << endl;
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + groupfile + " to determine the order. It contains " + toString(count) + " sequences.\n");
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SortSeqsCommand::readTax(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
+
+ vector<string> seqs; seqs.resize(names.size());
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; m->gobble(in);
+ in >> tax; m->gobble(in);
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = name + '\t' + tax;
+ }else { //if we cant find it then add it to the end
+ names[name] = seqs.size();
+ seqs.push_back((name + '\t' + tax));
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ }
+ in.close();
+
+ for (int i = 0; i < seqs.size(); i++) {
+ out << seqs[i] << endl;
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + taxfile + ".\n");
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; m->gobble(in);
+ in >> tax; m->gobble(in);
+
+ if (name != "") {
+ //if this name is in the accnos file
+ names[name] = count;
+ count++;
+ out << name << '\t' << tax << endl;
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + taxfile + " to determine the order. It contains " + toString(count) + " sequences.\n");
+ }
+
+ return 0;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readTax");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SortSeqsCommand::readAccnos(){
+ try {
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+ string name;
+ int count = 0;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { break; }
+
+ in >> name; m->gobble(in);
+
+ if (name != "") {
+ names[name] = count;
+ count++;
+ }
+ }
+ in.close();
+
+ m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(count) + " representative sequences.\n");
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readAccnos");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
+
+
projects / mothur.git / commitdiff