--- /dev/null
+/*
+ * getlineagecommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/24/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getlineagecommand.h"
+#include "sequence.hpp"
+#include "listvector.hpp"
+
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::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 plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
+ 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, "GetLineageCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetLineageCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n";
+ helpString += "It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n";
+ helpString += "The get.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";
+ 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";
+ helpString += "The taxon parameter allows you to select the taxons you would like to get and is required.\n";
+ helpString += "You may enter your taxons with confidence scores, doing so will get only those sequences that belong to the taxonomy and whose cofidence scores is above the scores you give.\n";
+ helpString += "If they belong to the taxonomy and have confidences below those you provide the sequence will not be selected.\n";
+ helpString += "The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
+ helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
+ 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";
+ helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\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, "GetLineageCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+GetLineageCommand::GetLineageCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetLineageCommand::GetLineageCommand(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["alignreport"] = tempOutNames;
+ outputTypes["list"] = 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("alignreport");
+ //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["alignreport"] = inputDir + it->second; }
+ }
+
+ 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("list");
+ //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["list"] = 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; }
+ }
+ }
+
+
+ //check for required parameters
+ 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); }
+
+ alignfile = validParameter.validFile(parameters, "alignreport", true);
+ if (alignfile == "not open") { abort = true; }
+ else if (alignfile == "not found") { alignfile = ""; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
+
+ taxfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxfile == "not open") { taxfile = ""; abort = true; }
+ else if (taxfile == "not found") {
+ taxfile = m->getTaxonomyFile();
+ if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTaxonomyFile(taxfile); }
+
+ string usedDups = "true";
+ string temp = validParameter.validFile(parameters, "dups", false);
+ if (temp == "not found") {
+ if (namefile != "") { temp = "true"; }
+ else { temp = "false"; usedDups = ""; }
+ }
+ dups = m->isTrue(temp);
+
+ taxons = validParameter.validFile(parameters, "taxon", false);
+ if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
+ else {
+ //rip off quotes
+ if (taxons[0] == '\'') { taxons = taxons.substr(1); }
+ if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
+ }
+ m->splitAtChar(taxons, listOfTaxons, '-');
+
+ 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; }
+
+ if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+ vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+ parser.getNameFile(files);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetLineageCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (m->control_pressed) { return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (taxfile != "") { readTax(); } //fills the set of names to get
+ if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
+ if (groupfile != "") { readGroup(); }
+ if (alignfile != "") { readAlign(); }
+ if (listfile != "") { readList(); }
+
+
+ if (m->control_pressed) { outputTypes.clear(); 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("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
+ }
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetLineageCommand::readFasta(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ string name;
+
+ bool wroteSomething = false;
+
+ 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
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ currSeq.printSequence(out);
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readFasta");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::readList(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //read in list vector
+ ListVector list(in);
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+
+ string newNames = "";
+ while (binnames.find_first_of(',') != -1) {
+ string name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //if that name is in the .accnos file, add it
+ if (names.count(name) != 0) { newNames += name + ","; }
+ }
+
+ //get last name
+ if (names.count(binnames) != 0) { newNames += binnames + ","; }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::readName(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string name, firstCol, secondCol;
+
+ bool wroteSomething = false;
+
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> firstCol;
+ in >> secondCol;
+
+ string hold = "";
+ if (dups) { hold = secondCol; }
+
+ vector<string> parsedNames;
+ m->splitAtComma(secondCol, parsedNames);
+
+ vector<string> validSecond;
+ for (int i = 0; i < parsedNames.size(); i++) {
+ if (names.count(parsedNames[i]) != 0) {
+ validSecond.push_back(parsedNames[i]);
+ }
+ }
+
+ if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
+ for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
+ out << firstCol << '\t' << hold << endl;
+ wroteSomething = true;
+ }else {
+ //if the name in the first column is in the set then print it and any other names in second column also in set
+ if (names.count(firstCol) != 0) {
+
+ wroteSomething = true;
+
+ out << firstCol << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+
+
+ //make first name in set you come to first column and then add the remaining names to second column
+ }else {
+ //you want part of this row
+ if (validSecond.size() != 0) {
+
+ wroteSomething = true;
+
+ out << validSecond[0] << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+ }
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetLineageCommand::readGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ out << name << '\t' << group << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetLineageCommand::readTax(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ //bool wroteSomething = false;
+ vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
+ vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
+ vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
+
+ for (int i = 0; i < listOfTaxons.size(); i++) {
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ int hasConPos = listOfTaxons[i].find_first_of('(');
+ if (hasConPos != string::npos) {
+ taxonsHasConfidence[i] = true;
+ searchTaxons[i] = getTaxons(listOfTaxons[i]);
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ m->removeConfidences(noConfidenceTaxons[i]);
+ }
+ }
+
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; //read from first column
+ in >> tax; //read from second column
+
+ for (int j = 0; j < listOfTaxons.size(); j++) {
+
+ string newtax = tax;
+
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
+ if (!taxonsHasConfidence[j]) {
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = tax;
+ m->removeConfidences(newtax);
+ }
+
+ int pos = newtax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else{//if listOfTaxons[i] has them and you don't them remove taxons
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences == string::npos) {
+
+ int pos = newtax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
+ //first remove confidences from both and see if the taxonomy exists
+
+ string noNewTax = tax;
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ noNewTax = tax;
+ m->removeConfidences(noNewTax);
+ }
+
+ int pos = noNewTax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //if yes, then are the confidences okay
+
+ bool good = true;
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
+
+ //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
+ //we want to "line them up", so we will find the the index where the searchstring starts
+ int index = 0;
+ for (int i = 0; i < usersTaxon.size(); i++) {
+
+ if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
+ index = i;
+ int spot = 0;
+ bool goodspot = true;
+ //is this really the start, or are we dealing with a taxon of the same name?
+ while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
+ if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
+ else { spot++; }
+ }
+
+ if (goodspot) { break; }
+ }
+ }
+
+ for (int i = 0; i < searchTaxons[j].size(); i++) {
+
+ if ((i+index) < usersTaxon.size()) { //just in case, should never be false
+ if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
+ good = false;
+ break;
+ }
+ }else {
+ good = false;
+ break;
+ }
+ }
+
+ //passed the test so add you
+ if (good) {
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ break;
+ }
+ }
+ }
+ }
+
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readTax");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
+ try {
+
+ vector< map<string, float> > t;
+ string taxon = "";
+ int taxLength = tax.length();
+ for(int i=0;i<taxLength;i++){
+ if(tax[i] == ';'){
+
+ int openParen = taxon.find_first_of('(');
+ int closeParen = taxon.find_last_of(')');
+
+ string newtaxon, confidence;
+ if ((openParen != string::npos) && (closeParen != string::npos)) {
+ newtaxon = taxon.substr(0, openParen); //rip off confidence
+ confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
+ }else{
+ newtaxon = taxon;
+ confidence = "0";
+ }
+ float con = 0;
+ convert(confidence, con);
+
+ map<string, float> temp;
+ temp[newtaxon] = con;
+ t.push_back(temp);
+
+ taxon = "";
+ }
+ else{
+ taxon += tax[i];
+ }
+ }
+
+ return t;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getTaxons");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//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
+int GetLineageCommand::readAlign(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(alignfile, in);
+ string name, junk;
+
+ bool wroteSomething = false;
+
+ //read column headers
+ for (int i = 0; i < 16; i++) {
+ if (!in.eof()) { in >> junk; out << junk << '\t'; }
+ else { break; }
+ }
+ out << endl;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+
+ in >> name; //read from first column
+
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ out << name << '\t';
+
+ //read rest
+ for (int i = 0; i < 15; i++) {
+ if (!in.eof()) { in >> junk; out << junk << '\t'; }
+ else { break; }
+ }
+ out << endl;
+
+ }else {//still read just don't do anything with it
+ //read rest
+ for (int i = 0; i < 15; i++) {
+ if (!in.eof()) { in >> junk; }
+ else { break; }
+ }
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "readAlign");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
+
projects / mothur.git / blobdiff