+++ /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