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/*
* removelineagecommand.cpp
* Mothur
*
* Created by westcott on 9/24/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "removelineagecommand.h"
#include "sequence.hpp"
#include "listvector.hpp"
#include "counttable.h"
#include "inputdata.h"
#include "taxonomy.hpp"
//**********************************************************************************************************************
vector<string> RemoveLineageCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT", "none","shared",false,false, true); parameters.push_back(pshared);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "tax", "FNGLT", "none","taxonomy",false,false, true); parameters.push_back(ptaxonomy);
CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "tax", "FNGLT", "none","constaxonomy",false,false, true); parameters.push_back(pconstaxonomy);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter ptaxon("taxon", "String", "", "", "", "", "","",false,true,true); parameters.push_back(ptaxon);
CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["count"] = tempOutNames;
outputTypes["constaxonomy"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
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, "RemoveLineageCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveLineageCommand::getHelpString(){
try {
string helpString = "";
helpString += "The remove.lineage command reads a taxonomy or constaxonomy file and any of the following file types: fasta, name, group, count, list, shared or alignreport file. The constaxonomy can only be used with a shared or list file.\n";
helpString += "It outputs a file containing only the sequences or OTUS from the taxonomy file that are not from the taxon you requested to be removed.\n";
helpString += "The remove.lineage command parameters are taxon, fasta, name, group, count, list, shared, taxonomy, alignreport, label and dups. You must provide taxonomy or constaxonomy 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 remove, and is required.\n";
helpString += "You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n";
helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
helpString += "The label parameter is used to analyze specific labels in your input. \n";
helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
helpString += "Example remove.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 remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
;
return helpString;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveLineageCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
else if (type == "constaxonomy") { pattern = "[filename],pick.cons.taxonomy"; }
else if (type == "name") { pattern = "[filename],pick,[extension]"; }
else if (type == "group") { pattern = "[filename],pick,[extension]"; }
else if (type == "count") { pattern = "[filename],pick,[extension]"; }
else if (type == "list") { pattern = "[filename],[distance],pick,[extension]"; }
else if (type == "shared") { pattern = "[filename],[distance],pick,[extension]"; }
else if (type == "alignreport") { pattern = "[filename],pick.[extension]"; }
else if (type == "accnos") { pattern = "[filename],accnos"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
RemoveLineageCommand::RemoveLineageCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { current->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
alignfile = validParameter.validFile(parameters, "alignreport");
if (alignfile == "not open") { abort = true; }
else if (alignfile == "not found") { alignfile = ""; }
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { current->setListFile(listfile); }
taxfile = validParameter.validFile(parameters, "taxonomy");
if (taxfile == "not open") { taxfile = ""; abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
else { current->setTaxonomyFile(taxfile); }
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { current->setSharedFile(sharedfile); }
constaxonomy = validParameter.validFile(parameters, "constaxonomy");
if (constaxonomy == "not open") { constaxonomy = ""; abort = true; }
else if (constaxonomy == "not found") { constaxonomy = ""; }
if ((constaxonomy == "") && (taxfile == "")) {
taxfile = current->getTaxonomyFile();
if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter.\n"); }
else {
m->mothurOut("You have no current taxonomy file and did not provide a constaxonomy file. The taxonomy or constaxonomy parameter is required.\n"); abort = true; }
}
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count.\n"); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count.\n"); abort=true;
}
string usedDups = "true";
string temp = validParameter.valid(parameters, "dups");
if (temp == "not found") {
if (namefile != "") { temp = "true"; }
else { temp = "false"; usedDups = ""; }
}
dups = util.isTrue(temp);
taxons = validParameter.valid(parameters, "taxon");
if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct.\n"); 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)); }
}
util.splitAtChar(taxons, listOfTaxons, '-');
if (m->getDebug()) { string taxonString = util.getStringFromVector(listOfTaxons, ", "); m->mothurOut("[DEBUG]: " + taxonString + "\n."); }
if ((fastafile == "") && (constaxonomy == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy, constaxonomy, shared or listfile.\n"); abort = true; }
if ((constaxonomy != "") && ((fastafile != "") || (namefile != "") || (groupfile != "") || (alignfile != "") || (taxfile != "") || (countfile != ""))) {
m->mothurOut("[ERROR]: can only use constaxonomy file with a list or shared file, aborting.\n"); abort = true;
}
if ((constaxonomy != "") && (taxfile != "")) {
m->mothurOut("[ERROR]: Choose only one: taxonomy or constaxonomy, aborting.\n"); abort = true;
}
if ((sharedfile != "") && (taxfile != "")) {
m->mothurOut("[ERROR]: sharedfile can only be used with constaxonomy file, aborting.\n"); abort = true;
}
if ((sharedfile != "") || (listfile != "")) {
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile.\n"); label=""; }
}
if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option.\n"); abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveLineageCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (m->getControl_pressed()) { return 0; }
//read through the correct file and output lines you want to keep
if (taxfile != "") {
string accnosFileName = readTax(); //fills the set of names to get
if (!util.isBlank(accnosFileName)) {
outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
runRemoveSeqs(accnosFileName);
}else{ m->mothurOut("\n*** No contaminants to remove ***\n"); util.mothurRemove(accnosFileName); }
}else {
string accnosFileName = readConsTax(); //writes accnos file with otuNames
if (!util.isBlank(accnosFileName)) {
outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
runRemoveOTUs(accnosFileName);
}else{ m->mothurOut("\n*** No contaminants to remove ***\n"); util.mothurRemove(accnosFileName); }
}
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOut("\nOutput File Names:\n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setNameFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setListFile(currentName); }
}
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setSharedFile(currentName); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setTaxonomyFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
//set constaxonomy file as new current constaxonomyfile
itTypes = outputTypes.find("constaxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setConsTaxonomyFile(currentName); }
}
//set constaxonomy file as new current constaxonomyfile
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setAccnosFile(currentName); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveLineageCommand::runRemoveSeqs(string accnosFileName){
try {
//use remove.seqs to create new list and shared files
if ((namefile != "") || (fastafile != "") || (countfile != "") || (groupfile != "") || (alignfile != "") || (listfile != "")) {
string inputString = "accnos=" + accnosFileName;
if (namefile != "") { inputString += ", name=" + namefile; }
if (countfile != "") { inputString += ", count=" + countfile; }
if (fastafile != "") { inputString += ", fasta=" + fastafile; }
if (groupfile != "") { inputString += ", group=" + groupfile; }
if (alignfile != "") { inputString += ", alignreport=" + alignfile; }
if (listfile != "") { inputString += ", list=" + listfile; }
m->mothurOut("\n/******************************************/\n");
m->mothurOut("Running command: remove.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* removeCommand = new RemoveSeqsCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
outputTypes.insert(filenames.begin(), filenames.end());
if (listfile != "") {
vector<string> files = filenames["list"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
if (namefile != "") {
vector<string> files = filenames["name"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
if (countfile != "") {
vector<string> files = filenames["count"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
if (fastafile != "") {
vector<string> files = filenames["fasta"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
if (groupfile != "") {
vector<string> files = filenames["group"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
if (alignfile != "") {
vector<string> files = filenames["alignreport"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "runRemoveSeqs");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveLineageCommand::runRemoveOTUs(string accnosFileName){
try {
//use remove.otus to create new list and shared files
if ((listfile != "") || (sharedfile != "")) {
string inputString = "accnos=" + accnosFileName;
if (listfile != "") { inputString += ", list=" + listfile; }
if (sharedfile != "") { inputString += ", shared=" + sharedfile; }
m->mothurOut("\n/******************************************/\n");
m->mothurOut("Running command: remove.otus(" + inputString + ")\n");
current->setMothurCalling(true);
Command* removeCommand = new RemoveOtusCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
outputTypes.insert(filenames.begin(), filenames.end());
if (listfile != "") {
vector<string> files = filenames["list"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
if (sharedfile != "") {
vector<string> files = filenames["shared"];
outputNames.insert(outputNames.end(), files.begin(), files.end());
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "runRemoveOTUs");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveLineageCommand::readTax(){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(taxfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(taxfile));
variables["[extension]"] = util.getExtension(taxfile);
string outputFileName = getOutputFileName("taxonomy", variables);
string accnosFileName = getOutputFileName("accnos", variables);
ofstream out, outAccnos;
util.openOutputFile(outputFileName, out);
util.openOutputFile(accnosFileName, outAccnos);
ifstream in; util.openInputFile(taxfile, in);
string name, tax;
bool wroteSomething = false;
vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
vector< vector<Taxon> > searchTaxons; searchTaxons.resize(listOfTaxons.size());
for (int i = 0; i < listOfTaxons.size(); i++) {
bool hasCon = false;
searchTaxons[i] = util.getTaxons(listOfTaxons[i], hasCon);
taxonsHasConfidence[i] = hasCon;
}
while(!in.eof()){
if (m->getControl_pressed()) { break; }
in >> name; gobble(in);
tax = util.getline(in); gobble(in);
Taxonomy thisSeq(name, tax);
vector<Taxon> otuTax = thisSeq.getTaxons();
util.removeQuotes(otuTax);
if (!util.searchTax(otuTax, taxonsHasConfidence, searchTaxons)) {
wroteSomething = true; out << name << '\t' << tax << endl;
}else { outAccnos << name << endl; }
}
in.close();
out.close();
outAccnos.close();
if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + ".\n"); }
outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
return accnosFileName;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "readTax");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveLineageCommand::readConsTax(){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(constaxonomy); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(constaxonomy));
string accnosFileName = getOutputFileName("accnos", variables);
string outputFileName = getOutputFileName("constaxonomy", variables);
ofstream out, outAccnos;
util.openOutputFile(outputFileName, out);
util.openOutputFile(accnosFileName, outAccnos);
ifstream in; util.openInputFile(constaxonomy, in);
string otuLabel, tax;
//read headers
string headers = util.getline(in);
out << headers << endl;
bool wroteSomething = false;
vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
vector< vector<Taxon> > searchTaxons; searchTaxons.resize(listOfTaxons.size());
for (int i = 0; i < listOfTaxons.size(); i++) {
bool hasCon = false;
searchTaxons[i] = util.getTaxons(listOfTaxons[i], hasCon);
taxonsHasConfidence[i] = hasCon;
}
int numR = 0;
while(!in.eof()){
if (m->getControl_pressed()) { break; }
Taxonomy thisOtu(in);
vector<Taxon> otuTax = thisOtu.getTaxons();
util.removeQuotes(otuTax);
if (!util.searchTax(otuTax, taxonsHasConfidence, searchTaxons)) {
thisOtu.printConsTax(out);
wroteSomething = true;
}else {
outAccnos << thisOtu.getName() << endl;
numR++;
}
}
in.close();
out.close();
outAccnos.close();
if (!wroteSomething) { m->mothurOut("Your constaxonomy file contains OTUs only from " + taxons + ".\n"); }
else { m->mothurOut("Removed " + toString(numR) + " OTUs from your cons.taxonomy file.\n"); }
outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName);
return accnosFileName;
}
catch(exception& e) {
m->errorOut(e, "RemoveLineageCommand", "readConsTax");
exit(1);
}
}
/**************************************************************************************************/
vector< map<string, float> > RemoveLineageCommand::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_last_of('(');
int closeParen = taxon.find_last_of(')');
string newtaxon, confidence;
if ((openParen != string::npos) && (closeParen != string::npos)) {
string confidenceScore = taxon.substr(openParen+1, (closeParen-(openParen+1)));
if (util.isNumeric1(confidenceScore)) { //its a confidence
newtaxon = taxon.substr(0, openParen); //rip off confidence
confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
}else { //its part of the taxon
newtaxon = taxon;
confidence = "0";
}
}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, "RemoveLineageCommand", "getTaxons");
exit(1);
}
}
//**********************************************************************************************************************
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