#include "listvector.hpp"
//**********************************************************************************************************************
-vector<string> RemoveLineageCommand::getValidParameters(){
+vector<string> RemoveLineageCommand::setParameters(){
try {
- string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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, "RemoveLineageCommand", "getValidParameters");
+ m->errorOut(e, "RemoveLineageCommand", "setParameters");
exit(1);
}
}
+//**********************************************************************************************************************
+string RemoveLineageCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The remove.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 not from the taxon you requested to be removed.\n";
+ helpString += "The remove.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 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 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";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+
//**********************************************************************************************************************
RemoveLineageCommand::RemoveLineageCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
}
}
//**********************************************************************************************************************
-vector<string> RemoveLineageCommand::getRequiredParameters(){
- try {
- string Array[] = {"taxonomy"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveLineageCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> RemoveLineageCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveLineageCommand", "getRequiredFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
RemoveLineageCommand::RemoveLineageCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { abort = true; }
- else if (taxfile == "not found") { taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine(); 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; }
+ }
string usedDups = "true";
- string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
+ 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);
}
//**********************************************************************************************************************
-void RemoveLineageCommand::help(){
- try {
- m->mothurOut("The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n");
- m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n");
- m->mothurOut("The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy and taxon.\n");
- m->mothurOut("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");
- m->mothurOut("The taxon parameter allows you to select the taxons you would like to remove.\n");
- m->mothurOut("The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
- m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
- m->mothurOut("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");
- m->mothurOut("Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveLineageCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int RemoveLineageCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
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;
in >> secondCol;
vector<string> parsedNames;
- //parse second column saving each name
- while (secondCol.find_first_of(',') != -1) {
- name = secondCol.substr(0,secondCol.find_first_of(','));
- secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- parsedNames.push_back(name);
- }
+ m->splitAtComma(secondCol, parsedNames);
- //get name after last ,
- parsedNames.push_back(secondCol);
-
vector<string> validSecond; validSecond.clear();
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) == 0) {
bool wroteSomething = false;
+ bool taxonsHasConfidence = false;
+ vector< map<string, float> > searchTaxons;
+ string noConfidenceTaxons = taxons;
+ int hasConPos = taxons.find_first_of('(');
+ if (hasConPos != string::npos) {
+ taxonsHasConfidence = true;
+ searchTaxons = getTaxons(taxons);
+ noConfidenceTaxons = removeConfidences(taxons);
+ }
+
+
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
string newtax = tax;
- //if the users file contains confidence scores we want to ignore them when searching for the taxons
- int hasConfidences = tax.find_first_of('(');
- if (hasConfidences != string::npos) {
- newtax = removeConfidences(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) {
+
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = removeConfidences(tax);
+ }
+
+ int pos = newtax.find(taxons);
+
+ if (pos == string::npos) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(name);
+ }
+
+ }else{//if taxons has them and you don't them remove taxons
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences == string::npos) {
+
+ int pos = newtax.find(noConfidenceTaxons);
+
+ if (pos == string::npos) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(name);
+ }
+ }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 = removeConfidences(tax);
+ }
+
+ int pos = noNewTax.find(noConfidenceTaxons);
+
+ if (pos != string::npos) { //if yes, then are the confidences okay
+
+ bool remove = false;
+ 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[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.size()) && ((i+spot) < usersTaxon.size())) {
+ if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
+ else { spot++; }
+ }
+
+ if (goodspot) { break; }
+ }
+ }
+
+ for (int i = 0; i < searchTaxons.size(); i++) {
+
+ if ((i+index) < usersTaxon.size()) { //just in case, should never be false
+ if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
+ remove = true;
+ break;
+ }
+ }else {
+ remove = true;
+ break;
+ }
+ }
+
+ //passed the test so remove you
+ if (remove) {
+ names.insert(name);
+ }else {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }
+ }else {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }
+ }
}
- int pos = newtax.find(taxons);
- if (pos == string::npos) {
- wroteSomething = true;
- out << name << '\t' << tax << endl;
- }else{ //this sequence contains the taxon the user wants to remove
- names.insert(name);
- }
+
m->gobble(in);
}
}
}
/**************************************************************************************************/
+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_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, "RemoveLineageCommand", "getTaxons");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
string RemoveLineageCommand::removeConfidences(string tax) {
try {
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