#include "sequence.hpp"
#include "listvector.hpp"
-//**********************************************************************************************************************
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetLineageCommand::GetLineageCommand(){
+ try {
+ abort = true; calledHelp = true;
+ 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);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"taxonomy","taxon"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetLineageCommand::GetLineageCommand(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
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 = ""; }
else if (taxfile == "not found") { taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); 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);
m->mothurOut("The get.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 get.\n");
+ m->mothurOut("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");
+ m->mothurOut("If they belong to the taxonomy and have confidences below those you provide the sequence will not be selected.\n");
m->mothurOut("The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
m->mothurOut("Example get.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");
int GetLineageCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
if (listfile != "") { readList(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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;
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
return 0;
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
return 0;
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
return 0;
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
return 0;
m->openInputFile(taxfile, in);
string name, tax;
- bool wroteSomething = false;
+ //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()){
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) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ }
+
+ }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) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ }
+ }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 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[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
+ good = false;
+ break;
+ }
+ }else {
+ good = false;
+ break;
+ }
+ }
+
+ //passed the test so add you
+ if (good) {
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ }
+ }
+ }
}
- int pos = newtax.find(taxons);
- if (pos != string::npos) { //this sequence contains the taxon the user wants
- names.insert(name);
- out << name << '\t' << tax << endl;
- }
m->gobble(in);
}
out.close();
if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
return 0;
}
}
/**************************************************************************************************/
+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);
+ }
+}
+/**************************************************************************************************/
string GetLineageCommand::removeConfidences(string tax) {
try {
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
return 0;
projects / mothur.git / blobdiff