#include "rabundvector.hpp"
#include "sabundvector.hpp"
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::setParameters(){
+ try {
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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, "PhylotypeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PhylotypeCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
+ helpString += "The phylotype command parameter options are taxonomy, name, count, cutoff and label. The taxonomy parameter is required.\n";
+ helpString += "The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n";
+ helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
+ helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
+ helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n";
+ helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
+ helpString += "The phylotype command should be in the following format: \n";
+ helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
+ helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PhylotypeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
-PhylotypeCommand::PhylotypeCommand(string option){
+PhylotypeCommand::PhylotypeCommand(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 if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
-
- //valid paramters for this command
- string AlignArray[] = {"taxonomy","cutoff","label"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ 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 (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+
+ //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("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; }
+ }
+
+ 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("count");
+ //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["count"] = inputDir + it->second; }
+ }
+ }
+
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
if (taxonomyFileName == "not found") {
- mothurOut("taxonomy is a required parameter for the phylotype command.");
- mothurOutEndLine();
- abort = true;
- }else if (taxonomyFileName == "not open") { abort = true; }
+ taxonomyFileName = m->getTaxonomyFile();
+ if (taxonomyFileName != "") { m->mothurOut("Using " + taxonomyFileName + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }
+ else { m->setTaxonomyFile(taxonomyFileName); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { readNamesFile(); m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ //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 = "";
+ outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
+ }
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
string temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "-1"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(taxonomyFileName);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
- errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
- exit(1);
- }
-}
-/**********************************************************************************************************************/
-
-void PhylotypeCommand::help(){
- try {
- mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
- mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
- mothurOut("The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n");
- mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
- mothurOut("For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n");
- mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n");
- mothurOut("For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n");
- mothurOut("The phylotype command should be in the following format: \n");
- mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
- mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "PhylotypeCommand", "help");
+ m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
exit(1);
}
}
/**********************************************************************************************************************/
-PhylotypeCommand::~PhylotypeCommand(){}
-
-/**********************************************************************************************************************/
-
int PhylotypeCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//reads in taxonomy file and makes all the taxonomies the same length
//by appending the last taxon to a given taxonomy as many times as needed to
//make it as long as the longest taxonomy in the file
- TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff);
+ TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
+
+ if (m->control_pressed) { delete taxEqual; return 0; }
string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
for (int i = 0; i < leaves.size(); i++) { currentNodes[leaves[i]] = leaves[i]; }
bool done = false;
- if (tree->get(leaves[0]).parent == -1) { mothurOut("Empty Tree"); mothurOutEndLine(); done = true; }
-
- ofstream outList;
- string outputListFile = getRootName(taxonomyFileName) + "tx.list";
- openOutputFile(outputListFile, outList);
- ofstream outSabund;
- string outputSabundFile = getRootName(taxonomyFileName) + "tx.sabund";
- openOutputFile(outputSabundFile, outSabund);
- ofstream outRabund;
- string outputRabundFile = getRootName(taxonomyFileName) + "tx.rabund";
- openOutputFile(outputRabundFile, outRabund);
+ if (tree->get(leaves[0]).parent == -1) { m->mothurOut("Empty Tree"); m->mothurOutEndLine(); done = true; }
+ if (m->control_pressed) { delete tree; return 0; }
+
+ ofstream outList, outRabund, outSabund;
+ map<string, string> variables;
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
+ variables["[filename]"] = fileroot;
+ variables["[clustertag]"] = "tx";
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+ string listFileName = getOutputFileName("list", variables);
+
+ if (countfile == "") {
+ m->openOutputFile(sabundFileName, outSabund);
+ m->openOutputFile(rabundFileName, outRabund);
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+
+ }
+ m->openOutputFile(listFileName, outList);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+
+
int count = 1;
//start at leaves of tree and work towards root, processing the labels the user wants
while((!done) && ((allLines == 1) || (labels.size() != 0))) {
string level = toString(count);
count++;
+ if (m->control_pressed) {
+ if (countfile == "") { outRabund.close(); outSabund.close(); } outList.close();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
+ delete tree; return 0;
+ }
+
//is this a level the user want output for
if(allLines == 1 || labels.count(level) == 1){
//output level
- mothurOut(level); mothurOutEndLine();
+ m->mothurOut(level); m->mothurOutEndLine();
ListVector list;
list.setLabel(level);
+
//go through nodes and build listvector
for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
//make the names compatable with listvector
string name = "";
- for (int i = 0; i < names.size(); i++) { name += names[i] + ","; }
+ for (int i = 0; i < names.size(); i++) {
+
+ if (names[i] != "unknown") {
+ if (namefile != "") {
+ map<string, string>::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile
+
+ if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile
+ else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ }else{ name += names[i] + ","; }
+ }
+ }
+
+ if (m->control_pressed) { break; }
+
name = name.substr(0, name.length()-1); //rip off extra ','
-
//add bin to list vector
- list.push_back(name);
+ if (name != "") { list.push_back(name); } //caused by unknown
}
//print listvector
- list.print(outList);
- //print rabund
- list.getRAbundVector().print(outRabund);
- //print sabund
- list.getSAbundVector().print(outSabund);
-
+ if (!m->printedListHeaders) { list.printHeaders(outList); }
+ list.print(outList);
+
+ if (countfile == "") {
+ //print rabund
+ list.getRAbundVector().print(outRabund);
+ //print sabund
+ list.getSAbundVector().print(outSabund);
+ }
labels.erase(level);
}else {
}
outList.close();
- outSabund.close();
- outRabund.close();
+ if (countfile == "") {
+ outSabund.close();
+ outRabund.close();
+ }
delete tree;
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
+ return 0;
+ }
+
+ //set list file as new current listfile
+ string current = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ //set rabund file as new current rabundfile
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ //set sabund file as new current sabundfile
+ itTypes = outputTypes.find("sabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+ }
+
+ 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();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "PhylotypeCommand", "execute");
+ m->errorOut(e, "PhylotypeCommand", "execute");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int PhylotypeCommand::readNamesFile() {
+ try {
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; m->gobble(in);
+
+ itNames = namemap.find(first);
+ if (itNames == namemap.end()) {
+ namemap[first] = second;
+ }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "readNamesFile");
exit(1);
}
}
+
/**********************************************************************************************************************/
projects / mothur.git / blobdiff