+++ /dev/null
-/*
- * phylotypecommand.cpp
- * Mothur
- *
- * Created by westcott on 11/20/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "phylotypecommand.h"
-#include "phylotree.h"
-#include "listvector.hpp"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-
-//**********************************************************************************************************************
-vector<string> PhylotypeCommand::setParameters(){
- try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); 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, 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);
- }
-}
-
-//**********************************************************************************************************************
-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) {
- 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["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; }
- }
- }
-
- taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
- if (taxonomyFileName == "not found") {
- 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); }
-
- //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
- }
-
- string temp = validParameter.validFile(parameters, "cutoff", false);
- if (temp == "not found") { temp = "-1"; }
- m->mothurConvert(temp, cutoff);
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; allLines = 1; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- if (namefile == "") {
- vector<string> files; files.push_back(taxonomyFileName);
- parser.getNameFile(files);
- }
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
- exit(1);
- }
-}
-/**********************************************************************************************************************/
-
-int PhylotypeCommand::execute(){
- try {
-
- 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, outputDir);
-
- if (m->control_pressed) { delete taxEqual; return 0; }
-
- string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
-
- delete taxEqual;
-
- //build taxonomy tree from equalized file
- PhyloTree* tree = new PhyloTree(equalizedTaxFile);
- vector<int> leaves = tree->getGenusNodes();
-
- //store leaf nodes in current map
- for (int i = 0; i < leaves.size(); i++) { currentNodes[leaves[i]] = leaves[i]; }
-
- bool done = false;
- if (tree->get(leaves[0]).parent == -1) { m->mothurOut("Empty Tree"); m->mothurOutEndLine(); done = true; }
-
- if (m->control_pressed) { delete tree; return 0; }
-
- string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
-
- ofstream outList;
- string outputListFile = fileroot + "tx.list";
- m->openOutputFile(outputListFile, outList);
- ofstream outSabund;
- string outputSabundFile = fileroot + "tx.sabund";
- m->openOutputFile(outputSabundFile, outSabund);
- ofstream outRabund;
- string outputRabundFile = fileroot + "tx.rabund";
- m->openOutputFile(outputRabundFile, outRabund);
-
- outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
- outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
- outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
-
- 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) {
- 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
- m->mothurOut(level); m->mothurOutEndLine();
-
- ListVector list;
- list.setLabel(level);
-
- //go through nodes and build listvector
- for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
-
- //get parents
- TaxNode node = tree->get(itCurrent->first);
- parentNodes[node.parent] = node.parent;
-
- vector<string> names = node.accessions;
-
- //make the names compatable with listvector
- string name = "";
- 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(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1); }
-
- }else{ name += names[i] + ","; }
- }
- }
- name = name.substr(0, name.length()-1); //rip off extra ','
- //add bin to list vector
- 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);
-
- labels.erase(level);
-
- }else {
-
- //just get parents
- for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
- int parent = tree->get(itCurrent->first).parent;
- parentNodes[parent] = parent;
- }
- }
-
- //move up a level
- currentNodes = parentNodes;
- parentNodes.clear();
-
- //have we reached the rootnode
- if (tree->get(currentNodes.begin()->first).parent == -1) { done = true; }
- }
-
- outList.close();
- 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) {
- 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);
- }
-}
-
-/**********************************************************************************************************************/
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