+++ /dev/null
-/*
- * clearcutcommand.cpp
- * Mothur
- *
- * Created by westcott on 5/11/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "clearcutcommand.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-#include "clearcut.h"
-#ifdef __cplusplus
-}
-#endif
-
-//**********************************************************************************************************************
-vector<string> ClearcutCommand::setParameters(){
- try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pverbose);
- CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pquiet);
- CommandParameter pversion("version", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pversion);
- CommandParameter pseed("seed", "String", "", "", "*", "", "",false,false); parameters.push_back(pseed);
- CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnorandom);
- CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshuffle);
- CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pneighbor);
- CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpblen);
- CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpdist);
- CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pDNA);
- CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pprotein);
- CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pjukes);
- CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkimura);
- CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pstdout);
- CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "",false,false); parameters.push_back(pntrees);
- CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "",false,false); parameters.push_back(pmatrixout);
- 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, "ClearcutCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ClearcutCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n";
- helpString += "For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n";
- helpString += "The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n";
- helpString += "The phylip parameter allows you to enter your phylip formatted distance matrix. \n";
- helpString += "The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n";
-
- helpString += "The version parameter prints out the version of clearcut you are using, default=F. \n";
- helpString += "The verbose parameter prints out more output from clearcut, default=F. \n";
- helpString += "The quiet parameter turns on silent operation mode, default=F. \n";
- helpString += "The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n";
- helpString += "The norandom parameter allows you to attempt joins deterministically, default=F. \n";
- helpString += "The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n";
- helpString += "The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n";
-
- helpString += "The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n";
- helpString += "The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n";
-
- helpString += "The stdout parameter outputs your tree to STDOUT, default=F. \n";
- helpString += "The matrixout parameter allows you to specify a filename to output a distance matrix to. \n";
- helpString += "The ntrees parameter allows you to specify the number of output trees, default=1. \n";
- helpString += "The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n";
- helpString += "The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n";
-
- helpString += "The clearcut command should be in the following format: \n";
- helpString += "clearcut(phylip=yourDistanceFile) \n";
- helpString += "Example: clearcut(phylip=abrecovery.phylip.dist) \n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-ClearcutCommand::ClearcutCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
- outputTypes["matrixout"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
- exit(1);
- }
-}
-/**************************************************************************************/
-ClearcutCommand::ClearcutCommand(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["tree"] = tempOutNames;
- outputTypes["matrixout"] = 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("fasta");
- //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["fasta"] = inputDir + it->second; }
- }
-
- it = parameters.find("phylip");
- //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["phylip"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { fastafile = ""; abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
- else { inputFile = fastafile; m->setFastaFile(fastafile); }
-
- phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { phylipfile = ""; abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputFile = phylipfile; m->setPhylipFile(phylipfile); }
-
- if ((phylipfile == "") && (fastafile == "")) {
- //is there are current file available for either of these?
- //give priority to phylip, then fasta
- phylipfile = m->getPhylipFile();
- if (phylipfile != "") { inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
- else {
- fastafile = m->getFastaFile();
- if (fastafile != "") { inputFile = fastafile; m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
- if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }
-
-
- //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 = m->hasPath(inputFile); }
-
- string temp;
- temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }
- version = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }
- verbose = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }
- quiet = m->isTrue(temp);
-
- seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }
-
- temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }
- norandom = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }
- shuffle = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "T"; }
- neighbor = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }
- DNA = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }
- protein = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }
- jukes = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }
- kimura = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }
- stdoutWanted = m->isTrue(temp);
-
- matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }
-
- ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }
-
- temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }
- expblen = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }
- expdist = m->isTrue(temp);
-
- if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
- exit(1);
- }
-}
-/**************************************************************************************/
-int ClearcutCommand::execute() {
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //prepare filename
- string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
- outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
-
- vector<char*> cPara;
-
- char* tempClearcut = new char[8];
- strcpy(tempClearcut, "clearcut");
- cPara.push_back(tempClearcut);
-
- //you gave us a distance matrix
- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); }
-
- //you gave us a fastafile
- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
-
- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); }
- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
- if (seed != "*") {
- string tempSeed = "--seed=" + seed;
- char* temp = new char[tempSeed.length()];
- strcpy(temp, tempSeed.c_str());
- cPara.push_back(temp);
- }
- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
-
- string tempIn = "--in=" + inputFile;
- char* tempI = new char[tempIn.length()];
- strcpy(tempI, tempIn.c_str());
- cPara.push_back(tempI);
-
- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
- else{
- string tempOut = "--out=" + outputName;
-
- char* temp = new char[tempOut.length()];
- strcpy(temp, tempOut.c_str());
- cPara.push_back(temp);
- }
-
- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); }
- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
- if (matrixout != "") {
- string tempMatrix = "--matrixout=" + outputDir + matrixout;
- char* temp = new char[tempMatrix.length()];
- strcpy(temp, tempMatrix.c_str());
- cPara.push_back(temp);
- outputNames.push_back((outputDir + matrixout));
- outputTypes["matrixout"].push_back((outputDir + matrixout));
- }
-
- if (ntrees != "1") {
- string tempNtrees = "--ntrees=" + ntrees;
- char* temp = new char[tempNtrees.length()];
- strcpy(temp, tempNtrees.c_str());
- cPara.push_back(temp);
- }
-
- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
-
- char** clearcutParameters;
- clearcutParameters = new char*[cPara.size()];
- for (int i = 0; i < cPara.size(); i++) { clearcutParameters[i] = cPara[i]; }
- int numArgs = cPara.size();
-
- clearcut_main(numArgs, clearcutParameters);
-
- //free memory
- for(int i = 0; i < cPara.size(); i++) { delete[] cPara[i]; }
- delete[] clearcutParameters;
-
- if (!stdoutWanted) {
-
- //set first tree file as new current treefile
- string currentTree = "";
- itTypes = outputTypes.find("tree");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
- }
-
- 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, "ClearcutCommand", "execute");
- exit(1);
- }
-}
-/**************************************************************************************/
-
-
-
-
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