--- /dev/null
+/*
+ * clearcutcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/11/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "clearcutcommand.h"
+#include "globaldata.hpp"
+
+/**************************************************************************************/
+ClearcutCommand::ClearcutCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
+ "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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; }
+ }
+
+ //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 = 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 = 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; }
+
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { inputFile = phylipfile; }
+
+ if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); 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 = ""; }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }
+ version = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }
+ verbose = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }
+ quiet = 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 = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }
+ shuffle = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }
+ neighbor = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "stdin", false); if (temp == "not found"){ temp = "F"; }
+ stdin = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }
+ DNA = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }
+ protein = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }
+ jukes = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }
+ kimura = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }
+ stdout = 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 = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }
+ expdist = 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);
+ }
+}
+//**********************************************************************************************************************
+
+void ClearcutCommand::help(){
+ try {
+ m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
+ m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
+ m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA, stdin. \n");
+ m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
+ m->mothurOut("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");
+
+ m->mothurOut("The version parameter prints out the version of clearcut you are using, default=F. \n");
+ m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");
+ m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \n");
+ m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");
+ m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");
+ m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");
+ m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");
+
+ m->mothurOut("The stdin parameter reads input from STDIN, default=F. \n");
+ m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");
+ m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");
+
+ m->mothurOut("The stdout parameter outputs your tree to STDOUT, default=F. \n");
+ m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");
+ m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");
+ m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");
+ m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n");
+
+ m->mothurOut("The clearcut command should be in the following format: \n");
+ m->mothurOut("clearcut(phylip=yourDistanceFile) \n");
+ m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "help");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+int ClearcutCommand::execute() {
+ try {
+
+ if (abort == true) { return 0; }
+
+ //prepare filename
+ string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
+
+ //get location of clearcut
+ GlobalData* globaldata = GlobalData::getInstance();
+ string path = globaldata->argv;
+ path = path.substr(0, (path.find_last_of('m')));
+
+ string clearcutCommand = path + "clearcut/clearcut ";
+
+ //you gave us a distance matrix
+ if (phylipfile != "") { clearcutCommand += "--distance "; }
+
+ //you gave us a fastafile
+ if (fastafile != "") { clearcutCommand += "--alignment "; }
+
+ if (version) { clearcutCommand += "--version "; }
+ if (verbose) { clearcutCommand += "--verbose "; }
+ if (quiet) { clearcutCommand += "--quiet "; }
+ if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }
+ if (norandom) { clearcutCommand += "--norandom "; }
+ if (shuffle) { clearcutCommand += "--shuffle "; }
+ if (neighbor) { clearcutCommand += "--neighbor "; }
+
+ if (stdin) { clearcutCommand += "--stdin "; }
+ else { clearcutCommand += "--in=" + inputFile + " "; }
+ if (stdout) { clearcutCommand += "--stdout "; }
+ else { clearcutCommand += "--out=" + outputName + " "; }
+
+ if (DNA) { clearcutCommand += "--DNA "; }
+ if (protein) { clearcutCommand += "--protein "; }
+ if (jukes) { clearcutCommand += "--jukes "; }
+ if (kimura) { clearcutCommand += "--kimura "; }
+ if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }
+ if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }
+ if (expblen) { clearcutCommand += "--expblen "; }
+ if (expdist) { clearcutCommand += "--expdist "; }
+
+ //run clearcut
+ system(clearcutCommand.c_str());
+
+ if (!stdout) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************/
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