-/*
- * 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 executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \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);
- }
-}
-/**************************************************************************************/
-
-
-
-
+/*\r
+ * clearcutcommand.cpp\r
+ * Mothur\r
+ *\r
+ * Created by westcott on 5/11/10.\r
+ * Copyright 2010 Schloss Lab. All rights reserved.\r
+ *\r
+ */\r
+\r
+#include "clearcutcommand.h"\r
+\r
+/**************************************************************************************/\r
+ClearcutCommand::ClearcutCommand(string option) { \r
+ try {\r
+ abort = false;\r
+ \r
+ //allow user to run help\r
+ if(option == "help") { help(); abort = true; }\r
+ \r
+ else {\r
+ //valid paramters for this command\r
+ string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",\r
+ "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};\r
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));\r
+ \r
+ OptionParser parser(option);\r
+ map<string,string> parameters = parser.getParameters();\r
+ \r
+ ValidParameters validParameter;\r
+ map<string, string>::iterator it;\r
+ \r
+ //check to make sure all parameters are valid for command\r
+ for (it = parameters.begin(); it != parameters.end(); it++) { \r
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }\r
+ }\r
+ \r
+ //if the user changes the input directory command factory will send this info to us in the output parameter \r
+ string inputDir = validParameter.validFile(parameters, "inputdir", false); \r
+ if (inputDir == "not found"){ inputDir = ""; }\r
+ else {\r
+ string path;\r
+ it = parameters.find("fasta");\r
+ //user has given a template file\r
+ if(it != parameters.end()){ \r
+ path = hasPath(it->second);\r
+ //if the user has not given a path then, add inputdir. else leave path alone.\r
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }\r
+ }\r
+ \r
+ it = parameters.find("phylip");\r
+ //user has given a template file\r
+ if(it != parameters.end()){ \r
+ path = hasPath(it->second);\r
+ //if the user has not given a path then, add inputdir. else leave path alone.\r
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }\r
+ }\r
+ }\r
+\r
+ //check for required parameters\r
+ fastafile = validParameter.validFile(parameters, "fasta", true);\r
+ if (fastafile == "not open") { fastafile = ""; abort = true; }\r
+ else if (fastafile == "not found") { fastafile = ""; } \r
+ else { inputFile = fastafile; }\r
+ \r
+ phylipfile = validParameter.validFile(parameters, "phylip", true);\r
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }\r
+ else if (phylipfile == "not found") { phylipfile = ""; }\r
+ else { inputFile = phylipfile; }\r
+ \r
+ if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); m->mothurOutEndLine(); abort=true; }\r
+ 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; }\r
+\r
+ \r
+ //if the user changes the output directory command factory will send this info to us in the output parameter \r
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }\r
+ \r
+ string temp;\r
+ temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }\r
+ version = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }\r
+ verbose = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }\r
+ quiet = isTrue(temp); \r
+ \r
+ seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }\r
+ \r
+ temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }\r
+ norandom = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }\r
+ shuffle = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }\r
+ neighbor = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "stdin", false); if (temp == "not found"){ temp = "F"; }\r
+ stdinWanted = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }\r
+ DNA = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }\r
+ protein = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }\r
+ jukes = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }\r
+ kimura = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }\r
+ stdoutWanted = isTrue(temp); \r
+ \r
+ matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }\r
+ \r
+ ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }\r
+ \r
+ temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }\r
+ expblen = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }\r
+ expdist = isTrue(temp);\r
+ \r
+ if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }\r
+ }\r
+\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "ClearcutCommand", "ClearcutCommand");\r
+ exit(1);\r
+ }\r
+}\r
+//**********************************************************************************************************************\r
+\r
+void ClearcutCommand::help(){\r
+ try {\r
+ 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");\r
+ m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");\r
+ m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");\r
+ m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdoutWanted, kimura, jukes, protein, DNA, stdinWanted. \n");\r
+ m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");\r
+ 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");\r
+ \r
+ m->mothurOut("The version parameter prints out the version of clearcut you are using, default=F. \n");\r
+ m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");\r
+ m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \n");\r
+ m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");\r
+ m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");\r
+ m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");\r
+ m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");\r
+ \r
+ m->mothurOut("The stdinWanted parameter reads input from STDIN, default=F. \n");\r
+ m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");\r
+ m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");\r
+ \r
+ m->mothurOut("The stdoutWanted parameter outputs your tree to STDOUT, default=F. \n");\r
+ m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");\r
+ m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");\r
+ m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");\r
+ m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n");\r
+\r
+ m->mothurOut("The clearcut command should be in the following format: \n");\r
+ m->mothurOut("clearcut(phylip=yourDistanceFile) \n");\r
+ m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n"); \r
+ \r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "ClearcutCommand", "help");\r
+ exit(1);\r
+ }\r
+}\r
+\r
+/**************************************************************************************/\r
+int ClearcutCommand::execute() { \r
+ try {\r
+ \r
+ if (abort == true) { return 0; }\r
+ \r
+ //prepare filename\r
+ string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";\r
+ \r
+ //get location of clearcut\r
+ GlobalData* globaldata = GlobalData::getInstance();\r
+ string path = globaldata->argv;\r
+ path = path.substr(0, (path.find_last_of('m')));\r
+ \r
+ string clearcutCommand = "";\r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ clearcutCommand = path + "clearcut/clearcut ";\r
+ #else\r
+ clearcutCommand = path + "clearcut\\clearcut ";\r
+ #endif\r
+ \r
+ //you gave us a distance matrix\r
+ if (phylipfile != "") { clearcutCommand += "--distance "; }\r
+ \r
+ //you gave us a fastafile\r
+ if (fastafile != "") { clearcutCommand += "--alignment "; }\r
+ \r
+ if (version) { clearcutCommand += "--version "; }\r
+ if (verbose) { clearcutCommand += "--verbose "; }\r
+ if (quiet) { clearcutCommand += "--quiet "; }\r
+ if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }\r
+ if (norandom) { clearcutCommand += "--norandom "; }\r
+ if (shuffle) { clearcutCommand += "--shuffle "; }\r
+ if (neighbor) { clearcutCommand += "--neighbor "; }\r
+ \r
+ if (stdinWanted) { clearcutCommand += "--stdin "; }\r
+ else{ \r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ clearcutCommand += "--in=" + inputFile + " "; }\r
+ #else\r
+ clearcutCommand += "--in=\"" + inputFile + "\" "; }\r
+ #endif\r
+ if (stdoutWanted) { clearcutCommand += "--stdout "; }\r
+ else{ \r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ clearcutCommand += "--out=" + outputName + " "; }\r
+ #else\r
+ clearcutCommand += "--out=\"" + outputName + "\" "; }\r
+ #endif\r
+ \r
+ if (DNA) { clearcutCommand += "--DNA "; }\r
+ if (protein) { clearcutCommand += "--protein "; }\r
+ if (jukes) { clearcutCommand += "--jukes "; }\r
+ if (kimura) { clearcutCommand += "--kimura "; }\r
+ if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }\r
+ if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }\r
+ if (expblen) { clearcutCommand += "--expblen "; }\r
+ if (expdist) { clearcutCommand += "--expdist "; }\r
+ \r
+ //run clearcut\r
+ system(clearcutCommand.c_str());\r
+ \r
+ if (!stdoutWanted) { \r
+ m->mothurOutEndLine();\r
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();\r
+ m->mothurOut(outputName); m->mothurOutEndLine(); \r
+ m->mothurOutEndLine();\r
+ }\r
+\r
+ return 0;\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "ClearcutCommand", "execute");\r
+ exit(1);\r
+ }\r
+}\r
+/**************************************************************************************/\r
+\r
+\r
+\r
+\r
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