5 * Created by Sarah Westcott on 5/7/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "distancecommand.h"
11 #include "ignoregaps.h"
12 #include "eachgapdist.h"
13 #include "eachgapignore.h"
14 #include "onegapdist.h"
15 #include "onegapignore.h"
17 //**********************************************************************************************************************
19 DistanceCommand::DistanceCommand(string option){
24 //allow user to run help
25 if(option == "help") { help(); abort = true; }
28 //valid paramters for this command
29 string Array[] = {"fasta", "phylip", "calc", "countends", "cutoff", "processors", "outputdir","inputdir"};
30 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
32 OptionParser parser(option);
33 map<string, string> parameters = parser.getParameters();
35 ValidParameters validParameter;
36 map<string, string>::iterator it2;
38 //check to make sure all parameters are valid for command
39 for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
40 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
43 //if the user changes the input directory command factory will send this info to us in the output parameter
44 string inputDir = validParameter.validFile(parameters, "inputdir", false);
45 if (inputDir == "not found"){ inputDir = ""; }
48 it2 = parameters.find("fasta");
49 //user has given a template file
50 if(it2 != parameters.end()){
51 path = hasPath(it2->second);
52 //if the user has not given a path then, add inputdir. else leave path alone.
53 if (path == "") { parameters["fasta"] = inputDir + it2->second; }
57 //check for required parameters
58 fastafile = validParameter.validFile(parameters, "fasta", true);
59 if (fastafile == "not found") { mothurOut("fasta is a required parameter for the dist.seqs command."); mothurOutEndLine(); abort = true; }
60 else if (fastafile == "not open") { abort = true; }
63 openInputFile(fastafile, inFASTA);
64 alignDB = SequenceDB(inFASTA);
68 //if the user changes the output directory command factory will send this info to us in the output parameter
69 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
71 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
74 //check for optional parameter and set defaults
75 // ...at some point should added some additional type checking...
76 calc = validParameter.validFile(parameters, "calc", false);
77 if (calc == "not found") { calc = "onegap"; }
79 if (calc == "default") { calc = "onegap"; }
81 splitAtDash(calc, Estimators);
84 temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
85 convert(temp, countends);
87 temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
88 convert(temp, cutoff);
90 temp = validParameter.validFile(parameters, "processors", false); if(temp == "not found"){ temp = "1"; }
91 convert(temp, processors);
93 phylip = validParameter.validFile(parameters, "phylip", false); if(phylip == "not found"){ phylip = "F"; }
96 ValidCalculators validCalculator;
98 if (isTrue(countends) == true) {
99 for (int i=0; i<Estimators.size(); i++) {
100 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
101 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
102 else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
103 else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
107 for (int i=0; i<Estimators.size(); i++) {
108 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
109 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
110 else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
111 else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
119 catch(exception& e) {
120 errorOut(e, "DistanceCommand", "DistanceCommand");
125 //**********************************************************************************************************************
127 DistanceCommand::~DistanceCommand(){
129 for(int i=0;i<lines.size();i++){
135 //**********************************************************************************************************************
137 void DistanceCommand::help(){
139 mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
140 mothurOut("The dist.seqs command parameters are fasta, calc, countends, cutoff and processors. \n");
141 mothurOut("The fasta parameter is required.\n");
142 mothurOut("The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
143 mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n");
144 mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
145 mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
146 mothurOut("The dist.seqs command should be in the following format: \n");
147 mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
148 mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
149 mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
151 catch(exception& e) {
152 errorOut(e, "DistanceCommand", "help");
156 //**********************************************************************************************************************
158 int DistanceCommand::execute(){
161 if (abort == true) { return 0; }
163 int numSeqs = alignDB.getNumSeqs();
168 //doses the user want the phylip formatted file as well
169 if (isTrue(phylip) == true) {
170 outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
171 remove(outputFile.c_str());
173 //output numSeqs to phylip formatted dist file
174 }else { //user wants column format
175 outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
176 remove(outputFile.c_str());
179 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
180 //if you don't need to fork anything
182 driver(0, numSeqs, outputFile, cutoff);
183 }else{ //you have multiple processors
185 for (int i = 0; i < processors; i++) {
186 lines.push_back(new linePair());
187 lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
188 lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
191 createProcesses(outputFile);
193 map<int, int>::iterator it = processIDS.begin();
194 rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
197 //append and remove temp files
198 for (; it != processIDS.end(); it++) {
199 appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
200 remove((outputFile + toString(it->second) + ".temp").c_str());
205 driver(0, numSeqs, outputFile, cutoff);
208 delete distCalculator;
213 catch(exception& e) {
214 errorOut(e, "DistanceCommand", "execute");
218 /**************************************************************************************************/
219 void DistanceCommand::createProcesses(string filename) {
221 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
225 //loop through and create all the processes you want
226 while (process != processors) {
230 processIDS[lines[process]->end] = pid; //create map from line number to pid so you can append files in correct order later
233 driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
235 }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
238 //force parent to wait until all the processes are done
239 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
240 int temp = it->second;
245 catch(exception& e) {
246 errorOut(e, "DistanceCommand", "createProcesses");
251 /**************************************************************************************************/
252 /////// need to fix to work with calcs and sequencedb
253 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
256 int startTime = time(NULL);
259 ofstream outFile(dFileName.c_str(), ios::trunc);
260 outFile.setf(ios::fixed, ios::showpoint);
261 outFile << setprecision(4);
263 if(isTrue(phylip) && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
265 for(int i=startLine;i<endLine;i++){
267 string name = alignDB.get(i).getName();
268 if (name.length() < 10) { //pad with spaces to make compatible
269 while (name.length() < 10) { name += " "; }
271 outFile << name << '\t';
273 for(int j=0;j<i;j++){
274 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
275 double dist = distCalculator->getDist();
278 if (!isTrue(phylip)) { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
280 if (isTrue(phylip)) { outFile << dist << '\t'; }
284 if (isTrue(phylip) == true) { outFile << endl; }
287 mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); mothurOutEndLine();
291 mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); mothurOutEndLine();
297 catch(exception& e) {
298 errorOut(e, "DistanceCommand", "driver");
303 /**************************************************************************************************
304 void DistanceCommand::appendFiles(string temp, string filename) {
309 //open output file in append mode
310 openOutputFileAppend(filename, output);
311 openInputFile(temp, input);
313 while(char c = input.get()){
314 if(input.eof()) { break; }
315 else { output << c; }
321 catch(exception& e) {
322 errorOut(e, "DistanceCommand", "appendFiles");
326 /**************************************************************************************************/