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", "output", "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") { m->mothurOut("fasta is a required parameter for the dist.seqs command."); m->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 output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
95 if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
97 ValidCalculators validCalculator;
99 if (isTrue(countends) == true) {
100 for (int i=0; i<Estimators.size(); i++) {
101 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
102 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
103 else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
104 else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
108 for (int i=0; i<Estimators.size(); i++) {
109 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
110 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
111 else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
112 else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
120 catch(exception& e) {
121 m->errorOut(e, "DistanceCommand", "DistanceCommand");
126 //**********************************************************************************************************************
128 DistanceCommand::~DistanceCommand(){
130 for(int i=0;i<lines.size();i++){
136 //**********************************************************************************************************************
138 void DistanceCommand::help(){
140 m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
141 m->mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors. \n");
142 m->mothurOut("The fasta parameter is required.\n");
143 m->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");
144 m->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");
145 m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
146 m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
147 m->mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
148 m->mothurOut("The dist.seqs command should be in the following format: \n");
149 m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
150 m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
151 m->mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
153 catch(exception& e) {
154 m->errorOut(e, "DistanceCommand", "help");
158 //**********************************************************************************************************************
160 int DistanceCommand::execute(){
163 if (abort == true) { return 0; }
165 int startTime = time(NULL);
167 int numSeqs = alignDB.getNumSeqs();
172 if (output == "lt") { //does the user want lower triangle phylip formatted file
173 outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
174 remove(outputFile.c_str());
176 //output numSeqs to phylip formatted dist file
177 }else if (output == "column") { //user wants column format
178 outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
179 remove(outputFile.c_str());
180 }else { //assume square
181 outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "square.dist";
182 remove(outputFile.c_str());
192 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
193 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
195 //each process gets where it should start and stop in the file
196 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
197 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
199 if (output != "lt") {
201 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
203 char filename[outputFile.length()];
204 strcpy(filename, outputFile.c_str());
206 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
208 if (pid == 0) { //you are the root process
212 driverMPI(start, end, outMPI, cutoff);
214 if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
217 for(int i = 1; i < processors; i++) {
218 if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
221 MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
223 }else { //you are a child process
225 driverMPI(start, end, outMPI, cutoff);
227 if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
231 //tell parent you are done.
232 MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
235 MPI_File_close(&outMPI);
237 }else { //lower triangle format
238 if (pid == 0) { //you are the root process
243 driverMPI(start, end, outputFile, mySize);
245 if (m->control_pressed) { delete distCalculator; return 0; }
247 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
251 char filename[outputFile.length()];
252 strcpy(filename, outputFile.c_str());
254 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
257 for(int b = 1; b < processors; b++) {
260 if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
262 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
264 string outTemp = outputFile + toString(b) + ".temp";
265 char buf[outTemp.length()];
266 strcpy(buf, outTemp.c_str());
268 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
271 while (count < fileSize) { //read 1000 characters at a time
274 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
275 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
279 MPI_File_close(&inMPI); //deleted on close
282 MPI_File_close(&outMPI);
283 }else { //you are a child process
286 driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
288 if (m->control_pressed) { delete distCalculator; return 0; }
290 //tell parent you are done.
291 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
296 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
297 //if you don't need to fork anything
299 driver(0, numSeqs, outputFile, cutoff);
300 }else{ //you have multiple processors
302 for (int i = 0; i < processors; i++) {
303 lines.push_back(new linePair());
304 lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
305 lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
308 createProcesses(outputFile);
310 map<int, int>::iterator it = processIDS.begin();
311 rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
314 //append and remove temp files
315 for (; it != processIDS.end(); it++) {
316 appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
317 remove((outputFile + toString(it->second) + ".temp").c_str());
322 driver(0, numSeqs, outputFile, cutoff);
326 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
329 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
331 if (pid == 0) { //only one process should output to screen
334 if (output == "square") { convertMatrix(outputFile); }
340 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
342 delete distCalculator;
344 m->mothurOutEndLine();
345 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
346 m->mothurOut(outputFile); m->mothurOutEndLine();
347 m->mothurOutEndLine();
348 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
352 catch(exception& e) {
353 m->errorOut(e, "DistanceCommand", "execute");
357 /**************************************************************************************************/
358 void DistanceCommand::createProcesses(string filename) {
360 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
364 //loop through and create all the processes you want
365 while (process != processors) {
369 processIDS[lines[process]->end] = pid; //create map from line number to pid so you can append files in correct order later
372 driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
374 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
377 //force parent to wait until all the processes are done
378 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
379 int temp = it->second;
384 catch(exception& e) {
385 m->errorOut(e, "DistanceCommand", "createProcesses");
390 /**************************************************************************************************/
391 /////// need to fix to work with calcs and sequencedb
392 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
395 int startTime = time(NULL);
398 ofstream outFile(dFileName.c_str(), ios::trunc);
399 outFile.setf(ios::fixed, ios::showpoint);
400 outFile << setprecision(4);
402 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
404 for(int i=startLine;i<endLine;i++){
406 string name = alignDB.get(i).getName();
407 if (name.length() < 10) { //pad with spaces to make compatible
408 while (name.length() < 10) { name += " "; }
410 outFile << name << '\t';
412 for(int j=0;j<i;j++){
414 if (m->control_pressed) { outFile.close(); return 0; }
416 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
417 double dist = distCalculator->getDist();
420 if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
422 if (output == "lt") { outFile << dist << '\t'; }
424 if (output == "square") { //make a square column you can convert to square phylip
425 outFile << alignDB.get(i).getName() << '\t' << alignDB.get(j).getName() << '\t' << dist << endl;
426 outFile << alignDB.get(j).getName() << '\t' << alignDB.get(i).getName() << '\t' << dist << endl;
431 if (output == "lt") { outFile << endl; }
434 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
438 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
444 catch(exception& e) {
445 m->errorOut(e, "DistanceCommand", "driver");
450 /**************************************************************************************************/
451 /////// need to fix to work with calcs and sequencedb
452 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
455 int startTime = time(NULL);
457 string outputString = "";
459 for(int i=startLine;i<endLine;i++){
461 for(int j=0;j<i;j++){
463 if (m->control_pressed) { return 0; }
465 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
466 double dist = distCalculator->getDist();
469 if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
472 if (output == "square") { //make a square column you can convert to square phylip
473 outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
474 outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
479 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
480 cout << i << '\t' << (time(NULL) - startTime) << endl;
484 //send results to parent
485 int length = outputString.length();
487 strcpy(buf, outputString.c_str());
489 MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
494 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
495 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
498 catch(exception& e) {
499 m->errorOut(e, "DistanceCommand", "driverMPI");
503 /**************************************************************************************************/
504 /////// need to fix to work with calcs and sequencedb
505 int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
510 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
512 char filename[file.length()];
513 strcpy(filename, file.c_str());
515 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
517 int startTime = time(NULL);
519 string outputString = "";
522 if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
524 for(int i=startLine;i<endLine;i++){
526 string name = alignDB.get(i).getName();
527 if (name.length() < 10) { //pad with spaces to make compatible
528 while (name.length() < 10) { name += " "; }
530 outputString += name + "\t";
532 for(int j=0;j<i;j++){
534 if (m->control_pressed) { return 0; }
536 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
537 double dist = distCalculator->getDist();
539 if (output == "lt") { outputString += toString(dist) + "\t"; }
542 if (output == "lt") { outputString += "\n"; }
546 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
547 cout << i << '\t' << (time(NULL) - startTime) << endl;
551 //send results to parent
552 int length = outputString.length();
554 strcpy(buf, outputString.c_str());
556 MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
557 size += outputString.length();
563 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
564 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
565 MPI_File_close(&outMPI);
569 catch(exception& e) {
570 m->errorOut(e, "DistanceCommand", "driverMPI");
575 /**************************************************************************************************/
576 int DistanceCommand::convertMatrix(string outputFile) {
579 //sort file by first column so the distances for each row are together
580 string outfile = getRootName(outputFile) + "sorted.dist.temp";
583 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
584 string command = "sort -n " + outputFile + " -o " + outfile;
585 system(command.c_str());
586 #else //sort using windows sort
587 string command = "sort " + outputFile + " /O " + outfile;
588 system(command.c_str());
592 //output to new file distance for each row and save positions in file where new row begins
594 openInputFile(outfile, in);
597 openOutputFile(outputFile, out);
599 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
601 out << alignDB.getNumSeqs() << endl;
603 //get first currentRow
604 string first, currentRow, second;
606 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
607 map<string, float>::iterator it;
612 rowDists[first] = 0.00; //distance to yourself is 0.0
615 //openInputFile(outfile, in);
618 if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
620 in >> first >> second >> dist; gobble(in);
622 if (first != currentRow) {
624 out << currentRow << '\t'; //print name
627 for (it = rowDists.begin(); it != rowDists.end(); it++) {
628 out << it->second << '\t';
635 rowDists[first] = 0.00;
636 rowDists[second] = dist;
638 rowDists[second] = dist;
642 out << currentRow << '\t'; //print name
645 for (it = rowDists.begin(); it != rowDists.end(); it++) {
646 out << it->second << '\t';
653 remove(outfile.c_str());
658 catch(exception& e) {
659 m->errorOut(e, "DistanceCommand", "convertMatrix");
663 /**************************************************************************************************/
664 int DistanceCommand::convertToLowerTriangle(string outputFile) {
667 //sort file by first column so the distances for each row are together
668 string outfile = getRootName(outputFile) + "sorted.dist.temp";
671 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
672 string command = "sort -n " + outputFile + " -o " + outfile;
673 system(command.c_str());
674 #else //sort using windows sort
675 string command = "sort " + outputFile + " /O " + outfile;
676 system(command.c_str());
680 //output to new file distance for each row and save positions in file where new row begins
682 openInputFile(outfile, in);
685 openOutputFile(outputFile, out);
687 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
689 out << alignDB.getNumSeqs() << endl;
691 //get first currentRow
692 string first, currentRow, second;
696 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
697 map<string, float>::iterator it;
702 rowDists[first] = 0.00; //distance to yourself is 0.0
705 //openInputFile(outfile, in);
708 if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
710 in >> first >> second >> dist; gobble(in);
712 if (first != currentRow) {
714 out << currentRow << '\t'; //print name
717 for (it = rowDists.begin(); it != rowDists.end(); it++) {
718 if (j >= i) { break; }
719 out << it->second << '\t';
727 rowDists[first] = 0.00;
728 rowDists[second] = dist;
732 rowDists[second] = dist;
736 out << currentRow << '\t'; //print name
739 for (it = rowDists.begin(); it != rowDists.end(); it++) {
740 out << it->second << '\t';
747 remove(outfile.c_str());
752 catch(exception& e) {
753 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
757 /**************************************************************************************************
758 void DistanceCommand::appendFiles(string temp, string filename) {
763 //open output file in append mode
764 openOutputFileAppend(filename, output);
765 openInputFile(temp, input);
767 while(char c = input.get()){
768 if(input.eof()) { break; }
769 else { output << c; }
775 catch(exception& e) {
776 m->errorOut(e, "DistanceCommand", "appendFiles");
780 /**************************************************************************************************/