2 * filterseqscommand.cpp
5 * Created by Thomas Ryabin on 5/4/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "filterseqscommand.h"
11 #include "sequence.hpp"
13 //**********************************************************************************************************************
14 vector<string> FilterSeqsCommand::getValidParameters(){
16 string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
17 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
21 m->errorOut(e, "FilterSeqsCommand", "getValidParameters");
25 //**********************************************************************************************************************
26 FilterSeqsCommand::FilterSeqsCommand(){
28 abort = true; calledHelp = true;
29 vector<string> tempOutNames;
30 outputTypes["fasta"] = tempOutNames;
31 outputTypes["filter"] = tempOutNames;
34 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
38 //**********************************************************************************************************************
39 vector<string> FilterSeqsCommand::getRequiredParameters(){
41 string Array[] = {"fasta"};
42 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
46 m->errorOut(e, "FilterSeqsCommand", "getRequiredParameters");
50 //**********************************************************************************************************************
51 vector<string> FilterSeqsCommand::getRequiredFiles(){
53 vector<string> myArray;
57 m->errorOut(e, "FilterSeqsCommand", "getRequiredFiles");
61 /**************************************************************************************/
62 FilterSeqsCommand::FilterSeqsCommand(string option) {
64 abort = false; calledHelp = false;
67 //allow user to run help
68 if(option == "help") { help(); abort = true; calledHelp = true; }
71 //valid paramters for this command
72 string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
73 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
75 OptionParser parser(option);
76 map<string,string> parameters = parser.getParameters();
78 ValidParameters validParameter("filter.seqs");
79 map<string,string>::iterator it;
81 //check to make sure all parameters are valid for command
82 for (it = parameters.begin(); it != parameters.end(); it++) {
83 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
86 //initialize outputTypes
87 vector<string> tempOutNames;
88 outputTypes["fasta"] = tempOutNames;
89 outputTypes["filter"] = tempOutNames;
91 //if the user changes the input directory command factory will send this info to us in the output parameter
92 string inputDir = validParameter.validFile(parameters, "inputdir", false);
93 if (inputDir == "not found"){ inputDir = ""; }
96 it = parameters.find("fasta");
97 //user has given a template file
98 if(it != parameters.end()){
99 path = m->hasPath(it->second);
100 //if the user has not given a path then, add inputdir. else leave path alone.
101 if (path == "") { parameters["fasta"] = inputDir + it->second; }
104 it = parameters.find("hard");
105 //user has given a template file
106 if(it != parameters.end()){
107 path = m->hasPath(it->second);
108 //if the user has not given a path then, add inputdir. else leave path alone.
109 if (path == "") { parameters["hard"] = inputDir + it->second; }
113 //check for required parameters
114 fasta = validParameter.validFile(parameters, "fasta", false);
115 if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true; }
117 m->splitAtDash(fasta, fastafileNames);
119 //go through files and make sure they are good, if not, then disregard them
120 for (int i = 0; i < fastafileNames.size(); i++) {
121 if (inputDir != "") {
122 string path = m->hasPath(fastafileNames[i]);
123 //if the user has not given a path then, add inputdir. else leave path alone.
124 if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; }
128 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
130 //if you can't open it, try default location
131 if (ableToOpen == 1) {
132 if (m->getDefaultPath() != "") { //default path is set
133 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
134 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
136 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
138 fastafileNames[i] = tryPath;
142 //if you can't open it, try default location
143 if (ableToOpen == 1) {
144 if (m->getOutputDir() != "") { //default path is set
145 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
146 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
148 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
150 fastafileNames[i] = tryPath;
156 if (ableToOpen == 1) {
157 m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
158 //erase from file list
159 fastafileNames.erase(fastafileNames.begin()+i);
162 string simpleName = m->getSimpleName(fastafileNames[i]);
163 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
168 //make sure there is at least one valid file left
169 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
173 //if the user changes the output directory command factory will send this info to us in the output parameter
174 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
176 outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
179 //check for optional parameter and set defaults
180 // ...at some point should added some additional type checking...
183 hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
184 else if (hard == "not open") { hard = ""; abort = true; }
186 temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
189 temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
190 else { soft = (float)atoi(temp.c_str()) / 100.0; }
192 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
193 convert(temp, processors);
195 vertical = validParameter.validFile(parameters, "vertical", false);
196 if (vertical == "not found") {
197 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
198 else { vertical = "F"; }
205 catch(exception& e) {
206 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
211 //**********************************************************************************************************************
213 void FilterSeqsCommand::help(){
216 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
217 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n");
218 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
219 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
220 m->mothurOut("The trump parameter .... The default is ...\n");
221 m->mothurOut("The soft parameter .... The default is ....\n");
222 m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
223 m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
224 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
225 m->mothurOut("The filter.seqs command should be in the following format: \n");
226 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
227 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
228 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
231 catch(exception& e) {
232 m->errorOut(e, "FilterSeqsCommand", "help");
237 /**************************************************************************************/
239 int FilterSeqsCommand::execute() {
242 if (abort == true) { if (calledHelp) { return 0; } return 2; }
245 m->openInputFile(fastafileNames[0], inFASTA);
247 Sequence testSeq(inFASTA);
248 alignmentLength = testSeq.getAlignLength();
251 ////////////create filter/////////////////
252 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
254 filter = createFilter();
256 m->mothurOutEndLine(); m->mothurOutEndLine();
258 if (m->control_pressed) { outputTypes.clear(); return 0; }
262 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
264 if (pid == 0) { //only one process should output the filter
269 //prevent giantic file name
271 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
272 else { filterFile = outputDir + filterFileName + ".filter"; }
274 m->openOutputFile(filterFile, outFilter);
275 outFilter << filter << endl;
277 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
283 ////////////run filter/////////////////
285 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
289 m->mothurOutEndLine(); m->mothurOutEndLine();
291 int filteredLength = 0;
292 for(int i=0;i<alignmentLength;i++){
293 if(filter[i] == '1'){ filteredLength++; }
296 if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
299 m->mothurOutEndLine();
300 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
301 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
302 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
303 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
305 //set fasta file as new current fastafile
307 itTypes = outputTypes.find("fasta");
308 if (itTypes != outputTypes.end()) {
309 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
312 m->mothurOutEndLine();
313 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
314 for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
315 m->mothurOutEndLine();
320 catch(exception& e) {
321 m->errorOut(e, "FilterSeqsCommand", "execute");
325 /**************************************************************************************/
326 int FilterSeqsCommand::filterSequences() {
331 for (int s = 0; s < fastafileNames.size(); s++) {
333 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
335 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
337 int pid, numSeqsPerProcessor, num;
339 vector<unsigned long int>MPIPos;
342 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
343 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
347 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
348 int inMode=MPI_MODE_RDONLY;
350 char outFilename[1024];
351 strcpy(outFilename, filteredFasta.c_str());
353 char inFileName[1024];
354 strcpy(inFileName, fastafileNames[s].c_str());
356 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
357 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
359 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
361 if (pid == 0) { //you are the root process
363 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
366 //send file positions to all processes
367 for(int i = 1; i < processors; i++) {
368 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
369 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
372 //figure out how many sequences you have to do
373 numSeqsPerProcessor = num / processors;
374 int startIndex = pid * numSeqsPerProcessor;
375 if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
379 driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
381 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
384 for(int i = 1; i < processors; i++) {
386 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
389 }else { //you are a child process
390 MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
391 MPIPos.resize(num+1);
393 MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
395 //figure out how many sequences you have to align
396 numSeqsPerProcessor = num / processors;
397 int startIndex = pid * numSeqsPerProcessor;
398 if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
402 driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
404 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
409 //tell parent you are done.
410 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
413 MPI_File_close(&outMPI);
414 MPI_File_close(&inMPI);
415 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
418 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
420 for (int i = 0; i < (positions.size()-1); i++) {
421 lines.push_back(new linePair(positions[i], positions[(i+1)]));
423 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
425 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
426 numSeqs += numFastaSeqs;
428 int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
429 numSeqs += numFastaSeqs;
431 rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
434 for(int i=1;i<processors;i++){
435 m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
436 remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
440 if (m->control_pressed) { return 1; }
442 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
443 numSeqs += numFastaSeqs;
445 if (m->control_pressed) { return 1; }
448 outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
453 catch(exception& e) {
454 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
459 /**************************************************************************************/
460 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
462 string outputString = "";
466 for(int i=0;i<num;i++){
468 if (m->control_pressed) { return 0; }
471 int length = MPIPos[start+i+1] - MPIPos[start+i];
472 char* buf4 = new char[length];
473 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
475 string tempBuf = buf4;
476 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
477 istringstream iss (tempBuf,istringstream::in);
480 Sequence seq(iss); m->gobble(iss);
482 if (seq.getName() != "") {
483 string align = seq.getAligned();
484 string filterSeq = "";
486 for(int j=0;j<alignmentLength;j++){
487 if(filter[j] == '1'){
488 filterSeq += align[j];
493 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
495 if(count % 10 == 0){ //output to file
496 //send results to parent
497 int length = outputString.length();
498 char* buf = new char[length];
499 memcpy(buf, outputString.c_str(), length);
501 MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
508 if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
511 if(outputString != ""){ //output to file
512 //send results to parent
513 int length = outputString.length();
514 char* buf = new char[length];
515 memcpy(buf, outputString.c_str(), length);
517 MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
522 if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
526 catch(exception& e) {
527 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
532 /**************************************************************************************/
533 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
536 m->openOutputFile(outputFilename, out);
539 m->openInputFile(inputFilename, in);
541 in.seekg(filePos->start);
548 if (m->control_pressed) { in.close(); out.close(); return 0; }
550 Sequence seq(in); m->gobble(in);
551 if (seq.getName() != "") {
552 string align = seq.getAligned();
553 string filterSeq = "";
555 for(int j=0;j<alignmentLength;j++){
556 if(filter[j] == '1'){
557 filterSeq += align[j];
561 out << '>' << seq.getName() << endl << filterSeq << endl;
565 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
566 unsigned long int pos = in.tellg();
567 if ((pos == -1) || (pos >= filePos->end)) { break; }
569 if (in.eof()) { break; }
573 if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
576 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
584 catch(exception& e) {
585 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
589 /**************************************************************************************************/
591 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
593 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
598 //loop through and create all the processes you want
599 while (process != processors) {
603 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
606 string filteredFasta = filename + toString(getpid()) + ".temp";
607 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
609 //pass numSeqs to parent
611 string tempFile = filename + toString(getpid()) + ".num.temp";
612 m->openOutputFile(tempFile, out);
618 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
619 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
624 //force parent to wait until all the processes are done
625 for (int i=0;i<processors;i++) {
626 int temp = processIDS[i];
630 for (int i = 0; i < processIDS.size(); i++) {
632 string tempFile = filename + toString(processIDS[i]) + ".num.temp";
633 m->openInputFile(tempFile, in);
634 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
635 in.close(); remove(tempFile.c_str());
642 catch(exception& e) {
643 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
647 /**************************************************************************************/
648 string FilterSeqsCommand::createFilter() {
650 string filterString = "";
653 if (soft != 0) { F.setSoft(soft); }
654 if (trump != '*') { F.setTrump(trump); }
656 F.setLength(alignmentLength);
658 if(trump != '*' || m->isTrue(vertical) || soft != 0){
662 if(hard.compare("") != 0) { F.doHard(hard); }
663 else { F.setFilter(string(alignmentLength, '1')); }
666 if(trump != '*' || m->isTrue(vertical) || soft != 0){
667 for (int s = 0; s < fastafileNames.size(); s++) {
669 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
672 int pid, numSeqsPerProcessor, num;
674 vector<unsigned long int> MPIPos;
678 MPI_Comm_size(MPI_COMM_WORLD, &processors);
679 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
681 //char* tempFileName = new char(fastafileNames[s].length());
682 //tempFileName = &(fastafileNames[s][0]);
684 char tempFileName[1024];
685 strcpy(tempFileName, fastafileNames[s].c_str());
687 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
689 if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
691 if (pid == 0) { //you are the root process
692 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
695 //send file positions to all processes
696 for(int i = 1; i < processors; i++) {
697 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
698 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
701 //figure out how many sequences you have to do
702 numSeqsPerProcessor = num / processors;
703 int startIndex = pid * numSeqsPerProcessor;
704 if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
708 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
710 if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
712 }else { //i am the child process
713 MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
714 MPIPos.resize(num+1);
716 MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
718 //figure out how many sequences you have to align
719 numSeqsPerProcessor = num / processors;
720 int startIndex = pid * numSeqsPerProcessor;
721 if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
725 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
727 if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
730 MPI_File_close(&inMPI);
731 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
734 vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
736 for (int i = 0; i < (positions.size()-1); i++) {
737 lines.push_back(new linePair(positions[i], positions[(i+1)]));
739 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
741 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
742 numSeqs += numFastaSeqs;
744 int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
745 numSeqs += numFastaSeqs;
748 if (m->control_pressed) { return filterString; }
750 int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
751 numSeqs += numFastaSeqs;
752 if (m->control_pressed) { return filterString; }
762 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
765 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
767 if(trump != '*' || m->isTrue(vertical) || soft != 0){
769 if (pid == 0) { //only one process should output the filter
771 vector<int> temp; temp.resize(alignmentLength+1);
773 //get the frequencies from the child processes
774 for(int i = 1; i < processors; i++) {
776 for (int j = 0; j < 5; j++) {
778 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
779 int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what letter count this is for
781 if (receiveTag == Atag) { //you are recieveing the A frequencies
782 for (int k = 0; k < alignmentLength; k++) { F.a[k] += temp[k]; }
783 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
784 for (int k = 0; k < alignmentLength; k++) { F.t[k] += temp[k]; }
785 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
786 for (int k = 0; k < alignmentLength; k++) { F.c[k] += temp[k]; }
787 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
788 for (int k = 0; k < alignmentLength; k++) { F.g[k] += temp[k]; }
789 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
790 for (int k = 0; k < alignmentLength; k++) { F.gap[k] += temp[k]; }
796 //send my fequency counts
798 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
800 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
802 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
804 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
805 F.gap.push_back(Gaptag);
806 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
811 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
813 if (pid == 0) { //only one process should output the filter
816 F.setNumSeqs(numSeqs);
817 if(m->isTrue(vertical) == 1) { F.doVertical(); }
818 if(soft != 0) { F.doSoft(); }
819 filterString = F.getFilter();
822 //send filter string to kids
823 //for(int i = 1; i < processors; i++) {
824 // MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
826 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
828 //recieve filterString
829 char* tempBuf = new char[alignmentLength];
830 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
831 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
833 filterString = tempBuf;
834 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); }
838 MPI_Barrier(MPI_COMM_WORLD);
843 catch(exception& e) {
844 m->errorOut(e, "FilterSeqsCommand", "createFilter");
848 /**************************************************************************************/
849 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
853 m->openInputFile(filename, in);
855 in.seekg(filePos->start);
862 if (m->control_pressed) { in.close(); return 1; }
864 Sequence seq(in); m->gobble(in);
865 if (seq.getName() != "") {
866 if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
868 if(trump != '*') { F.doTrump(seq); }
869 if(m->isTrue(vertical) || soft != 0) { F.getFreqs(seq); }
874 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
875 unsigned long int pos = in.tellg();
876 if ((pos == -1) || (pos >= filePos->end)) { break; }
878 if (in.eof()) { break; }
882 if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
885 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
890 catch(exception& e) {
891 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
896 /**************************************************************************************/
897 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
902 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
904 for(int i=0;i<num;i++){
906 if (m->control_pressed) { return 0; }
909 int length = MPIPos[start+i+1] - MPIPos[start+i];
911 char* buf4 = new char[length];
912 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
914 string tempBuf = buf4;
915 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
916 istringstream iss (tempBuf,istringstream::in);
921 if (seq.getAligned().length() != alignmentLength) { cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1); }
923 if(trump != '*'){ F.doTrump(seq); }
924 if(m->isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
928 if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
932 if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
936 catch(exception& e) {
937 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
942 /**************************************************************************************************/
944 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
946 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
951 //loop through and create all the processes you want
952 while (process != processors) {
956 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
959 //reset child's filter counts to 0;
960 F.a.clear(); F.a.resize(alignmentLength, 0);
961 F.t.clear(); F.t.resize(alignmentLength, 0);
962 F.g.clear(); F.g.resize(alignmentLength, 0);
963 F.c.clear(); F.c.resize(alignmentLength, 0);
964 F.gap.clear(); F.gap.resize(alignmentLength, 0);
966 num = driverCreateFilter(F, filename, lines[process]);
968 //write out filter counts to file
969 filename += toString(getpid()) + "filterValues.temp";
971 m->openOutputFile(filename, out);
974 out << F.getFilter() << endl;
975 for (int k = 0; k < alignmentLength; k++) { out << F.a[k] << '\t'; } out << endl;
976 for (int k = 0; k < alignmentLength; k++) { out << F.t[k] << '\t'; } out << endl;
977 for (int k = 0; k < alignmentLength; k++) { out << F.g[k] << '\t'; } out << endl;
978 for (int k = 0; k < alignmentLength; k++) { out << F.c[k] << '\t'; } out << endl;
979 for (int k = 0; k < alignmentLength; k++) { out << F.gap[k] << '\t'; } out << endl;
981 //cout << F.getFilter() << endl;
986 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
987 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
992 //parent do your part
993 num = driverCreateFilter(F, filename, lines[0]);
995 //force parent to wait until all the processes are done
996 for (int i=0;i<(processors-1);i++) {
997 int temp = processIDS[i];
1001 //parent reads in and combines Filter info
1002 for (int i = 0; i < processIDS.size(); i++) {
1003 string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1005 m->openInputFile(tempFilename, in);
1008 string tempFilterString;
1010 in >> tempNum; m->gobble(in); num += tempNum;
1012 in >> tempFilterString;
1013 F.mergeFilter(tempFilterString);
1015 for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } m->gobble(in);
1016 for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } m->gobble(in);
1017 for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } m->gobble(in);
1018 for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } m->gobble(in);
1019 for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in);
1022 remove(tempFilename.c_str());
1028 catch(exception& e) {
1029 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1033 /**************************************************************************************/