* allows for a global alignment and not the local alignment provided by bLAst. Furthermore, it has the potential to
* provide a better alignment because of the banding method employed by blast (I'm not sure about this).
*
- * to compile type:
- * make
- *
- * for basic instructions on how to run nastPlus type:
- * ./nastPlus
*/
#include "aligncommand.h"
#include "sequence.hpp"
-#include "alignment.hpp"
#include "gotohoverlap.hpp"
#include "needlemanoverlap.hpp"
#include "blastalign.hpp"
#include "noalign.hpp"
-#include "database.hpp"
#include "kmerdb.hpp"
#include "suffixdb.hpp"
#include "blastdb.hpp"
-#include "distancedb.hpp"
#include "nast.hpp"
#include "nastreport.hpp"
//**********************************************************************************************************************
-AlignCommand::AlignCommand(){
+
+AlignCommand::AlignCommand(string option){
try {
- globaldata = GlobalData::getInstance();
- candidateFileName = globaldata->inputFileName;
- templateFileName = globaldata->getTemplateFile();
- openInputFile(candidateFileName, in);
- convert(globaldata->getKSize(), kmerSize);
- convert(globaldata->getMatch(), match);
- convert(globaldata->getMismatch(), misMatch);
- convert(globaldata->getGapopen(), gapOpen);
- convert(globaldata->getGapextend(), gapExtend);
- distanceFileName = "????";
+ // globaldata = GlobalData::getInstance();
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+
+ //valid paramters for this command
+ string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //check for required parameters
+ templateFileName = validParameter.validFile(parameters, "template", true);
+ if (templateFileName == "not found") { cout << "template is a required parameter for the align.seqs command." << endl; abort = true; }
+ else if (templateFileName == "not open") { abort = true; }
+
+ candidateFileName = validParameter.validFile(parameters, "candidate", true);
+ if (candidateFileName == "not found") { cout << "candidate is a required parameter for the align.seqs command." << endl; abort = true; }
+ else if (candidateFileName == "not open") { abort = true; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string temp;
+ temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
+ convert(temp, kmerSize);
+
+ temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
+ convert(temp, match);
+
+ temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
+ convert(temp, misMatch);
+
+ temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
+ convert(temp, gapOpen);
+
+ temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
+ convert(temp, gapExtend);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
+ search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
+
+ align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
+ }
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function AlignCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
//**********************************************************************************************************************
-AlignCommand::~AlignCommand(){
-
+AlignCommand::~AlignCommand(){
+
+ if (abort == false) {
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete templateDB;
+ delete alignment;
+ }
+}
+
+//**********************************************************************************************************************
+
+void AlignCommand::help(){
+ try {
+ cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
+ cout << "The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
+ cout << "The template and candidate parameters are required." << "\n";
+ cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer." << "\n";
+ cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman." << "\n";
+ cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n";
+ cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
+ cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n";
+ cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n";
+ cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n";
+ cout << "The align.seqs command should be in the following format: " << "\n";
+ cout << "align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
+ cout << "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the AlignCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
int AlignCommand::execute(){
try {
- srand( (unsigned)time( NULL ) ); //needed to assign names to temporary files
-
- Database* templateDB;
- if(globaldata->getSearch() == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); }
- else if(globaldata->getSearch() == "suffix") { templateDB = new SuffixDB(templateFileName); }
- else if(globaldata->getSearch() == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); }
- else if(globaldata->getSearch() == "distance") { templateDB = new DistanceDB(templateFileName, distanceFileName); }
- else { cout << globaldata->getSearch() << " is not a valid search option. I will run the command using suffix." << endl;
- templateDB = new SuffixDB(templateFileName); }
-
- Alignment* alignment;
- if(globaldata->getAlign() == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000); }
- else if(globaldata->getAlign() == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000); }
- else if(globaldata->getAlign() == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(globaldata->getAlign() == "noalign") { alignment = new NoAlign(); }
- else { cout << globaldata->getAlign() << " is not a valid alignment option. I will run the command using blast." << endl;
- alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
-
- int numFastaSeqs=count(istreambuf_iterator<char>(in),istreambuf_iterator<char>(), '>');
- in.seekg(0);
-
- string candidateAligngmentFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + globaldata->getSearch() + '.' + globaldata->getAlign() + ".nast.align";
- ofstream candidateAlignmentFile;
- openOutputFile(candidateAligngmentFName, candidateAlignmentFile);
-
- string candidateReportFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + globaldata->getSearch() + '.' + globaldata->getAlign() + ".nast.report";
- NastReport report(candidateReportFName);
-
- cout << "We are going to align the " << numFastaSeqs << " sequences in " << candidateFileName << "..." << endl;
- cout.flush();
-
+ if (abort == true) { return 0; }
+
+ if(search == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); }
+ else if(search == "suffix") { templateDB = new SuffixDB(templateFileName); }
+ else if(search == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); }
+ else {
+ cout << search << " is not a valid search option. I will run the command using kmer, ksize=8." << endl; kmerSize = 8;
+ templateDB = new KmerDB(templateFileName, kmerSize);
+ }
+
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000); }
+ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
+ else if(align == "noalign") { alignment = new NoAlign(); }
+ else {
+ cout << align << " is not a valid alignment option. I will run the command using needleman." << endl;
+ alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);
+ }
+
+ string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
+ string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
+
+ int numFastaSeqs = 0;
int start = time(NULL);
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(candidateFileName, inFASTA);
+ numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driver(lines[0], alignFileName, reportFileName);
+
+ }
+ else{
+ vector<int> positions;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(candidateFileName, inFASTA);
+
+ while(!inFASTA.eof()){
+ char c = inFASTA.get();
+ if(c == '>'){ positions.push_back(inFASTA.tellg()); }
+ while (!inFASTA.eof()) { c = inFASTA.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ }
+ inFASTA.close();
+
+ numFastaSeqs = positions.size();
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+ createProcesses(alignFileName, reportFileName);
+
+ rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
+ rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
+
+ for(int i=1;i<processors;i++){
+ appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+ remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+
+ appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
+ remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
+ }
+
+ }
+#else
+ ifstream inFASTA;
+ openInputFile(candidateFileName, inFASTA);
+ numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driver(lines[0], alignFileName, reportFileName);
+#endif
+
+ cout << "It took " << time(NULL) - start << " secs to align " << numFastaSeqs << " sequences" << endl;
+ cout << endl;
+
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the AlignCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
- for(int i=0;i<numFastaSeqs;i++){
+//**********************************************************************************************************************
- Sequence* candidateSeq = new Sequence(in);
+int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
+ try {
+ ofstream alignmentFile;
+ openOutputFile(alignFName, alignmentFile);
+ NastReport report(reportFName);
+
+ ifstream inFASTA;
+ openInputFile(candidateFileName, inFASTA);
+ inFASTA.seekg(line->start);
+
+ for(int i=0;i<line->numSeqs;i++){
+
+ Sequence* candidateSeq = new Sequence(inFASTA);
report.setCandidate(candidateSeq);
-
- Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq);
+
+ Sequence temp = templateDB->findClosestSequence(candidateSeq);
+ Sequence* templateSeq = &temp;
+
report.setTemplate(templateSeq);
- report.setSearchParameters(globaldata->getSearch(), templateDB->getSearchScore());
-
+ report.setSearchParameters(search, templateDB->getSearchScore());
+
Nast nast(alignment, candidateSeq, templateSeq);
- report.setAlignmentParameters(globaldata->getAlign(), alignment);
+ report.setAlignmentParameters(align, alignment);
report.setNastParameters(nast);
+
+ alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
+
+ report.print();
+
+ delete candidateSeq;
+ }
+
+ alignmentFile.close();
+ inFASTA.close();
+
+ return 1;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the AlignCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
- candidateAlignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
- candidateAlignmentFile.flush();
+/**************************************************************************************************/
- if((i+1) % 100 == 0){
- cout << "It has taken " << time(NULL) - start << " secs to align " << i+1 << " sequences" << endl;
- }
- report.print();
+void AlignCommand::createProcesses(string alignFileName, string reportFileName) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ // processIDS.resize(0);
- delete candidateSeq;
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp");
+ exit(0);
+ }else { cout << "unable to spawn the necessary processes." << endl; exit(0); }
}
- cout << "It took " << time(NULL) - start << " secs to align " << numFastaSeqs << " sequences" << endl;
- cout << endl;
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+#endif
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the AlignCommand class function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
- delete templateDB;
- delete alignment;
+/**************************************************************************************************/
-
- return 0;
+void AlignCommand::appendAlignFiles(string temp, string filename) {
+ try{
+
+ //open output file in append mode
+ ofstream output;
+ openOutputFileAppend(filename, output);
+
+ //open temp file for reading
+ ifstream input;
+ openInputFile(temp, input);
+
+ string line;
+ //read input file and write to output file
+ while(input.eof() != true) {
+ getline(input, line); //getline removes the newline char
+ if (line != "") {
+ output << line << endl; // Appending back newline char
+ }
+ }
+
+ input.close();
+ output.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the AlignCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the DistanceCommand class function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
-//**********************************************************************************************************************
\ No newline at end of file
+/**************************************************************************************************/
+
+void AlignCommand::appendReportFiles(string temp, string filename) {
+ try{
+
+ //open output file in append mode
+ ofstream output;
+ openOutputFileAppend(filename, output);
+
+ //open temp file for reading
+ ifstream input;
+ openInputFile(temp, input);
+ while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
+
+ string line;
+ //read input file and write to output file
+ while(input.eof() != true) {
+ getline(input, line); //getline removes the newline char
+ if (line != "") {
+ output << line << endl; // Appending back newline char
+ }
+ }
+
+ input.close();
+ output.close();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DistanceCommand class function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
projects / mothur.git / blobdiff