//**********************************************************************************************************************
-AlignCommand::AlignCommand(){
+AlignCommand::AlignCommand(string option){
try {
globaldata = GlobalData::getInstance();
- if(globaldata->getFastaFile() == ""){
- cout << "you forgot a template file" << endl;
- }
- openInputFile(globaldata->getCandidateFile(), in);
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"fasta","candidate","search","ksize","align","match","mismatch","gapopen","gapextend"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ parser = new OptionParser();
+
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //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; }
+ }
+
+ //check for required parameters
+ templateFileName = validParameter->validFile(parameters, "fasta", true);
+ if (templateFileName == "not found") { cout << "fasta is a required parameter for the align.seqs command." << endl; abort = true; }
+ else if (templateFileName == "not open") { abort = true; }
+ else { globaldata->setFastaFile(templateFileName); }
+
+ 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; }
+ else {
+ globaldata->setCandidateFile(candidateFileName);
+ openInputFile(candidateFileName, in);
+ }
+
+
+ //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 = "-1.0"; }
+ convert(temp, gapOpen);
+
+ temp = validParameter->validFile(parameters, "gapextend", false); if (temp == "not found") { temp = "-2.0"; }
+ convert(temp, gapExtend);
- convert(globaldata->getKSize(), kmerSize);
- convert(globaldata->getMatch(), match);
- convert(globaldata->getMismatch(), misMatch);
- convert(globaldata->getGapopen(), gapOpen);
- convert(globaldata->getGapextend(), gapExtend);
+ search = validParameter->validFile(parameters, "search", false); if (search == "not found") { search = "kmer"; }
+ align = validParameter->validFile(parameters, "align", false); if (align == "not found") { align = "needleman"; }
+
+ delete validParameter;
+ }
+
}
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(){
}
+//**********************************************************************************************************************
+
+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 fasta, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
+ cout << "The fasta 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(fasta=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, fasta=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. fasta), '=' 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 {
+ if (abort == true) { return 0; }
+
srand( (unsigned)time( NULL ) ); //needed to assign names to temporary files
Database* templateDB;
- if(globaldata->getSearch() == "kmer") { templateDB = new KmerDB(globaldata->getFastaFile() , kmerSize); }
- else if(globaldata->getSearch() == "suffix") { templateDB = new SuffixDB(globaldata->getFastaFile()); }
- else if(globaldata->getSearch() == "blast") { templateDB = new BlastDB(globaldata->getFastaFile(), gapOpen, gapExtend, match, misMatch); }
+ 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 << globaldata->getSearch() << " is not a valid search option. I will run the command using kmer, ksize=8." << endl;
- templateDB = new KmerDB(globaldata->getFastaFile(), kmerSize);
+ 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);
}
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(); }
+ 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 << globaldata->getAlign() << " is not a valid alignment option. I will run the command using needleman." << endl;
+ cout << align << " is not a valid alignment option. I will run the command using needleman." << endl;
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);
}
int numFastaSeqs=count(istreambuf_iterator<char>(in),istreambuf_iterator<char>(), '>');
in.seekg(0);
- candidateFileName = globaldata->getCandidateFile();
string candidateAligngmentFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
ofstream candidateAlignmentFile;
openOutputFile(candidateAligngmentFName, candidateAlignmentFile);
Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq);
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);
candidateAlignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
projects / mothur.git / blobdiff