X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.cpp;h=9013e7d33f66f38b7ce1283ee92a45be3d4ab76c;hb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;hp=b810b9f09fdca369bd5e8e0ccdba830d247eaf37;hpb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;p=mothur.git diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp index b810b9f..9013e7d 100644 --- a/chimeraseqscommand.cpp +++ b/chimeraseqscommand.cpp @@ -9,222 +9,59 @@ #include "chimeraseqscommand.h" -//*************************************************************************************************************** - -ChimeraSeqsCommand::ChimeraSeqsCommand(string option){ +//********************************************************************************************************************** +vector ChimeraSeqsCommand::getValidParameters(){ try { - abort = false; - - //allow user to run help - if(option == "help") { help(); abort = true; } - - else { - //valid paramters for this command - string Array[] = {"fasta", "filter", "correction", "processors", "method" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - - //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true; } - - string temp; - temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; } - filter = isTrue(temp); - - temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; } - correction = isTrue(temp); - - temp = validParameter.validFile(parameters, "processors", true); if (temp == "not found") { temp = "1"; } - convert(temp, processors); - - method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "bellerophon"; } - - } + vector myArray; + return myArray; } catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand"); + m->errorOut(e, "ChimeraSeqsCommand", "getValidParameters"); exit(1); } } //********************************************************************************************************************** - -void ChimeraSeqsCommand::help(){ +vector ChimeraSeqsCommand::getRequiredParameters(){ try { - mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n"); - mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method. fasta is required.\n"); - mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter. The default is false. \n"); - mothurOut("The correction parameter allows you to ..... The default is true. \n"); - mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); - mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is bellerophon. \n"); - mothurOut("The chimera.seqs command should be in the following format: \n"); - mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n"); - mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n"); - mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); + vector myArray; + return myArray; } catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "help"); + m->errorOut(e, "ChimeraSeqsCommand", "getRequiredParameters"); exit(1); } } - -//*************************************************************************************************************** - -ChimeraSeqsCommand::~ChimeraSeqsCommand(){ /* do nothing */ } - -//*************************************************************************************************************** - -int ChimeraSeqsCommand::execute(){ - try{ - - if (abort == true) { return 0; } - - //do soft filter - if (filter) { - string optionString = "fasta=" + fastafile + ", soft=50.0, vertical=F"; - filterSeqs = new FilterSeqsCommand(optionString); - filterSeqs->execute(); - delete filterSeqs; - - //reset fastafile to filtered file - fastafile = getRootName(fastafile) + "filter.fasta"; - } - - //read in sequences - readSeqs(); - - //int numSeqs = seqs.size(); - - //find average midpoint of seqs - midpoint = findAverageMidPoint(); - - //this should be parallelized - //generatePreferences(); - - - //output results to screen - mothurOutEndLine(); - mothurOut("\t\t"); mothurOutEndLine(); - //mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); mothurOutEndLine(); - //mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); mothurOutEndLine(); - //mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); mothurOutEndLine(); - //mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); mothurOutEndLine(); - //mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); mothurOutEndLine(); - //mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); mothurOutEndLine(); - //mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); mothurOutEndLine(); - //mothurOut("# of Seqs:\t" + toString(numSeqs)); mothurOutEndLine(); - - //outSummary.close(); - return 0; +//********************************************************************************************************************** +vector ChimeraSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; } catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "execute"); + m->errorOut(e, "ChimeraSeqsCommand", "getRequiredFiles"); exit(1); } } - //*************************************************************************************************************** -void ChimeraSeqsCommand::readSeqs(){ - try { - ifstream inFASTA; - openInputFile(fastafile, inFASTA); - - //read in seqs and store in vector - while(!inFASTA.eof()){ - Sequence current(inFASTA); - - seqs.push_back(current); - - gobble(inFASTA); - } - inFASTA.close(); - } - catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "readSeqs"); - exit(1); - } -} +ChimeraSeqsCommand::ChimeraSeqsCommand(string option) {} +//********************************************************************************************************************** +void ChimeraSeqsCommand::help(){} //*************************************************************************************************************** -int ChimeraSeqsCommand::findAverageMidPoint(){ - try { - int totalMids = 0; - int averageMid = 0; - - //loop through the seqs and find midpoint - for (int i = 0; i < seqs.size(); i++) { - - //get unaligned sequence - seqs[i].setUnaligned(seqs[i].getUnaligned()); //if you read an aligned file the unaligned is really aligned, so we need to make sure its unaligned - - string unaligned = seqs[i].getUnaligned(); - string aligned = seqs[i].getAligned(); - - //find midpoint of this seq - int count = 0; - int thismid = 0; - for (int j = 0; j < aligned.length(); j++) { - - thismid++; - - //if you are part of the unaligned sequence increment - if (isalpha(aligned[j])) { count++; } - - //if you have reached the halfway point stop - if (count >= (unaligned.length() / 2)) { break; } - } - - //add this mid to total - totalMids += thismid; - - } - - averageMid = (totalMids / seqs.size()); - - return averageMid; - - - } - catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "findAverageMidPoint"); - exit(1); - } -} -/*************************************************************************************************************** -int ChimeraSeqsCommand::createSparseMatrix(int startLine, int endLine, SparseMatrix* sparse){ - try { +ChimeraSeqsCommand::~ChimeraSeqsCommand(){ /* do nothing */ } - for(int i=startLine; icalcDist(seqs.get(i), seqs.get(j)); - double dist = distCalculator->getDist(); - - - - } - +//*************************************************************************************************************** + +int ChimeraSeqsCommand::execute(){ - return 1; - } - catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "createSparseMatrix"); - exit(1); - } + m->mothurOut("The chimera.seqs command has been broken up into 5 separate commands.\n"); + m->mothurOut("The chimera.bellerophon, chimera.ccode, chimera.check, chimera.pintail and chimera.slayer commands.\n"); + + return 0; } -/**************************************************************************************************/ +//********************************************************************************************************************** +