--- /dev/null
+//
+// primerdesigncommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 1/18/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#include "primerdesigncommand.h"
+
+//**********************************************************************************************************************
+vector<string> PrimerDesignCommand::setParameters(){
+ try {
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","summary-list",false,true,true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,true, true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter plength("length", "Number", "", "18", "", "", "","",false,false); parameters.push_back(plength);
+ CommandParameter pmintm("mintm", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmintm);
+ CommandParameter pmaxtm("maxtm", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxtm);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors);
+ CommandParameter potunumber("otunumber", "Number", "", "-1", "", "", "","",false,true,true); parameters.push_back(potunumber);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PrimerDesignCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The primer.design allows you to design sequence fragments that are specific to particular OTUs.\n";
+ helpString += "The primer.design command parameters are: list, fasta, name, count, otunumber, cutoff, length, pdiffs, mintm, maxtm, processors and label.\n";
+ helpString += "The list parameter allows you to provide a list file and is required.\n";
+ helpString += "The fasta parameter allows you to provide a fasta file and is required.\n";
+ helpString += "The name parameter allows you to provide a name file associated with your fasta file.\n";
+ helpString += "The count parameter allows you to provide a count file associated with your fasta file.\n";
+ helpString += "The label parameter is used to indicate the label you want to use from your list file.\n";
+ helpString += "The otunumber parameter is used to indicate the otu you want to use from your list file. It is required.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
+ helpString += "The length parameter is used to indicate the length of the primer. The default is 18.\n";
+ helpString += "The mintm parameter is used to indicate minimum melting temperature.\n";
+ helpString += "The maxtm parameter is used to indicate maximum melting temperature.\n";
+ helpString += "The processors parameter allows you to indicate the number of processors you want to use. Default=1.\n";
+ helpString += "The cutoff parameter allows you set a percentage of sequences that support the base. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.\n";
+ helpString += "The primer.desing command should be in the following format: primer.design(list=yourListFile, fasta=yourFastaFile, name=yourNameFile)\n";
+ helpString += "primer.design(list=final.an.list, fasta=final.fasta, name=final.names, label=0.03)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PrimerDesignCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[distance],otu.cons.fasta"; }
+ else if (type == "summary") { pattern = "[filename],[distance],primer.summary"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PrimerDesignCommand::PrimerDesignCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "PrimerDesignCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PrimerDesignCommand::PrimerDesignCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ //valid paramters for this command
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+ //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; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+ }
+
+ //check for parameters
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ //get fastafile - it is required
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { fastafile = ""; abort=true; }
+ else if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
+
+ //get listfile - it is required
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort=true; }
+ else if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setListFile(listfile); }
+
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = m->hasPath(listfile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, cutoff);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "length", false); if (temp == "not found") { temp = "18"; }
+ m->mothurConvert(temp, length);
+
+ temp = validParameter.validFile(parameters, "mintm", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, minTM);
+
+ temp = validParameter.validFile(parameters, "maxtm", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, maxTM);
+
+ temp = validParameter.validFile(parameters, "otunumber", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, otunumber);
+ if (otunumber < 1) { m->mothurOut("[ERROR]: You must provide an OTU number, aborting.\n"); abort = true; }
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
+
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "PrimerDesignCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int PrimerDesignCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
+ //////////////////////////////////////////////////////////////////////////////
+ // get file inputs //
+ //////////////////////////////////////////////////////////////////////////////
+
+ //reads list file and selects the label the users specified or the first label
+ getListVector();
+ if (otunumber > list->getNumBins()) { m->mothurOut("[ERROR]: You selected an OTU number larger than the number of OTUs you have in your list file, quitting.\n"); return 0; }
+
+ map<string, int> nameMap;
+ unsigned long int numSeqs; //used to sanity check the files. numSeqs = total seqs for namefile and uniques for count.
+ //list file should have all seqs if namefile was used to create it and only uniques in count file was used.
+
+ if (namefile != "") { nameMap = m->readNames(namefile, numSeqs); }
+ else if (countfile != "") { nameMap = readCount(numSeqs); }
+ else { numSeqs = list->getNumSeqs(); }
+
+ //sanity check
+ if (numSeqs != list->getNumSeqs()) {
+ if (namefile != "") { m->mothurOut("[ERROR]: Your list file contains " + toString(list->getNumSeqs()) + " sequences, and your name file contains " + toString(numSeqs) + " sequences, aborting. Do you have the correct files? Perhaps you forgot to include the name file when you clustered? \n"); }
+ else if (countfile != "") {
+ m->mothurOut("[ERROR]: Your list file contains " + toString(list->getNumSeqs()) + " sequences, and your count file contains " + toString(numSeqs) + " unique sequences, aborting. Do you have the correct files? Perhaps you forgot to include the count file when you clustered? \n");
+ }
+ m->control_pressed = true;
+ }
+
+ if (m->control_pressed) { delete list; return 0; }
+
+ //////////////////////////////////////////////////////////////////////////////
+ // process data //
+ //////////////////////////////////////////////////////////////////////////////
+ m->mothurOut("\nFinding consensus sequences for each otu..."); cout.flush();
+
+ vector<Sequence> conSeqs = createProcessesConSeqs(nameMap, numSeqs);
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = list->getLabel();
+ string consFastaFile = getOutputFileName("fasta", variables);
+ outputNames.push_back(consFastaFile); outputTypes["fasta"].push_back(consFastaFile);
+ ofstream out;
+ m->openOutputFile(consFastaFile, out);
+ for (int i = 0; i < conSeqs.size(); i++) { conSeqs[i].printSequence(out); }
+ out.close();
+
+ m->mothurOut("Done.\n\n");
+
+ set<string> primers = getPrimer(conSeqs[otunumber-1]);
+
+ if (m->control_pressed) { delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ string consSummaryFile = getOutputFileName("summary", variables);
+ outputNames.push_back(consSummaryFile); outputTypes["summary"].push_back(consSummaryFile);
+ ofstream outSum;
+ m->openOutputFile(consSummaryFile, outSum);
+
+ outSum << "PrimerOtu: " << otunumber << " Members: " << list->get(otunumber-1) << endl << "Primers\tminTm\tmaxTm" << endl;
+
+ //find min and max melting points
+ vector<double> minTms;
+ vector<double> maxTms;
+ string primerString = "";
+ for (set<string>::iterator it = primers.begin(); it != primers.end();) {
+
+ double minTm, maxTm;
+ findMeltingPoint(*it, minTm, maxTm);
+ if ((minTM == -1) && (maxTM == -1)) { //user did not set min or max Tm so save this primer
+ minTms.push_back(minTm);
+ maxTms.push_back(maxTm);
+ outSum << *it << '\t' << minTm << '\t' << maxTm << endl;
+ it++;
+ }else if ((minTM == -1) && (maxTm <= maxTM)){ //user set max and no min, keep if below max
+ minTms.push_back(minTm);
+ maxTms.push_back(maxTm);
+ outSum << *it << '\t' << minTm << '\t' << maxTm << endl;
+ it++;
+ }else if ((maxTM == -1) && (minTm >= minTM)){ //user set min and no max, keep if above min
+ minTms.push_back(minTm);
+ maxTms.push_back(maxTm);
+ outSum << *it << '\t' << minTm << '\t' << maxTm << endl;
+ it++;
+ }else if ((maxTm <= maxTM) && (minTm >= minTM)) { //keep if above min and below max
+ minTms.push_back(minTm);
+ maxTms.push_back(maxTm);
+ outSum << *it << '\t' << minTm << '\t' << maxTm << endl;
+ it++;
+ }else { primers.erase(it++); } //erase because it didn't qualify
+ }
+
+ outSum << "\nOTUNumber\tPrimer\tStart\tEnd\tLength\tMismatches\tminTm\tmaxTm\n";
+ outSum.close();
+
+ //check each otu's conseq for each primer in otunumber
+ set<int> otuToRemove = createProcesses(consSummaryFile, minTms, maxTms, primers, conSeqs);
+
+ if (m->control_pressed) { delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //print new list file
+ map<string, string> mvariables;
+ mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ mvariables["[extension]"] = m->getExtension(listfile);
+ string newListFile = getOutputFileName("list", mvariables);
+ outputNames.push_back(newListFile); outputTypes["list"].push_back(newListFile);
+ ofstream outList;
+ m->openOutputFile(newListFile, outList);
+
+ outList << list->getLabel() << '\t' << (list->getNumBins()-otuToRemove.size()) << '\t';
+ for (int j = 0; j < list->getNumBins(); j++) {
+ if (m->control_pressed) { break; }
+ //good otus
+ if (otuToRemove.count(j) == 0) {
+ string bin = list->get(j);
+ if (bin != "") { outList << bin << '\t'; }
+ }
+ }
+ outList << endl;
+ outList.close();
+
+ if (m->control_pressed) { delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ delete list;
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(list->getNumBins()) + " OTUs.\n");
+
+
+ //output files created by command
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "execute");
+ exit(1);
+ }
+}
+//********************************************************************/
+//used http://www.biophp.org/minitools/melting_temperature/ as a reference to substitute degenerate bases
+// in order to find the min and max Tm values.
+//Tm = 64.9°C + 41°C x (number of G’s and C’s in the primer – 16.4)/N
+
+/* A = adenine
+ * C = cytosine
+ * G = guanine
+ * T = thymine
+ * R = G A (purine)
+ * Y = T C (pyrimidine)
+ * K = G T (keto)
+ * M = A C (amino)
+ * S = G C (strong bonds)
+ * W = A T (weak bonds)
+ * B = G T C (all but A)
+ * D = G A T (all but C)
+ * H = A C T (all but G)
+ * V = G C A (all but T)
+ * N = A G C T (any) */
+
+int PrimerDesignCommand::findMeltingPoint(string primer, double& minTm, double& maxTm){
+ try {
+ string minTmprimer = primer;
+ string maxTmprimer = primer;
+
+ //find minimum Tm string substituting for degenerate bases
+ for (int i = 0; i < minTmprimer.length(); i++) {
+ minTmprimer[i] = toupper(minTmprimer[i]);
+
+ if (minTmprimer[i] == 'Y') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'R') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'W') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'K') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'M') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'D') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'V') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'H') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'B') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'N') { minTmprimer[i] = 'A'; }
+ else if (minTmprimer[i] == 'S') { minTmprimer[i] = 'G'; }
+ }
+
+ //find maximum Tm string substituting for degenerate bases
+ for (int i = 0; i < maxTmprimer.length(); i++) {
+ maxTmprimer[i] = toupper(maxTmprimer[i]);
+
+ if (maxTmprimer[i] == 'Y') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'R') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'W') { maxTmprimer[i] = 'A'; }
+ else if (maxTmprimer[i] == 'K') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'M') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'D') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'V') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'H') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'B') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'N') { maxTmprimer[i] = 'G'; }
+ else if (maxTmprimer[i] == 'S') { maxTmprimer[i] = 'G'; }
+ }
+
+ int numGC = 0;
+ for (int i = 0; i < minTmprimer.length(); i++) {
+ if (minTmprimer[i] == 'G') { numGC++; }
+ else if (minTmprimer[i] == 'C') { numGC++; }
+ }
+
+ minTm = 64.9 + 41 * (numGC - 16.4) / (double) minTmprimer.length();
+
+ numGC = 0;
+ for (int i = 0; i < maxTmprimer.length(); i++) {
+ if (maxTmprimer[i] == 'G') { numGC++; }
+ else if (maxTmprimer[i] == 'C') { numGC++; }
+ }
+
+ maxTm = 64.9 + 41 * (numGC - 16.4) / (double) maxTmprimer.length();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "findMeltingPoint");
+ exit(1);
+ }
+}
+//********************************************************************/
+//search for a primer over the sequence string
+bool PrimerDesignCommand::findPrimer(string rawSequence, string primer, vector<int>& primerStart, vector<int>& primerEnd, vector<int>& mismatches){
+ try {
+ bool foundAtLeastOne = false; //innocent til proven guilty
+
+ //look for exact match
+ if(rawSequence.length() < primer.length()) { return false; }
+
+ //search for primer
+ for (int j = 0; j < rawSequence.length()-length; j++){
+
+ if (m->control_pressed) { return foundAtLeastOne; }
+
+ string rawChunk = rawSequence.substr(j, length);
+
+ int numDiff = countDiffs(primer, rawChunk);
+
+ if(numDiff <= pdiffs){
+ primerStart.push_back(j);
+ primerEnd.push_back(j+length);
+ mismatches.push_back(numDiff);
+ foundAtLeastOne = true;
+ }
+ }
+
+ return foundAtLeastOne;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "findPrimer");
+ exit(1);
+ }
+}
+//********************************************************************/
+//find all primers for the given sequence
+set<string> PrimerDesignCommand::getPrimer(Sequence primerSeq){
+ try {
+ set<string> primers;
+
+ string rawSequence = primerSeq.getUnaligned();
+
+ for (int j = 0; j < rawSequence.length()-length; j++){
+ if (m->control_pressed) { break; }
+
+ string primer = rawSequence.substr(j, length);
+ primers.insert(primer);
+ }
+
+ return primers;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "getPrimer");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+set<int> PrimerDesignCommand::createProcesses(string newSummaryFile, vector<double>& minTms, vector<double>& maxTms, set<string>& primers, vector<Sequence>& conSeqs) {
+ try {
+
+ vector<int> processIDS;
+ int process = 1;
+ set<int> otusToRemove;
+ int numBinsProcessed = 0;
+
+ //sanity check
+ int numBins = conSeqs.size();
+ if (numBins < processors) { processors = numBins; }
+
+ //divide the otus between the processors
+ vector<linePair> lines;
+ int numOtusPerProcessor = numBins / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numOtusPerProcessor;
+ int endIndex = (i+1) * numOtusPerProcessor;
+ if(i == (processors - 1)){ endIndex = numBins; }
+ lines.push_back(linePair(startIndex, endIndex));
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //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){
+ //clear old file because we append in driver
+ m->mothurRemove(newSummaryFile + toString(getpid()) + ".temp");
+
+ otusToRemove = driver(newSummaryFile + toString(getpid()) + ".temp", minTms, maxTms, primers, conSeqs, lines[process].start, lines[process].end, numBinsProcessed);
+
+ string tempFile = toString(getpid()) + ".otus2Remove.temp";
+ ofstream outTemp;
+ m->openOutputFile(tempFile, outTemp);
+
+ outTemp << numBinsProcessed << endl;
+ outTemp << otusToRemove.size() << endl;
+ for (set<int>::iterator it = otusToRemove.begin(); it != otusToRemove.end(); it++) { outTemp << *it << endl; }
+ outTemp.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ otusToRemove = driver(newSummaryFile, minTms, maxTms, primers, conSeqs, lines[0].start, lines[0].end, numBinsProcessed);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFile = toString(processIDS[i]) + ".otus2Remove.temp";
+ ifstream intemp;
+ m->openInputFile(tempFile, intemp);
+
+ int num;
+ intemp >> num; m->gobble(intemp);
+ if (num != (lines[i+1].end - lines[i+1].start)) { m->mothurOut("[ERROR]: process " + toString(processIDS[i]) + " did not complete processing all OTUs assigned to it, quitting.\n"); m->control_pressed = true; }
+ intemp >> num; m->gobble(intemp);
+ for (int k = 0; k < num; k++) {
+ int otu;
+ intemp >> otu; m->gobble(intemp);
+ otusToRemove.insert(otu);
+ }
+ intemp.close();
+ m->mothurRemove(tempFile);
+ }
+
+
+ #else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the primerDesignData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<primerDesignData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+ m->mothurRemove(newSummaryFile+extension);
+
+ primerDesignData* tempPrimer = new primerDesignData((newSummaryFile+extension), m, lines[i].start, lines[i].end, minTms, maxTms, primers, conSeqs, pdiffs, otunumber, length, i);
+ pDataArray.push_back(tempPrimer);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyPrimerThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+
+ //using the main process as a worker saves time and memory
+ otusToRemove = driver(newSummaryFile, minTms, maxTms, primers, conSeqs, lines[0].start, lines[0].end, numBinsProcessed);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (set<int>::iterator it = pDataArray[i]->otusToRemove.begin(); it != pDataArray[i]->otusToRemove.end(); it++) {
+ otusToRemove.insert(*it);
+ }
+ int num = pDataArray[i]->numBinsProcessed;
+ if (num != (lines[processIDS[i]].end - lines[processIDS[i]].start)) { m->mothurOut("[ERROR]: process " + toString(processIDS[i]) + " did not complete processing all OTUs assigned to it, quitting.\n"); m->control_pressed = true; }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ m->appendFiles((newSummaryFile + toString(processIDS[i]) + ".temp"), newSummaryFile);
+ m->mothurRemove((newSummaryFile + toString(processIDS[i]) + ".temp"));
+ }
+
+ return otusToRemove;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+set<int> PrimerDesignCommand::driver(string summaryFileName, vector<double>& minTms, vector<double>& maxTms, set<string>& primers, vector<Sequence>& conSeqs, int start, int end, int& numBinsProcessed){
+ try {
+ set<int> otuToRemove;
+
+ ofstream outSum;
+ m->openOutputFileAppend(summaryFileName, outSum);
+
+ for (int i = start; i < end; i++) {
+
+ if (m->control_pressed) { break; }
+
+ if (i != (otunumber-1)) {
+ int primerIndex = 0;
+ for (set<string>::iterator it = primers.begin(); it != primers.end(); it++) {
+ vector<int> primerStarts;
+ vector<int> primerEnds;
+ vector<int> mismatches;
+
+ bool found = findPrimer(conSeqs[i].getUnaligned(), (*it), primerStarts, primerEnds, mismatches);
+
+ //if we found it report to the table
+ if (found) {
+ for (int j = 0; j < primerStarts.size(); j++) {
+ outSum << (i+1) << '\t' << *it << '\t' << primerStarts[j] << '\t' << primerEnds[j] << '\t' << length << '\t' << mismatches[j] << '\t' << minTms[primerIndex] << '\t' << maxTms[primerIndex] << endl;
+ }
+ otuToRemove.insert(i);
+ }
+ primerIndex++;
+ }
+ }
+ numBinsProcessed++;
+ }
+ outSum.close();
+
+
+ return otuToRemove;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "driver");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< vector< vector<unsigned int> > > PrimerDesignCommand::driverGetCounts(map<string, int>& nameMap, unsigned long int& fastaCount, vector<unsigned int>& otuCounts, unsigned long long& start, unsigned long long& end){
+ try {
+ vector< vector< vector<unsigned int> > > counts;
+ map<string, int> seq2Bin;
+ alignedLength = 0;
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ in.seekg(start);
+
+ bool done = false;
+ fastaCount = 0;
+
+ while (!done) {
+ if (m->control_pressed) { in.close(); return counts; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+ if (fastaCount == 0) { alignedLength = seq.getAligned().length(); initializeCounts(counts, alignedLength, seq2Bin, nameMap, otuCounts); }
+ else if (alignedLength != seq.getAligned().length()) {
+ m->mothurOut("[ERROR]: your sequences are not all the same length. primer.design requires sequences to be aligned."); m->mothurOutEndLine(); m->control_pressed = true; break;
+ }
+
+ int num = 1;
+ map<string, int>::iterator itCount;
+ if (namefile != "") {
+ itCount = nameMap.find(seq.getName());
+ if (itCount == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your name file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ else { num = itCount->second; }
+ fastaCount+=num;
+ }else if (countfile != "") {
+ itCount = nameMap.find(seq.getName());
+ if (itCount == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your count file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ else { num = itCount->second; }
+ fastaCount++;
+ }else {
+ fastaCount++;
+ }
+
+ //increment counts
+ itCount = seq2Bin.find(seq.getName());
+ if (itCount == seq2Bin.end()) {
+ if ((namefile != "") || (countfile != "")) {
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your list file, aborting. Perhaps you forgot to include your name or count file while clustering.\n"); m->mothurOutEndLine(); m->control_pressed = true; break;
+ }else{
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your list file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; break;
+ }
+ }else {
+ otuCounts[itCount->second] += num;
+ string aligned = seq.getAligned();
+ for (int i = 0; i < alignedLength; i++) {
+ char base = toupper(aligned[i]);
+ if (base == 'A') { counts[itCount->second][i][0]+=num; }
+ else if (base == 'T') { counts[itCount->second][i][1]+=num; }
+ else if (base == 'G') { counts[itCount->second][i][2]+=num; }
+ else if (base == 'C') { counts[itCount->second][i][3]+=num; }
+ else { counts[itCount->second][i][4]+=num; }
+ }
+ }
+
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+ }
+
+ in.close();
+
+ return counts;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "driverGetCounts");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<Sequence> PrimerDesignCommand::createProcessesConSeqs(map<string, int>& nameMap, unsigned long int& numSeqs) {
+ try {
+ vector< vector< vector<unsigned int> > > counts;
+ vector<unsigned int> otuCounts;
+ vector<int> processIDS;
+ int process = 1;
+ unsigned long int fastaCount = 0;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ vector<unsigned long long> positions;
+ vector<fastaLinePair> lines;
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(fastaLinePair(positions[i], positions[(i+1)])); }
+
+ //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){
+ counts = driverGetCounts(nameMap, fastaCount, otuCounts, lines[process].start, lines[process].end);
+
+ string tempFile = toString(getpid()) + ".cons_counts.temp";
+ ofstream outTemp;
+ m->openOutputFile(tempFile, outTemp);
+
+ outTemp << fastaCount << endl;
+ //pass counts
+ outTemp << counts.size() << endl;
+ for (int i = 0; i < counts.size(); i++) {
+ outTemp << counts[i].size() << endl;
+ for (int j = 0; j < counts[i].size(); j++) {
+ for (int k = 0; k < 5; k++) { outTemp << counts[i][j][k] << '\t'; }
+ outTemp << endl;
+ }
+ }
+ //pass otuCounts
+ outTemp << otuCounts.size() << endl;
+ for (int i = 0; i < otuCounts.size(); i++) { outTemp << otuCounts[i] << '\t'; }
+ outTemp << endl;
+ outTemp.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ counts = driverGetCounts(nameMap, fastaCount, otuCounts, lines[0].start, lines[0].end);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFile = toString(processIDS[i]) + ".cons_counts.temp";
+ ifstream intemp;
+ m->openInputFile(tempFile, intemp);
+
+ unsigned long int num;
+ intemp >> num; m->gobble(intemp); fastaCount += num;
+ intemp >> num; m->gobble(intemp);
+ if (num != counts.size()) { m->mothurOut("[ERROR]: " + tempFile + " was not built correctly by the child process, quitting.\n"); m->control_pressed = true; }
+ else {
+ //read counts
+ for (int k = 0; k < num; k++) {
+ int alength;
+ intemp >> alength; m->gobble(intemp);
+ if (alength != alignedLength) { m->mothurOut("[ERROR]: your sequences are not all the same length. primer.design requires sequences to be aligned."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ for (int j = 0; j < alength; j++) {
+ for (int l = 0; l < 5; l++) { unsigned int numTemp; intemp >> numTemp; m->gobble(intemp); counts[k][j][l] += numTemp; }
+ }
+ }
+ }
+ //read otuCounts
+ intemp >> num; m->gobble(intemp);
+ for (int k = 0; k < num; k++) {
+ unsigned int numTemp; intemp >> numTemp; m->gobble(intemp);
+ otuCounts[k] += numTemp;
+ }
+ }
+ intemp.close();
+ m->mothurRemove(tempFile);
+ }
+
+
+#else
+ counts = driverGetCounts(nameMap, fastaCount, otuCounts, 0, 1000);
+#endif
+
+ //you will have a nameMap error if there is a namefile or countfile, but if those aren't given we want to make sure the fasta and list file match.
+ if (fastaCount != numSeqs) {
+ if ((namefile == "") && (countfile == "")) { m->mothurOut("[ERROR]: Your list file contains " + toString(list->getNumSeqs()) + " sequences, and your fasta file contains " + toString(fastaCount) + " sequences, aborting. Do you have the correct files? Perhaps you forgot to include the name or count file? \n"); }
+ m->control_pressed = true;
+ }
+
+ vector<Sequence> conSeqs;
+
+ if (m->control_pressed) { return conSeqs; }
+
+ //build consensus seqs
+ string snumBins = toString(counts.size());
+ for (int i = 0; i < counts.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ string otuLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { otuLabel += "0"; }
+ }
+ otuLabel += sbinNumber;
+
+ string cons = "";
+ for (int j = 0; j < counts[i].size(); j++) {
+ cons += getBase(counts[i][j], otuCounts[i]);
+ }
+ Sequence consSeq(otuLabel, cons);
+ conSeqs.push_back(consSeq);
+ }
+
+ if (m->control_pressed) { conSeqs.clear(); return conSeqs; }
+
+ return conSeqs;
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "createProcessesConSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+char PrimerDesignCommand::getBase(vector<unsigned int> counts, int size){ //A,T,G,C,Gap
+ try{
+ /* A = adenine
+ * C = cytosine
+ * G = guanine
+ * T = thymine
+ * R = G A (purine)
+ * Y = T C (pyrimidine)
+ * K = G T (keto)
+ * M = A C (amino)
+ * S = G C (strong bonds)
+ * W = A T (weak bonds)
+ * B = G T C (all but A)
+ * D = G A T (all but C)
+ * H = A C T (all but G)
+ * V = G C A (all but T)
+ * N = A G C T (any) */
+
+ char conBase = 'N';
+
+ //zero out counts that don't make the cutoff
+ float percentage = (100.0 - cutoff) / 100.0;
+
+ for (int i = 0; i < counts.size(); i++) {
+ float countPercentage = counts[i] / (float) size;
+ if (countPercentage < percentage) { counts[i] = 0; }
+ }
+
+ //any
+ if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
+ //any no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'N'; }
+ //all but T
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'v'; }
+ //all but T no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'V'; }
+ //all but G
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'h'; }
+ //all but G no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'H'; }
+ //all but C
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'd'; }
+ //all but C no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'D'; }
+ //all but A
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'b'; }
+ //all but A no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'B'; }
+ //W = A T (weak bonds)
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'w'; }
+ //W = A T (weak bonds) no gap
+ else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'W'; }
+ //S = G C (strong bonds)
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 's'; }
+ //S = G C (strong bonds) no gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'S'; }
+ //M = A C (amino)
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'm'; }
+ //M = A C (amino) no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'M'; }
+ //K = G T (keto)
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'k'; }
+ //K = G T (keto) no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'K'; }
+ //Y = T C (pyrimidine)
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'y'; }
+ //Y = T C (pyrimidine) no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'Y'; }
+ //R = G A (purine)
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'r'; }
+ //R = G A (purine) no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'R'; }
+ //only A
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'a'; }
+ //only A no gap
+ else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'A'; }
+ //only T
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 't'; }
+ //only T no gap
+ else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'T'; }
+ //only G
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'g'; }
+ //only G no gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'G'; }
+ //only C
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'c'; }
+ //only C no gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
+ //only gap
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
+ //cutoff removed all counts
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
+ else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
+
+ return conBase;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "getBase");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int PrimerDesignCommand::initializeCounts(vector< vector< vector<unsigned int> > >& counts, int length, map<string, int>& seq2Bin, map<string, int>& nameMap, vector<unsigned int>& otuCounts){
+ try {
+ counts.clear();
+ otuCounts.clear();
+ seq2Bin.clear();
+
+ //vector< vector< vector<unsigned int> > > counts - otu < spot_in_alignment < counts_for_A,T,G,C,Gap > > >
+ for (int i = 0; i < list->getNumBins(); i++) {
+ string binNames = list->get(i);
+ vector<string> names;
+ m->splitAtComma(binNames, names);
+ otuCounts.push_back(0);
+
+ //lets be smart and only map the unique names if a name or count file was given to save search time and memory
+ if ((namefile != "") || (countfile != "")) {
+ for (int j = 0; j < names.size(); j++) {
+ map<string, int>::iterator itNames = nameMap.find(names[j]);
+ if (itNames != nameMap.end()) { //add name because its a unique one
+ seq2Bin[names[j]] = i;
+ }
+ }
+ }else { //map everyone
+ for (int j = 0; j < names.size(); j++) { seq2Bin[names[j]] = i; }
+ }
+
+ vector<unsigned int> temp; temp.resize(5, 0); //A,T,G,C,Gap
+ vector< vector<unsigned int> > temp2;
+ for (int j = 0; j < length; j++) {
+ temp2.push_back(temp);
+ }
+ counts.push_back(temp2);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "initializeCounts");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+map<string, int> PrimerDesignCommand::readCount(unsigned long int& numSeqs){
+ try {
+ map<string, int> nameMap;
+
+ CountTable ct;
+ ct.readTable(countfile);
+ vector<string> namesOfSeqs = ct.getNamesOfSeqs();
+ numSeqs = ct.getNumUniqueSeqs();
+
+ for (int i = 0; i < namesOfSeqs.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ nameMap[namesOfSeqs[i]] = ct.getNumSeqs(namesOfSeqs[i]);
+ }
+
+ return nameMap;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "readCount");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int PrimerDesignCommand::getListVector(){
+ try {
+ InputData input(listfile, "list");
+ list = input.getListVector();
+ string lastLabel = list->getLabel();
+
+ if (label == "") { label = lastLabel; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return 0; }
+
+ if(labels.count(list->getLabel()) == 1){
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector(lastLabel);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = list->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ delete list;
+ list = input.getListVector();
+ }
+
+
+ if (m->control_pressed) { return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ delete list;
+ list = input.getListVector(lastLabel);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "getListVector");
+ exit(1);
+ }
+}
+//********************************************************************/
+/* A = adenine
+ * C = cytosine
+ * G = guanine
+ * T = thymine
+ * R = G A (purine)
+ * Y = T C (pyrimidine)
+ * K = G T (keto)
+ * M = A C (amino)
+ * S = G C (strong bonds)
+ * W = A T (weak bonds)
+ * B = G T C (all but A)
+ * D = G A T (all but C)
+ * H = A C T (all but G)
+ * V = G C A (all but T)
+ * N = A G C T (any) */
+int PrimerDesignCommand::countDiffs(string oligo, string seq){
+ try {
+
+ int length = oligo.length();
+ int countDiffs = 0;
+
+ for(int i=0;i<length;i++){
+
+ oligo[i] = toupper(oligo[i]);
+ seq[i] = toupper(seq[i]);
+
+ if(oligo[i] != seq[i]){
+ if(oligo[i] == 'A' && (seq[i] != 'A' && seq[i] != 'M' && seq[i] != 'R' && seq[i] != 'W' && seq[i] != 'D' && seq[i] != 'H' && seq[i] != 'V')) { countDiffs++; }
+ else if(oligo[i] == 'C' && (seq[i] != 'C' && seq[i] != 'Y' && seq[i] != 'M' && seq[i] != 'S' && seq[i] != 'B' && seq[i] != 'H' && seq[i] != 'V')) { countDiffs++; }
+ else if(oligo[i] == 'G' && (seq[i] != 'G' && seq[i] != 'R' && seq[i] != 'K' && seq[i] != 'S' && seq[i] != 'B' && seq[i] != 'D' && seq[i] != 'V')) { countDiffs++; }
+ else if(oligo[i] == 'T' && (seq[i] != 'T' && seq[i] != 'Y' && seq[i] != 'K' && seq[i] != 'W' && seq[i] != 'B' && seq[i] != 'D' && seq[i] != 'H')) { countDiffs++; }
+ else if((oligo[i] == '.' || oligo[i] == '-')) { countDiffs++; }
+ else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
+ else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { countDiffs++; }
+ else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { countDiffs++; }
+ else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { countDiffs++; }
+ else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
+ else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; }
+ else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
+ }
+
+ }
+
+ return countDiffs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "countDiffs");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff