--- /dev/null
+/*
+ * chimeraperseuscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 10/26/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "chimeraperseuscommand.h"
+#include "deconvolutecommand.h"
+#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> ChimeraPerseusCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter palpha("alpha", "Number", "", "-5.54", "", "", "",false,false); parameters.push_back(palpha);
+ CommandParameter pbeta("beta", "Number", "", "0.33", "", "", "",false,false); parameters.push_back(pbeta);
+
+ 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, "ChimeraPerseusCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChimeraPerseusCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The chimera.perseus command reads a fastafile and namefile and outputs potentially chimeric sequences.\n";
+ helpString += "The chimera.perseus command parameters are fasta, name, group, cutoff, processors, alpha and beta.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
+ helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
+ helpString += "The group parameter allows you to provide a group file. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "The alpha parameter .... The default is -5.54. \n";
+ helpString += "The beta parameter .... The default is 0.33. \n";
+ helpString += "The cutoff parameter .... The default is 0.50. \n";
+ helpString += "The chimera.perseus command should be in the following format: \n";
+ helpString += "chimera.perseus(fasta=yourFastaFile, name=yourNameFile) \n";
+ helpString += "Example: chimera.perseus(fasta=AD.align, name=AD.names) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChimeraPerseusCommand::ChimeraPerseusCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "ChimeraPerseusCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+ChimeraPerseusCommand::ChimeraPerseusCommand(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 {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter("chimera.uchime");
+ 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["chimera"] = tempOutNames;
+ outputTypes["accnos"] = 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 = ""; }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", false);
+ if (fastafile == "not found") {
+ //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " 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->splitAtDash(fastafile, fastaFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+
+ bool ignore = false;
+ if (fastaFileNames[i] == "current") {
+ fastaFileNames[i] = m->getFastaFile();
+ if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
+ }
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+
+ //check for required parameters
+ bool hasName = true;
+ namefile = validParameter.validFile(parameters, "name", false);
+ if (namefile == "not found") {
+ //if there is a current fasta file, use it
+ string filename = m->getNameFile();
+ if (filename != "") { nameFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ hasName = false;
+ }else {
+ m->splitAtDash(namefile, nameFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < nameFileNames.size(); i++) {
+
+ bool ignore = false;
+ if (nameFileNames[i] == "current") {
+ nameFileNames[i] = m->getNameFile();
+ if (nameFileNames[i] != "") { m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ nameFileNames.erase(nameFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(nameFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
+ m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ nameFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
+ m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ nameFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ nameFileNames.erase(nameFileNames.begin()+i);
+ i--;
+ }else {
+ m->setNameFile(nameFileNames[i]);
+ }
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
+
+ bool hasGroup = true;
+ groupfile = validParameter.validFile(parameters, "group", false);
+ if (groupfile == "not found") { groupfile = ""; hasGroup = false; }
+ else {
+ m->splitAtDash(groupfile, groupFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < groupFileNames.size(); i++) {
+
+ bool ignore = false;
+ if (groupFileNames[i] == "current") {
+ groupFileNames[i] = m->getGroupFile();
+ if (groupFileNames[i] != "") { m->mothurOut("Using " + groupFileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ groupFileNames.erase(groupFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(groupFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { groupFileNames[i] = inputDir + groupFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ ableToOpen = m->openInputFile(groupFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(groupFileNames[i]);
+ m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
+ m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ groupFileNames.erase(groupFileNames.begin()+i);
+ i--;
+ }else {
+ m->setGroupFile(groupFileNames[i]);
+ }
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (groupFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid group files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if (hasGroup && (groupFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of groupfiles does not match the number of fastafiles, please correct."); 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 = ""; }
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.50"; }
+ m->mothurConvert(temp, cutoff);
+
+ temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found"){ temp = "-5.54"; }
+ m->mothurConvert(temp, alpha);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.33"; }
+ m->mothurConvert(temp, beta);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "ChimeraPerseusCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int ChimeraPerseusCommand::execute(){
+ try{
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+
+ //process each file
+ for (int s = 0; s < fastaFileNames.size(); s++) {
+
+ m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+
+ int start = time(NULL);
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "perseus.chimera";
+ string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "perseus.accnos";
+ //string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
+
+ //you provided a groupfile
+ string groupFile = "";
+ if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; }
+
+ string nameFile = "";
+ if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
+ nameFile = nameFileNames[s];
+ }else { nameFile = getNamesFile(fastaFileNames[s]); }
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ int numSeqs = 0;
+ int numChimeras = 0;
+
+ if (groupFile != "") {
+ //Parse sequences by group
+ SequenceParser parser(groupFile, fastaFileNames[s], nameFile);
+ vector<string> groups = parser.getNamesOfGroups();
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ //clears files
+ ofstream out, out1, out2;
+ m->openOutputFile(outputFileName, out); out.close();
+ m->openOutputFile(accnosFileName, out1); out1.close();
+
+ if(processors == 1) { numSeqs = driverGroups(parser, outputFileName, accnosFileName, 0, groups.size(), groups); }
+ else { numSeqs = createProcessesGroups(parser, outputFileName, accnosFileName, groups, groupFile, fastaFileNames[s], nameFile); }
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ numChimeras = deconvoluteResults(parser, outputFileName, accnosFileName);
+
+ m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine();
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ }else{
+ if (processors != 1) { m->mothurOut("Without a groupfile, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
+
+ //read sequences and store sorted by frequency
+ vector<seqData> sequences = readFiles(fastaFileNames[s], nameFile);
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ numSeqs = driver(outputFileName, sequences, accnosFileName, numChimeras);
+ }
+
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences. " + toString(numChimeras) + " chimeras were found."); m->mothurOutEndLine();
+ outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
+ outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
+ }
+
+ //set accnos file as new current accnosfile
+ string current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
+ 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, "ChimeraPerseusCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ChimeraPerseusCommand::getNamesFile(string& inputFile){
+ try {
+ string nameFile = "";
+
+ m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ //use unique.seqs to create new name and fastafile
+ string inputString = "fasta=" + inputFile;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* uniqueCommand = new DeconvoluteCommand(inputString);
+ uniqueCommand->execute();
+
+ map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
+
+ delete uniqueCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ nameFile = filenames["name"][0];
+ inputFile = filenames["fasta"][0];
+
+ return nameFile;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "getNamesFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraPerseusCommand::driverGroups(SequenceParser& parser, string outputFName, string accnos, int start, int end, vector<string> groups){
+ try {
+
+ int totalSeqs = 0;
+ int numChimeras = 0;
+
+ for (int i = start; i < end; i++) {
+
+ m->mothurOutEndLine(); m->mothurOut("Checking sequences from group " + groups[i] + "..."); m->mothurOutEndLine();
+
+ int start = time(NULL); if (m->control_pressed) { return 0; }
+
+ vector<seqData> sequences = loadSequences(parser, groups[i]);
+
+ if (m->control_pressed) { return 0; }
+
+ int numSeqs = driver((outputFName + groups[i]), sequences, (accnos+groups[i]), numChimeras);
+ totalSeqs += numSeqs;
+
+ if (m->control_pressed) { return 0; }
+
+ //append files
+ m->appendFiles((outputFName+groups[i]), outputFName); m->mothurRemove((outputFName+groups[i]));
+ m->appendFiles((accnos+groups[i]), accnos); m->mothurRemove((accnos+groups[i]));
+
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + groups[i] + "."); m->mothurOutEndLine();
+ }
+
+ return totalSeqs;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "driverGroups");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<seqData> ChimeraPerseusCommand::loadSequences(SequenceParser& parser, string group){
+ try {
+
+ vector<Sequence> thisGroupsSeqs = parser.getSeqs(group);
+ map<string, string> nameMap = parser.getNameMap(group);
+ map<string, string>::iterator it;
+
+ vector<seqData> sequences;
+ bool error = false;
+ alignLength = 0;
+
+ for (int i = 0; i < thisGroupsSeqs.size(); i++) {
+
+ if (m->control_pressed) { return sequences; }
+
+ it = nameMap.find(thisGroupsSeqs[i].getName());
+ if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
+ else {
+ int num = m->getNumNames(it->second);
+ sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
+ if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
+ }
+ }
+
+ if (error) { m->control_pressed = true; }
+
+ //sort by frequency
+ sort(sequences.rbegin(), sequences.rend());
+
+ return sequences;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "loadSequences");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, string name){
+ try {
+ map<string, int>::iterator it;
+ map<string, int> nameMap = m->readNames(name);
+
+ //read fasta file and create sequenceData structure - checking for file mismatches
+ vector<seqData> sequences;
+ bool error = false;
+ ifstream in;
+ m->openInputFile(inputFile, in);
+ alignLength = 0;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return sequences; }
+
+ Sequence temp(in); m->gobble(in);
+
+ it = nameMap.find(temp.getName());
+ if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
+ else {
+ sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
+ if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
+ }
+ }
+ in.close();
+
+ if (error) { m->control_pressed = true; }
+
+ //sort by frequency
+ sort(sequences.rbegin(), sequences.rend());
+
+ return sequences;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "getNamesFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& sequences, string accnosFileName, int& numChimeras){
+ try {
+
+ vector<vector<double> > correctModel(4); //could be an option in the future to input own model matrix
+ for(int i=0;i<4;i++){ correctModel[i].resize(4); }
+
+ correctModel[0][0] = 0.000000; //AA
+ correctModel[1][0] = 11.619259; //CA
+ correctModel[2][0] = 11.694004; //TA
+ correctModel[3][0] = 7.748623; //GA
+
+ correctModel[1][1] = 0.000000; //CC
+ correctModel[2][1] = 7.619657; //TC
+ correctModel[3][1] = 12.852562; //GC
+
+ correctModel[2][2] = 0.000000; //TT
+ correctModel[3][2] = 10.964048; //TG
+
+ correctModel[3][3] = 0.000000; //GG
+
+ for(int i=0;i<4;i++){
+ for(int j=0;j<i;j++){
+ correctModel[j][i] = correctModel[i][j];
+ }
+ }
+
+ int numSeqs = sequences.size();
+ //int alignLength = sequences[0].sequence.size();
+
+ ofstream chimeraFile;
+ ofstream accnosFile;
+ m->openOutputFile(chimeraFileName, chimeraFile);
+ m->openOutputFile(accnosFileName, accnosFile);
+
+ Perseus myPerseus;
+ vector<vector<double> > binMatrix = myPerseus.binomial(alignLength);
+
+ chimeraFile << "SequenceIndex\tName\tDiffsToBestMatch\tBestMatchIndex\tBestMatchName\tDiffstToChimera\tIndexofLeftParent\tIndexOfRightParent\tNameOfLeftParent\tNameOfRightParent\tDistanceToBestMatch\tcIndex\t(cIndex - singleDist)\tloonIndex\tMismatchesToChimera\tMismatchToTrimera\tChimeraBreakPoint\tLogisticProbability\tTypeOfSequence\n";
+
+ vector<bool> chimeras(numSeqs, 0);
+
+ for(int i=0;i<numSeqs;i++){
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ vector<bool> restricted = chimeras;
+
+ vector<vector<int> > leftDiffs(numSeqs);
+ vector<vector<int> > leftMaps(numSeqs);
+ vector<vector<int> > rightDiffs(numSeqs);
+ vector<vector<int> > rightMaps(numSeqs);
+
+ vector<int> singleLeft, bestLeft;
+ vector<int> singleRight, bestRight;
+
+ int bestSingleIndex, bestSingleDiff;
+ vector<pwAlign> alignments(numSeqs);
+
+ int comparisons = myPerseus.getAlignments(i, sequences, alignments, leftDiffs, leftMaps, rightDiffs, rightMaps, bestSingleIndex, bestSingleDiff, restricted);
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ int minMismatchToChimera, leftParentBi, rightParentBi, breakPointBi;
+
+ string dummyA, dummyB;
+
+ if (sequences[i].sequence.size() < 3) {
+ chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
+ }else if(comparisons >= 2){
+ minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ int minMismatchToTrimera = numeric_limits<int>::max();
+ int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
+
+ if(minMismatchToChimera >= 3 && comparisons >= 3){
+ minMismatchToTrimera = myPerseus.getTrimera(sequences, leftDiffs, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight, restricted);
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+ }
+
+ double singleDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, sequences[bestSingleIndex].sequence, dummyA, dummyB, correctModel);
+
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ string type;
+ string chimeraRefSeq;
+
+ if(minMismatchToChimera - minMismatchToTrimera >= 3){
+ type = "trimera";
+ chimeraRefSeq = myPerseus.stitchTrimera(alignments, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, leftMaps, rightMaps);
+ }
+ else{
+ type = "chimera";
+ chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, leftMaps, rightMaps);
+ }
+ ;
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ double chimeraDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq, dummyA, dummyB, correctModel);
+
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ double cIndex = chimeraDist;//modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq);
+ double loonIndex = myPerseus.calcLoonIndex(sequences[i].sequence, sequences[leftParentBi].sequence, sequences[rightParentBi].sequence, breakPointBi, binMatrix);
+
+ if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
+
+ chimeraFile << i << '\t' << sequences[i].seqName << '\t' << bestSingleDiff << '\t' << bestSingleIndex << '\t' << sequences[bestSingleIndex].seqName << '\t';
+ chimeraFile << minMismatchToChimera << '\t' << leftParentBi << '\t' << rightParentBi << '\t' << sequences[leftParentBi].seqName << '\t' << sequences[rightParentBi].seqName << '\t';
+ chimeraFile << singleDist << '\t' << cIndex << '\t' << (cIndex - singleDist) << '\t' << loonIndex << '\t';
+ chimeraFile << minMismatchToChimera << '\t' << minMismatchToTrimera << '\t' << breakPointBi << '\t';
+
+ double probability = myPerseus.classifyChimera(singleDist, cIndex, loonIndex, alpha, beta);
+
+ chimeraFile << probability << '\t';
+
+ if(probability > cutoff){
+ chimeraFile << type << endl;
+ accnosFile << sequences[i].seqName << endl;
+ chimeras[i] = 1;
+ numChimeras++;
+ }
+ else{
+ chimeraFile << "good" << endl;
+ }
+
+ }
+ else{
+ chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
+ }
+
+ //report progress
+ if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1) + "\n"); }
+ }
+
+ if((numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n"); }
+
+ chimeraFile.close();
+ accnosFile.close();
+
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "driver");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int ChimeraPerseusCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string accnos, vector<string> groups, string group, string fasta, string name) {
+ try {
+
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
+
+ //sanity check
+ if (groups.size() < processors) { processors = groups.size(); }
+
+ //divide the groups between the processors
+ vector<linePair> lines;
+ int numGroupsPerProcessor = groups.size() / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numGroupsPerProcessor;
+ int endIndex = (i+1) * numGroupsPerProcessor;
+ if(i == (processors - 1)){ endIndex = groups.size(); }
+ 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){
+ num = driverGroups(parser, outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputFName + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.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
+ num = driverGroups(parser, outputFName, accnos, lines[0].start, lines[0].end, groups);
+
+ //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++) {
+ ifstream in;
+ string tempFile = outputFName + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); m->mothurRemove(tempFile);
+ }
+
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<perseusData*> 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";
+
+ perseusData* tempPerseus = new perseusData(alpha, beta, cutoff, outputFName+extension, fasta, name, group, accnos+extension, groups, m, lines[i].start, lines[i].end, i);
+
+ pDataArray.push_back(tempPerseus);
+ processIDS.push_back(i);
+
+ //MyPerseusThreadFunction 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, MyPerseusThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+
+ //using the main process as a worker saves time and memory
+ num = driverGroups(parser, outputFName, accnos, lines[0].start, lines[0].end, groups);
+
+ //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++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
+ m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
+ m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
+ }
+
+ return num;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "createProcessesGroups");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ChimeraPerseusCommand::deconvoluteResults(SequenceParser& parser, string outputFileName, string accnosFileName){
+ try {
+ map<string, string> uniqueNames = parser.getAllSeqsMap();
+ map<string, string>::iterator itUnique;
+ int total = 0;
+
+ //edit accnos file
+ ifstream in2;
+ m->openInputFile(accnosFileName, in2);
+
+ ofstream out2;
+ m->openOutputFile(accnosFileName+".temp", out2);
+
+ string name;
+ set<string> namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once
+ set<string>::iterator itNames;
+ set<string> chimerasInFile;
+ set<string>::iterator itChimeras;
+
+
+ while (!in2.eof()) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+
+ in2 >> name; m->gobble(in2);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ itChimeras = chimerasInFile.find((itUnique->second));
+
+ if (itChimeras == chimerasInFile.end()) {
+ out2 << itUnique->second << endl;
+ chimerasInFile.insert((itUnique->second));
+ total++;
+ }
+ }
+ }
+ in2.close();
+ out2.close();
+
+ m->mothurRemove(accnosFileName);
+ rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
+
+ //edit chimera file
+ ifstream in;
+ m->openInputFile(outputFileName, in);
+
+ ofstream out;
+ m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ int DiffsToBestMatch, BestMatchIndex, DiffstToChimera, IndexofLeftParent, IndexOfRightParent;
+ float temp1,temp2, temp3, temp4, temp5, temp6, temp7, temp8;
+ string index, BestMatchName, parent1, parent2, flag;
+ name = "";
+ namesInFile.clear();
+ //assumptions - in file each read will always look like
+ /*
+ SequenceIndex Name DiffsToBestMatch BestMatchIndex BestMatchName DiffstToChimera IndexofLeftParent IndexOfRightParent NameOfLeftParent NameOfRightParent DistanceToBestMatch cIndex (cIndex - singleDist) loonIndex MismatchesToChimera MismatchToTrimera ChimeraBreakPoint LogisticProbability TypeOfSequence
+ 0 F01QG4L02JVBQY 0 0 Null 0 0 0 Null Null 0.0 0.0 0.0 0.0 0 0 0 0.0 0.0 good
+ 1 F01QG4L02ICTC6 0 0 Null 0 0 0 Null Null 0.0 0.0 0.0 0.0 0 0 0 0.0 0.0 good
+ 2 F01QG4L02JZOEC 48 0 F01QG4L02JVBQY 47 0 0 F01QG4L02JVBQY F01QG4L02JVBQY 2.0449 2.03545 -0.00944493 0 47 2147483647 138 0 good
+ 3 F01QG4L02G7JEC 42 0 F01QG4L02JVBQY 40 1 0 F01QG4L02ICTC6 F01QG4L02JVBQY 1.87477 1.81113 -0.0636404 5.80145 40 2147483647 25 0 good
+ */
+
+ //get and print headers
+ BestMatchName = m->getline(in); m->gobble(in);
+ out << BestMatchName << endl;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
+
+ bool print = false;
+ in >> index; m->gobble(in);
+
+ if (index != "SequenceIndex") { //if you are not a header line, there will be a header line for each group if group file is given
+ in >> name; m->gobble(in);
+ in >> DiffsToBestMatch; m->gobble(in);
+ in >> BestMatchIndex; m->gobble(in);
+ in >> BestMatchName; m->gobble(in);
+ in >> DiffstToChimera; m->gobble(in);
+ in >> IndexofLeftParent; m->gobble(in);
+ in >> IndexOfRightParent; m->gobble(in);
+ in >> parent1; m->gobble(in);
+ in >> parent2; m->gobble(in);
+ in >> temp1 >> temp2 >> temp3 >> temp4 >> temp5 >> temp6 >> temp7 >> temp8 >> flag; m->gobble(in);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ name = itUnique->second;
+ //is this name already in the file
+ itNames = namesInFile.find((name));
+
+ if (itNames == namesInFile.end()) { //no not in file
+ if (flag == "good") { //are you really a no??
+ //is this sequence really not chimeric??
+ itChimeras = chimerasInFile.find(name);
+
+ //then you really are a no so print, otherwise skip
+ if (itChimeras == chimerasInFile.end()) { print = true; }
+ }else{ print = true; }
+ }
+ }
+
+ if (print) {
+ out << index << '\t' << name << '\t' << DiffsToBestMatch << '\t' << BestMatchIndex << '\t';
+ namesInFile.insert(name);
+
+ if (BestMatchName != "Null") {
+ itUnique = uniqueNames.find(BestMatchName);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find BestMatchName "+ BestMatchName + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << '\t'; }
+ }else { out << "Null" << '\t'; }
+
+ out << DiffstToChimera << '\t' << IndexofLeftParent << '\t' << IndexOfRightParent << '\t';
+
+ if (parent1 != "Null") {
+ itUnique = uniqueNames.find(parent1);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parent1 "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << '\t'; }
+ }else { out << "Null" << '\t'; }
+
+ if (parent1 != "Null") {
+ itUnique = uniqueNames.find(parent2);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parent2 "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << '\t'; }
+ }else { out << "Null" << '\t'; }
+
+ out << temp1 << '\t' << temp2 << '\t' << temp3 << '\t' << temp4 << '\t' << temp5 << '\t' << temp6 << '\t' << temp7 << '\t' << temp8 << '\t' << flag << endl;
+ }
+ }else { index = m->getline(in); m->gobble(in); }
+ }
+ in.close();
+ out.close();
+
+ m->mothurRemove(outputFileName);
+ rename((outputFileName+".temp").c_str(), outputFileName.c_str());
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "deconvoluteResults");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff