--- /dev/null
+/*
+ * splitabundcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "splitabundcommand.h"
+
+//**********************************************************************************************************************
+vector<string> SplitAbundCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(paccnos);
+ 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, "SplitAbundCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SplitAbundCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n";
+ helpString += "The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n";
+ helpString += "The fasta and a list or name parameter are required, and you must provide a cutoff value.\n";
+ helpString += "The cutoff parameter is used to qualify what is abundant and rare.\n";
+ helpString += "The group parameter allows you to parse a group file into rare and abundant groups.\n";
+ helpString += "The label parameter is used to read specific labels in your listfile you want to use.\n";
+ helpString += "The accnos parameter allows you to output a .rare.accnos and .abund.accnos files to use with the get.seqs and remove.seqs commands.\n";
+ helpString += "The groups parameter allows you to parse the files into rare and abundant files by group. \n";
+ helpString += "For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files. \n";
+ helpString += "If you want .abund and .rare files for all groups, set groups=all. \n";
+ helpString += "The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n";
+ helpString += "Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+SplitAbundCommand::SplitAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SplitAbundCommand::SplitAbundCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //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;
+ 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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["fasta"] = 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("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; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = 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; }
+ }
+
+ }
+
+
+ //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 = ""; }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else{ inputFile = listfile; m->setListFile(listfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else{ inputFile = namefile; m->setNameFile(namefile); }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { 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); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else {
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ m->setGroupFile(groupfile);
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else if (groups == "all") {
+ if (groupfile != "") { Groups = groupMap->getNamesOfGroups(); }
+ else { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; }
+ }else {
+ m->splitAtDash(groups, Groups);
+ }
+
+ if ((groupfile == "") && (groups != "")) { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; Groups.clear(); }
+
+ //do you have all files needed
+ if ((listfile == "") && (namefile == "")) {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else {
+ 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 list or namefile and the list or name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; allLines = 1; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ string temp = validParameter.validFile(parameters, "accnos", false); if (temp == "not found") { temp = "F"; }
+ accnos = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, cutoff);
+
+ if (cutoff == 0) { m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SplitAbundCommand::~SplitAbundCommand(){
+ if (groupfile != "") { delete groupMap; }
+}
+//**********************************************************************************************************************
+int SplitAbundCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (listfile != "") { //you are using a listfile to determine abundance
+ if (outputDir == "") { outputDir = m->hasPath(listfile); }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ input = new InputData(listfile, "list");
+ list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ //do you have a namefile or do we need to similate one?
+ if (namefile != "") { readNamesFile(); }
+ else { createNameMap(list); }
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ splitList(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(lastLabel); //get new list vector to process
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ splitList(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(); //get new list vector to process
+ }
+
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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();
+ }
+
+ }
+
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel); //get new list vector to process
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ splitList(list);
+
+ delete list;
+ }
+
+ delete input;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ }else { //you are using the namefile to determine abundance
+ if (outputDir == "") { outputDir = m->hasPath(namefile); }
+
+ splitNames();
+ writeNames();
+
+ string tag = "";
+ if (groupfile != "") { parseGroup(tag); }
+ if (accnos) { writeAccnos(tag); }
+ if (fastafile != "") { parseFasta(tag); }
+ }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(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, "SplitAbundCommand", "execute");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::splitList(ListVector* thisList) {
+ try {
+ rareNames.clear();
+ abundNames.clear();
+
+ //get rareNames and abundNames
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string bin = thisList->get(i);
+
+ vector<string> names;
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
+ int size = names.size();
+
+ if (size <= cutoff) {
+ for (int j = 0; j < names.size(); j++) { rareNames.insert(names[j]); }
+ }else{
+ for (int j = 0; j < names.size(); j++) { abundNames.insert(names[j]); }
+ }
+ }//end for
+
+
+ string tag = thisList->getLabel() + ".";
+
+ writeList(thisList, tag);
+
+ if (groupfile != "") { parseGroup(tag); }
+ if (accnos) { writeAccnos(tag); }
+ if (fastafile != "") { parseFasta(tag); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "splitList");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::writeList(ListVector* thisList, string tag) {
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ SAbundVector* sabund = new SAbundVector();
+ *sabund = thisList->getSAbundVector();
+
+ //find out how many bins are rare and how many are abundant so you can process the list vector one bin at a time
+ // and don't have to store the bins until you are done with the whole vector, this save alot of space.
+ int numRareBins = 0;
+ for (int i = 0; i <= sabund->getMaxRank(); i++) {
+ if (i > cutoff) { break; }
+ numRareBins += sabund->get(i);
+ }
+ int numAbundBins = thisList->getNumBins() - numRareBins;
+ delete sabund;
+
+ ofstream aout;
+ ofstream rout;
+
+ string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare.list";
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["list"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund.list";
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["list"].push_back(abund);
+
+ if (rareNames.size() != 0) { rout << thisList->getLabel() << '\t' << numRareBins << '\t'; }
+ if (abundNames.size() != 0) { aout << thisList->getLabel() << '\t' << numAbundBins << '\t'; }
+
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
+ string bin = list->get(i);
+
+ int size = m->getNumNames(bin);
+
+ if (size <= cutoff) { rout << bin << '\t'; }
+ else { aout << bin << '\t'; }
+ }
+
+ if (rareNames.size() != 0) { rout << endl; }
+ if (abundNames.size() != 0) { aout << endl; }
+
+ rout.close();
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+ ofstream* temp;
+ ofstream* temp2;
+ //map<string, bool> wroteFile;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ m->openOutputFile(fileroot + Groups[i] + tag + ".rare.list", *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + Groups[i] + tag + ".abund.list", *(filehandles[Groups[i]+".abund"]));
+ outputNames.push_back(fileroot + Groups[i] + tag + ".rare.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".rare.list");
+ outputNames.push_back(fileroot + Groups[i] + tag + ".abund.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".abund.list");
+ }
+
+ map<string, string> groupVector;
+ map<string, string>::iterator itGroup;
+ map<string, int> groupNumBins;
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ groupNumBins[it3->first] = 0;
+ groupVector[it3->first] = "";
+ }
+
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
+ map<string, string> groupBins;
+ string bin = list->get(i);
+
+ vector<string> names;
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
+
+ //parse bin into list of sequences in each group
+ for (int j = 0; j < names.size(); j++) {
+ string rareAbund;
+ if (rareNames.count(names[j]) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ string group = groupMap->getGroup(names[j]);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ itGroup = groupBins.find(group+rareAbund);
+ if(itGroup == groupBins.end()) {
+ groupBins[group+rareAbund] = names[j]; //add first name
+ groupNumBins[group+rareAbund]++;
+ }else{ //add another name
+ groupBins[group+rareAbund] += "," + names[j];
+ }
+ }else if(group == "not found") {
+ m->mothurOut(names[j] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+
+
+ for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
+ groupVector[itGroup->first] += itGroup->second + '\t';
+ }
+ }
+
+ //end list vector
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group
+ (*(filehandles[it3->first])).close();
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "writeList");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::splitNames() { //namefile
+ try {
+
+ rareNames.clear();
+ abundNames.clear();
+
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; m->gobble(in);
+
+ nameMap[firstCol] = secondCol;
+
+ int size = m->getNumNames(secondCol);
+
+ if (size <= cutoff) {
+ rareNames.insert(firstCol);
+ }else{
+ abundNames.insert(firstCol);
+ }
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "splitNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::readNamesFile() {
+ try {
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; m->gobble(in);
+
+ nameMap[firstCol] = secondCol;
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "readNamesFile");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::createNameMap(ListVector* thisList) {
+ try {
+
+ if (thisList != NULL) {
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string bin = thisList->get(i);
+
+ vector<string> names;
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
+
+ for (int j = 0; j < names.size(); j++) { nameMap[names[j]] = names[j]; }
+ }//end for
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "createNameMap");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::writeNames() { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ string rare = outputDir + m->getRootName(m->getSimpleName(namefile)) + "rare.names";
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["name"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(namefile)) + "abund.names";
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["name"].push_back(abund);
+
+ if (rareNames.size() != 0) {
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ rout << (*itRare) << '\t' << nameMap[(*itRare)] << endl;
+ }
+ }
+ rout.close();
+
+ if (abundNames.size() != 0) {
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ aout << (*itAbund) << '\t' << nameMap[(*itAbund)] << endl;
+ }
+ }
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(namefile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ m->openOutputFile(fileroot + Groups[i] + ".rare.names", *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + Groups[i] + ".abund.names", *(filehandles[Groups[i]+".abund"]));
+ }
+
+ for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
+ vector<string> names;
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
+
+ string rareAbund;
+ if (rareNames.count(itName->first) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ map<string, string> outputStrings;
+ map<string, string>::iterator itout;
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(names[i]);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ itout = outputStrings.find(group+rareAbund);
+ if (itout == outputStrings.end()) {
+ outputStrings[group+rareAbund] = names[i] + '\t' + names[i];
+ }else { outputStrings[group+rareAbund] += "," + names[i]; }
+ }else if(group == "not found") {
+ m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+
+ for (itout = outputStrings.begin(); itout != outputStrings.end(); itout++) { *(filehandles[itout->first]) << itout->second << endl; }
+ }
+
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ outputNames.push_back(fileroot + it3->first + ".names"); outputTypes["name"].push_back(fileroot + it3->first + ".names");
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "writeNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+//just write the unique names - if a namesfile is given
+int SplitAbundCommand::writeAccnos(string tag) {
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+
+ string rare = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "rare.accnos";
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["accnos"].push_back(rare);
+
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ rout << (*itRare) << endl;
+ }
+ rout.close();
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "abund.accnos";
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
+
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ aout << (*itAbund) << endl;
+ }
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ m->openOutputFile(fileroot + tag + Groups[i] + ".rare.accnos", *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + tag + Groups[i] + ".abund.accnos", *(filehandles[Groups[i]+".abund"]));
+ }
+
+ //write rare
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ string group = groupMap->getGroup(*itRare);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+".rare"]) << *itRare << endl;
+ }
+ }
+
+ //write abund
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ string group = groupMap->getGroup(*itAbund);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+".abund"]) << *itAbund << endl;
+ }
+ }
+
+ //close files
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ outputNames.push_back(fileroot + tag + it3->first + ".accnos"); outputTypes["accnos"].push_back(fileroot + tag + it3->first + ".accnos");
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "writeAccnos");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::parseGroup(string tag) { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ string rare = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "rare.groups";
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["group"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "abund.groups";
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["group"].push_back(abund);
+
+ for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
+ vector<string> names;
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
+
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(names[i]);
+
+ if (group == "not found") {
+ m->mothurOut(names[i] + " is not in your groupfile, ignoring, please correct."); m->mothurOutEndLine();
+ }else {
+ if (rareNames.count(itName->first) != 0) { //you are a rare name
+ rout << names[i] << '\t' << group << endl;
+ }else{ //you are a abund name
+ aout << names[i] << '\t' << group << endl;
+ }
+ }
+ }
+ }
+
+ rout.close();
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ m->openOutputFile(fileroot + tag + Groups[i] + ".rare.groups", *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + tag + Groups[i] + ".abund.groups", *(filehandles[Groups[i]+".abund"]));
+ }
+
+ for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
+ vector<string> names;
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
+
+ string rareAbund;
+ if (rareNames.count(itName->first) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(names[i]);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+rareAbund]) << names[i] << '\t' << group << endl;
+ }
+ }
+ }
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ outputNames.push_back(fileroot + tag + it3->first + ".groups"); outputTypes["group"].push_back(fileroot + tag + it3->first + ".groups");
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "parseGroups");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::parseFasta(string tag) { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ string rare = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "rare.fasta";
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "abund.fasta";
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+
+ map<string, string>::iterator itNames;
+
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) {
+ m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
+ }else{
+ if (rareNames.count(seq.getName()) != 0) { //you are a rare name
+ seq.printSequence(rout);
+ }else{ //you are a abund name
+ seq.printSequence(aout);
+ }
+ }
+ }
+ }
+ in.close();
+ rout.close();
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ m->openOutputFile(fileroot + tag + Groups[i] + ".rare.fasta", *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + tag + Groups[i] + ".abund.fasta", *(filehandles[Groups[i]+".abund"]));
+ }
+
+ //open input file
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+ map<string, string>::iterator itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) {
+ m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
+ }else{
+ vector<string> names;
+ m->splitAtComma(itNames->second, names); //parses bin into individual sequence names
+
+ string rareAbund;
+ if (rareNames.count(itNames->first) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(seq.getName());
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ seq.printSequence(*(filehandles[group+rareAbund]));
+ }else if(group == "not found") {
+ m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+ }
+ }
+ }
+ in.close();
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ outputNames.push_back(fileroot + tag + it3->first + ".fasta"); outputTypes["fasta"].push_back(fileroot + tag + it3->first + ".fasta");
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "parseFasta");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+
projects / mothur.git / blobdiff