+++ /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