+++ /dev/null
-/*
- * subsamplecommand.cpp
- * Mothur
- *
- * Created by westcott on 10/27/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "subsamplecommand.h"
-#include "sharedutilities.h"
-#include "deconvolutecommand.h"
-#include "subsample.h"
-
-//**********************************************************************************************************************
-vector<string> SubSampleCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "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", "FLSSR", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
- 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, "SubSampleCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string SubSampleCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n";
- helpString += "The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size, persample and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
- helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
- helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
- helpString += "The size parameter allows you indicate the size of your subsample.\n";
- helpString += "The persample parameter allows you indicate you want to select subsample of the same size from each of your groups, default=false. It is only used with the list and fasta files if a groupfile is given.\n";
- helpString += "persample=false will select a random set of sequences of the size you select, but the number of seqs from each group may differ.\n";
- helpString += "The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files if a groupfile is given and persample=true, then size=number of seqs in smallest sample, otherwise size=10% of number of seqs.\n";
- helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
- helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
- helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
- helpString += "The sub.sample command outputs a .subsample file.\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SubSampleCommand::SubSampleCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["shared"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SubSampleCommand::SubSampleCommand(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;
-
- //check to make sure all parameters are valid for command
- map<string,string>::iterator it;
- 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["shared"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
-
- //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 = ""; }
-
- //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("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("shared");
- //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["shared"] = 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("sabund");
- //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["sabund"] = inputDir + it->second; }
- }
-
- it = parameters.find("rabund");
- //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["rabund"] = 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; }
- }
- }
-
- //check for required parameters
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { listfile = ""; abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { m->setListFile(listfile); }
-
- sabundfile = validParameter.validFile(parameters, "sabund", true);
- if (sabundfile == "not open") { sabundfile = ""; abort = true; }
- else if (sabundfile == "not found") { sabundfile = ""; }
- else { m->setSabundFile(sabundfile); }
-
- rabundfile = validParameter.validFile(parameters, "rabund", true);
- if (rabundfile == "not open") { rabundfile = ""; abort = true; }
- else if (rabundfile == "not found") { rabundfile = ""; }
- else { m->setRabundFile(rabundfile); }
-
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { fastafile = ""; abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
- else { m->setFastaFile(fastafile); }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { m->setSharedFile(sharedfile); }
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { namefile = ""; abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { groupfile = ""; abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- //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 = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; pickedGroups = false; }
- else {
- pickedGroups = true;
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- string temp = validParameter.validFile(parameters, "size", false); if (temp == "not found"){ temp = "0"; }
- m->mothurConvert(temp, size);
-
- temp = validParameter.validFile(parameters, "persample", false); if (temp == "not found"){ temp = "f"; }
- persample = m->isTrue(temp);
-
- if (groupfile == "") { persample = false; }
-
- if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
-
- if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
- m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
-
- if (pickedGroups && ((groupfile == "") && (sharedfile == ""))) {
- m->mothurOut("You cannot pick groups without a valid group file or shared file."); m->mothurOutEndLine(); abort = true; }
-
- if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
- m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
-
- if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
- m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
-
- if ((fastafile != "") && (namefile == "")) {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int SubSampleCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if (sharedfile != "") { getSubSampleShared(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); return 0; } }
-
- if (listfile != "") { getSubSampleList(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); return 0; } }
-
- if (rabundfile != "") { getSubSampleRabund(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); return 0; } }
-
- if (sabundfile != "") { getSubSampleSabund(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); return 0; } }
-
- if (fastafile != "") { getSubSampleFasta(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); return 0; } }
-
- //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("shared");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
- }
-
- itTypes = outputTypes.find("rabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
- }
-
- itTypes = outputTypes.find("sabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(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, "SubSampleCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleFasta() {
- try {
-
- if (namefile != "") { readNames(); } //fills names with all names in namefile.
- else { getNames(); }//no name file, so get list of names to pick from
-
- GroupMap* groupMap;
- if (groupfile != "") {
-
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- //takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> namesGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, namesGroups);
- delete util;
-
- //file mismatch quit
- if (names.size() != groupMap->getNumSeqs()) {
- m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
- m->mothurOutEndLine();
- delete groupMap;
- return 0;
- }
- }
-
- if (m->control_pressed) { return 0; }
-
-
- //make sure that if your picked groups size is not too big
- int thisSize = names.size();
- if (persample) {
- if (size == 0) { //user has not set size, set size = smallest samples size
- size = groupMap->getNumSeqs(Groups[0]);
- for (int i = 1; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
-
- if (thisSize < size) { size = thisSize; }
- }
- }else { //make sure size is not too large
- vector<string> newGroups;
- for (int i = 0; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
-
- if (thisSize >= size) { newGroups.push_back(Groups[i]); }
- else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
- }
- Groups = newGroups;
- }
-
- m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
- }else {
- if (pickedGroups) {
- int total = 0;
- for(int i = 0; i < Groups.size(); i++) {
- total += groupMap->getNumSeqs(Groups[i]);
- }
-
- if (size == 0) { //user has not set size, set size = 10% samples size
- size = int (total * 0.10);
- }
-
- if (total < size) {
- if (size != 0) {
- m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
- }
- size = int (total * 0.10);
- }
-
- m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
- }
-
- if (size == 0) { //user has not set size, set size = 10% samples size
- size = int (names.size() * 0.10);
- }
-
- if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
- size = thisSize;
- }
-
- if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
-
- }
- random_shuffle(names.begin(), names.end());
-
- set<string> subset; //dont want repeat sequence names added
- if (persample) {
- //initialize counts
- map<string, int> groupCounts;
- map<string, int>::iterator itGroupCounts;
- for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
-
- for (int j = 0; j < names.size(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
- else{
- itGroupCounts = groupCounts.find(group);
- if (itGroupCounts != groupCounts.end()) {
- if (groupCounts[group] < size) { subset.insert(names[j]); groupCounts[group]++; }
- }
- }
- }
- }else {
-
- //randomly select a subset of those names to include in the subsample
- //since names was randomly shuffled just grab the next one
- for (int j = 0; j < names.size(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
- if (m->inUsersGroups(group, Groups)) {
- subset.insert(names[j]);
- }
- }else{
- subset.insert(names[j]);
- }
- }else{ //save everyone, group
- subset.insert(names[j]);
- }
-
- //do we have enough??
- if (subset.size() == size) { break; }
- }
- }
-
- if (subset.size() == 0) { m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine(); return 0; }
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- //read through fasta file outputting only the names on the subsample list
- ifstream in;
- m->openInputFile(fastafile, in);
-
- string thisname;
- int count = 0;
- map<string, vector<string> >::iterator itNameMap;
-
- while(!in.eof()){
-
- if (m->control_pressed) { in.close(); out.close(); return 0; }
-
- Sequence currSeq(in);
- thisname = currSeq.getName();
-
- if (thisname != "") {
-
- //does the subset contain a sequence that this sequence represents
- itNameMap = nameMap.find(thisname);
- if (itNameMap != nameMap.end()) {
- vector<string> nameRepresents = itNameMap->second;
-
- for (int i = 0; i < nameRepresents.size(); i++){
- if (subset.count(nameRepresents[i]) != 0) {
- out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
- count++;
- }
- }
- }else{
- m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
- }
- }
- m->gobble(in);
- }
- in.close();
- out.close();
-
- if (count != subset.size()) {
- m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
- }
-
- if (namefile != "") {
- m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
-
- //use unique.seqs to create new name and fastafile
- string inputString = "fasta=" + outputFileName;
- 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;
-
- outputTypes["name"].push_back(filenames["name"][0]); outputNames.push_back(filenames["name"][0]);
- m->mothurRemove(outputFileName);
- outputFileName = filenames["fasta"][0];
-
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
-
- m->mothurOut("Done."); m->mothurOutEndLine();
- }
-
- outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- //if a groupfile is provided read through the group file only outputting the names on the subsample list
- if (groupfile != "") {
-
- string groupOutputDir = outputDir;
- if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
- string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
-
- ofstream outGroup;
- m->openOutputFile(groupOutputFileName, outGroup);
- outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName);
-
- ifstream inGroup;
- m->openInputFile(groupfile, inGroup);
- string name, group;
-
- while(!inGroup.eof()){
-
- if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
-
- inGroup >> name; m->gobble(inGroup); //read from first column
- inGroup >> group; //read from second column
-
- //if this name is in the accnos file
- if (subset.count(name) != 0) {
- outGroup << name << '\t' << group << endl;
- subset.erase(name);
- }
-
- m->gobble(inGroup);
- }
- inGroup.close();
- outGroup.close();
-
- //sanity check
- if (subset.size() != 0) {
- m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
- for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
- m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
- }
- }
- }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::getNames() {
- try {
-
- ifstream in;
- m->openInputFile(fastafile, in);
-
- string thisname;
- while(!in.eof()){
-
- if (m->control_pressed) { in.close(); return 0; }
-
- Sequence currSeq(in);
- thisname = currSeq.getName();
-
- if (thisname != "") {
- vector<string> temp; temp.push_back(thisname);
- nameMap[thisname] = temp;
- names.push_back(thisname);
- }
- m->gobble(in);
- }
- in.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getNames");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::readNames() {
- try {
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, vector<string> >::iterator it;
-
- while(!in.eof()){
-
- if (m->control_pressed) { in.close(); return 0; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
- if (it == nameMap.end()) {
-
- vector<string> splitRepNames;
- m->splitAtComma(repnames, splitRepNames);
-
- nameMap[thisname] = splitRepNames;
- for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
-
- }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
-
- m->gobble(in);
- }
- in.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "readNames");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleShared() {
- try {
-
- InputData* input = new InputData(sharedfile, "sharedfile");
- vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
- string lastLabel = lookup[0]->getLabel();
-
- //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;
-
- if (size == 0) { //user has not set size, set size = smallest samples size
- size = lookup[0]->getNumSeqs();
- for (int i = 1; i < lookup.size(); i++) {
- int thisSize = lookup[i]->getNumSeqs();
-
- if (thisSize < size) { size = thisSize; }
- }
- }else {
- m->clearGroups();
- Groups.clear();
- vector<SharedRAbundVector*> temp;
- for (int i = 0; i < lookup.size(); i++) {
- if (lookup[i]->getNumSeqs() < size) {
- m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
- delete lookup[i];
- }else {
- Groups.push_back(lookup[i]->getGroup());
- temp.push_back(lookup[i]);
- }
- }
- lookup = temp;
- m->setGroups(Groups);
- }
-
- if (lookup.size() == 0) { m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
-
- m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } return 0; }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- processShared(lookup);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- }
-
- if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = lookup[0]->getLabel();
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
- lookup = input->getSharedRAbundVectors(lastLabel);
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- processShared(lookup);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
- lastLabel = lookup[0]->getLabel();
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- }
-
-
- if (m->control_pressed) { return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
- lookup = input->getSharedRAbundVectors(lastLabel);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- processShared(lookup);
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
- delete input;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
- try {
-
- //save mothurOut's binLabels to restore for next label
- vector<string> saveBinLabels = m->currentBinLabels;
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
-
- SubSample sample;
- vector<string> subsampledLabels = sample.getSample(thislookup, size);
-
- if (m->control_pressed) { return 0; }
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- m->currentBinLabels = subsampledLabels;
-
- thislookup[0]->printHeaders(out);
-
- for (int i = 0; i < thislookup.size(); i++) {
- out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(out);
- }
- out.close();
-
-
- //save mothurOut's binLabels to restore for next label
- m->currentBinLabels = saveBinLabels;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "processShared");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleList() {
- try {
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- InputData* input = new InputData(listfile, "list");
- ListVector* list = input->getListVector();
- string lastLabel = list->getLabel();
-
- //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;
-
- ofstream outGroup;
- GroupMap* groupMap;
- if (groupfile != "") {
-
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- //takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> namesGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, namesGroups);
- delete util;
-
- //create outputfiles
- string groupOutputDir = outputDir;
- if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
- string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
-
- m->openOutputFile(groupOutputFileName, outGroup);
- outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName);
-
- //file mismatch quit
- if (list->getNumSeqs() != groupMap->getNumSeqs()) {
- m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
- m->mothurOutEndLine();
- delete groupMap;
- delete list;
- delete input;
- out.close();
- outGroup.close();
- return 0;
- }
- }
-
- //make sure that if your picked groups size is not too big
- if (persample) {
- if (size == 0) { //user has not set size, set size = smallest samples size
- size = groupMap->getNumSeqs(Groups[0]);
- for (int i = 1; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
-
- if (thisSize < size) { size = thisSize; }
- }
- }else { //make sure size is not too large
- vector<string> newGroups;
- for (int i = 0; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
-
- if (thisSize >= size) { newGroups.push_back(Groups[i]); }
- else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
- }
- Groups = newGroups;
- }
-
- m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
- }else{
- if (pickedGroups) {
- int total = 0;
- for(int i = 0; i < Groups.size(); i++) {
- total += groupMap->getNumSeqs(Groups[i]);
- }
-
- if (size == 0) { //user has not set size, set size = 10% samples size
- size = int (total * 0.10);
- }
-
- if (total < size) {
- m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
- size = int (total * 0.10);
- }
-
- m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
- }else{
-
- if (size == 0) { //user has not set size, set size = 10% samples size
- size = int (list->getNumSeqs() * 0.10);
- }
-
- int thisSize = list->getNumSeqs();
- if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
- size = thisSize;
- }
-
- m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine();
- }
- }
-
-
- //fill names
- for (int i = 0; i < list->getNumBins(); i++) {
- string binnames = list->get(i);
-
- //parse names
- string individual = "";
- int length = binnames.length();
- for(int j=0;j<length;j++){
- if(binnames[j] == ','){
-
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
- if (m->inUsersGroups(group, Groups)) {
- names.push_back(individual);
- }
- }else{
- names.push_back(individual);
- }
- }else{ //save everyone, group
- names.push_back(individual);
- }
- individual = "";
- }
- else{
- individual += binnames[j];
- }
- }
- //save last name
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
- if (m->inUsersGroups(group, Groups)) {
- names.push_back(individual);
- }
- }else{
- names.push_back(individual);
- }
- }else{ //save everyone, group
- names.push_back(individual);
- }
- }
-
- random_shuffle(names.begin(), names.end());
-
- //randomly select a subset of those names to include in the subsample
- set<string> subset; //dont want repeat sequence names added
- if (persample) {
- //initialize counts
- map<string, int> groupCounts;
- map<string, int>::iterator itGroupCounts;
- for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
-
- for (int j = 0; j < names.size(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
- else{
- itGroupCounts = groupCounts.find(group);
- if (itGroupCounts != groupCounts.end()) {
- if (groupCounts[group] < size) { subset.insert(names[j]); groupCounts[group]++; }
- }
- }
- }
- }else{
- for (int j = 0; j < size; j++) {
-
- if (m->control_pressed) { break; }
-
- subset.insert(names[j]);
- }
- }
-
- if (groupfile != "") {
- //write out new groupfile
- for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
- string group = groupMap->getGroup(*it);
- if (group == "not found") { group = "NOTFOUND"; }
-
- outGroup << *it << '\t' << group << endl;
- }
- outGroup.close(); delete groupMap;
- }
-
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { delete list; delete input; out.close(); return 0; }
-
- if(allLines == 1 || labels.count(list->getLabel()) == 1){
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list, out, subset);
-
- 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);
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list, out, subset);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
- }
-
- lastLabel = list->getLabel();
-
- delete list; list = NULL;
-
- //get next line to process
- list = input->getListVector();
- }
-
-
- if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- list = input->getListVector(lastLabel);
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list, out, subset);
-
- delete list; list = NULL;
- }
-
- out.close();
- if (list != NULL) { delete list; }
- delete input;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getSubSampleList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
- try {
-
- int numBins = list->getNumBins();
-
- ListVector* temp = new ListVector();
- temp->setLabel(list->getLabel());
-
- for (int i = 0; i < numBins; i++) {
-
- if (m->control_pressed) { break; }
-
- string binnames = list->get(i);
-
- //parse names
- string individual = "";
- string newNames = "";
- int length = binnames.length();
- for(int j=0;j<length;j++){
- if(binnames[j] == ','){
- if (subset.count(individual) != 0) { newNames += individual + ","; }
- individual = "";
- }else{
- individual += binnames[j];
- }
- }
- if (subset.count(individual) != 0) { newNames += individual + ","; }
-
-
- //if there are names in this bin add to new list
- if (newNames != "") {
- newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
- temp->push_back(newNames);
- }
- }
-
- delete list;
- list = temp;
-
- if (m->control_pressed) { return 0; }
-
- list->print(out);
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "processList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleRabund() {
- try {
- InputData* input = new InputData(rabundfile, "rabund");
- RAbundVector* rabund = input->getRAbundVector();
- string lastLabel = rabund->getLabel();
-
- //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;
-
- if (size == 0) { //user has not set size, set size = 10%
- size = int((rabund->getNumSeqs()) * 0.10);
- }else if (size > rabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping rabund file."); m->mothurOutEndLine(); delete input; delete rabund; return 0; }
-
- m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; delete rabund; out.close(); return 0; }
-
- if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
-
- m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
-
- processRabund(rabund, out);
-
- processedLabels.insert(rabund->getLabel());
- userLabels.erase(rabund->getLabel());
- }
-
- if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = rabund->getLabel();
-
- delete rabund;
-
- rabund = input->getRAbundVector(lastLabel);
- m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
-
- processRabund(rabund, out);
-
- processedLabels.insert(rabund->getLabel());
- userLabels.erase(rabund->getLabel());
-
- //restore real lastlabel to save below
- rabund->setLabel(saveLabel);
- }
-
- lastLabel = rabund->getLabel();
-
- //prevent memory leak
- delete rabund; rabund = NULL;
-
- //get next line to process
- rabund = input->getRAbundVector();
- }
-
-
- if (m->control_pressed) { out.close(); return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (rabund != NULL) { delete rabund; }
-
- rabund = input->getRAbundVector(lastLabel);
-
- m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
-
- processRabund(rabund, out);
-
- delete rabund;
- }
-
- delete input;
- out.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
- try {
-
- int numBins = rabund->getNumBins();
- int thisSize = rabund->getNumSeqs();
-
- if (thisSize != size) {
-
- OrderVector* order = new OrderVector();
- for(int p=0;p<numBins;p++){
- for(int j=0;j<rabund->get(p);j++){
- order->push_back(p);
- }
- }
- random_shuffle(order->begin(), order->end());
-
- RAbundVector* temp = new RAbundVector(numBins);
- temp->setLabel(rabund->getLabel());
-
- delete rabund;
- rabund = temp;
-
- for (int j = 0; j < size; j++) {
-
- if (m->control_pressed) { delete order; return 0; }
-
- int bin = order->get(j);
-
- int abund = rabund->get(bin);
- rabund->set(bin, (abund+1));
- }
-
- delete order;
- }
-
- if (m->control_pressed) { return 0; }
-
- rabund->print(out);
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "processRabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleSabund() {
- try {
-
- InputData* input = new InputData(sabundfile, "sabund");
- SAbundVector* sabund = input->getSAbundVector();
- string lastLabel = sabund->getLabel();
-
- //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;
-
- if (size == 0) { //user has not set size, set size = 10%
- size = int((sabund->getNumSeqs()) * 0.10);
- }else if (size > sabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping sabund file."); m->mothurOutEndLine(); delete input; delete sabund; return 0; }
-
-
- m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; delete sabund; out.close(); return 0; }
-
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
-
- processSabund(sabund, out);
-
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = sabund->getLabel();
-
- delete sabund;
-
- sabund = input->getSAbundVector(lastLabel);
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
-
- processSabund(sabund, out);
-
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
- //restore real lastlabel to save below
- sabund->setLabel(saveLabel);
- }
-
- lastLabel = sabund->getLabel();
-
- //prevent memory leak
- delete sabund; sabund = NULL;
-
- //get next line to process
- sabund = input->getSAbundVector();
- }
-
-
- if (m->control_pressed) { out.close(); return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (sabund != NULL) { delete sabund; }
-
- sabund = input->getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
-
- processSabund(sabund, out);
-
- delete sabund;
- }
-
- delete input;
- out.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
- try {
-
- RAbundVector* rabund = new RAbundVector();
- *rabund = sabund->getRAbundVector();
-
- int numBins = rabund->getNumBins();
- int thisSize = rabund->getNumSeqs();
-
- if (thisSize != size) {
-
- OrderVector* order = new OrderVector();
- for(int p=0;p<numBins;p++){
- for(int j=0;j<rabund->get(p);j++){
- order->push_back(p);
- }
- }
- random_shuffle(order->begin(), order->end());
-
- RAbundVector* temp = new RAbundVector(numBins);
- temp->setLabel(rabund->getLabel());
-
- delete rabund;
- rabund = temp;
-
- for (int j = 0; j < size; j++) {
-
- if (m->control_pressed) { delete order; return 0; }
-
- int bin = order->get(j);
-
- int abund = rabund->get(bin);
- rabund->set(bin, (abund+1));
- }
-
- delete order;
- }
-
- if (m->control_pressed) { return 0; }
-
- delete sabund;
- sabund = new SAbundVector();
- *sabund = rabund->getSAbundVector();
- delete rabund;
-
- sabund->print(out);
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "processSabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
-
projects / mothur.git / blobdiff