*/
#include "subsamplecommand.h"
+#include "sharedutilities.h"
+#include "deconvolutecommand.h"
//**********************************************************************************************************************
-vector<string> SubSampleCommand::getValidParameters(){
- try {
- string Array[] = {"fasta", "group", "list","shared","rabund", "name","sabund","size","groups","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+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", "getValidParameters");
+ 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;
- //initialize outputTypes
+ abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["list"] = tempOutNames;
}
}
//**********************************************************************************************************************
-vector<string> SubSampleCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","list","shared","rabund", "sabund","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SubSampleCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getRequiredFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta", "group", "list","shared","rabund", "sabund","name","size","groups","label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
- else if (listfile == "not found") { listfile = ""; }
+ 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...
else {
pickedGroups = true;
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->setGroups(Groups);
}
string temp = validParameter.validFile(parameters, "size", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, size);
+ 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 ((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);
+ }
}
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void SubSampleCommand::help(){
- try {
- m->mothurOut("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");
- m->mothurOut("The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n");
- m->mothurOut("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");
- m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
- m->mothurOut("The size parameter allows you indicate the size of your subsample.\n");
- m->mothurOut("The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files, 10% of number of seqs.\n");
- m->mothurOut("The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
- m->mothurOut("The sub.sample command outputs a .subsample file.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-SubSampleCommand::~SubSampleCommand(){}
-
//**********************************************************************************************************************
int SubSampleCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (sharedfile != "") { getSubSampleShared(); }
- //if (listfile != "") { getSubSampleList(); }
- //if (rabund != "") { getSubSampleRabund(); }
- //if (sabundfile != "") { getSubSampleSabund(); }
- //if (fastafile != "") { getSubSampleFasta(); }
-
+ 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(); }
}
}
//**********************************************************************************************************************
-int SubSampleCommand::getSubSampleShared() {
+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(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile);
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
ofstream out;
m->openOutputFile(outputFileName, out);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ //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) { out.close(); return 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, out);
-
+ 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, out);
+ processShared(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
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) { out.close(); return 0; }
-
+ if (m->control_pressed) { return 0; }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
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]; } }
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- processShared(lookup, out);
+ processShared(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
-
- out.close();
-
+
+ delete input;
+
return 0;
-
+
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
}
}
//**********************************************************************************************************************
-int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofstream& out) {
+int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
try {
- if (pickedGroups) { eliminateZeroOTUS(thislookup); }
+ //save mothurOut's binLabels to restore for next label
+ vector<string> saveBinLabels = m->currentBinLabels;
- if (size == 0) { //user has not set size, set size = smallest samples size
- size = thislookup[0]->getNumSeqs();
- for (int i = 1; i < thislookup.size(); i++) {
- int thisSize = thislookup[i]->getNumSeqs();
-
- if (thisSize < size) { size = thisSize; }
- }
- }
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
+
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
int numBins = thislookup[0]->getNumBins();
for (int i = 0; i < thislookup.size(); i++) {
int thisSize = thislookup[i]->getNumSeqs();
-
+
if (thisSize != size) {
string thisgroup = thislookup[i]->getGroup();
-
+
OrderVector* order = new OrderVector();
for(int p=0;p<numBins;p++){
for(int j=0;j<thislookup[i]->getAbundance(p);j++){
for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { delete order; out.close(); return 0; }
+
//get random number to sample from order between 0 and thisSize-1.
- int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
+ //don't need this because of the random shuffle above
+ //int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
- int bin = order->get(myrand);
+ int bin = order->get(j);
int abund = thislookup[i]->getAbundance(bin);
thislookup[i]->set(bin, (abund+1), thisgroup);
//subsampling may have created some otus with no sequences in them
eliminateZeroOTUS(thislookup);
+ if (m->control_pressed) { out.close(); return 0; }
+
+ 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", "eliminateZeroOTUS");
+ 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);
+ }
+}
+//**********************************************************************************************************************
int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
try {
}
//for each bin
+ vector<string> newBinLabels;
+ string snumBins = toString(thislookup[0]->getNumBins());
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
for (int j = 0; j < thislookup.size(); j++) {
newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
}
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
}
}
thislookup.clear();
thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
return 0;
projects / mothur.git / blobdiff