commands["remove.otulabels"] = "remove.otulabels";
commands["make.contigs"] = "make.contigs";
commands["load.logfile"] = "load.logfile";
+ commands["make.table"] = "make.table";
commands["quit"] = "MPIEnabled";
}
else if(commandName == "make.shared") { command = new SharedCommand(optionString); }
else if(commandName == "get.commandinfo") { command = new GetCommandInfoCommand(optionString); }
else if(commandName == "deunique.tree") { command = new DeuniqueTreeCommand(optionString); }
- else if(commandName == "count.seqs") { command = new CountSeqsCommand(optionString); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(optionString); }
else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { command = new SummaryTaxCommand(optionString); }
else if(commandName == "make.shared") { pipecommand = new SharedCommand(optionString); }
else if(commandName == "get.commandinfo") { pipecommand = new GetCommandInfoCommand(optionString); }
else if(commandName == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(optionString); }
- else if(commandName == "count.seqs") { pipecommand = new CountSeqsCommand(optionString); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(optionString); }
else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(optionString); }
else if(commandName == "make.shared") { shellcommand = new SharedCommand(); }
else if(commandName == "get.commandinfo") { shellcommand = new GetCommandInfoCommand(); }
else if(commandName == "deunique.tree") { shellcommand = new DeuniqueTreeCommand(); }
- else if(commandName == "count.seqs") { shellcommand = new CountSeqsCommand(); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { shellcommand = new CountSeqsCommand(); }
else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); }
else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); }
try {
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
string CountSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.seqs command reads a name file and outputs a .seq.count file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count.table file. You may also provide a group file to get the counts broken down by group.\n";
helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
+ helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
- helpString += "Example count.seqs(name=amazon.names).\n";
+ helpString += "Example count.seqs(name=amazon.names) or make.table(name=amazon.names).\n";
helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";
return helpString;
}
it = outputTypes.find(type);
if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
else {
- if (type == "summary") { outputFileName = "seq.count"; }
+ if (type == "counttable") { outputFileName = "count.table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
}
return outputFileName;
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["counttable"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["counttable"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
m->splitAtDash(groups, Groups);
+
+ string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
+ large = m->isTrue(temp);
//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 = m->hasPath(namefile); }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("summary");
- m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
- out << "Representative_Sequence\ttotal\t";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("counttable");
+
+ int total = 0;
+ if (!large) { total = processSmall(outputFileName); }
+ else { total = processLarge(outputFileName); }
+
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+
+ //set rabund file as new current rabundfile
+ itTypes = outputTypes.find("counttable");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
- GroupMap* groupMap;
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::processSmall(string outputFileName){
+ try {
+ ofstream out;
+ m->openOutputFile(outputFileName, out); outputTypes["counttable"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName);
+ out << "Representative_Sequence\ttotal\t";
+
+ GroupMap* groupMap;
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
if (m->control_pressed) { break; }
string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
+ in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
vector<string> names;
m->splitAtChar(secondCol, names, ',');
total += names.size();
}
in.close();
+ out.close();
if (groupfile != "") { delete groupMap; }
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processSmall");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::processLarge(string outputFileName){
+ try {
+ set<string> namesOfGroups;
+ map<string, int> initial;
+ for (set<string>::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0; }
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName);
+ out << "Representative_Sequence\ttotal\t";
+ if (groupfile == "") { out << endl; }
+
+ map<string, unsigned long long> namesToIndex;
+ string outfile = m->getRootName(groupfile) + "sorted.groups.temp";
+ string outName = m->getRootName(namefile) + "sorted.name.temp";
+ map<int, string> indexToName;
+ map<int, string> indexToGroup;
+ if (groupfile != "") {
+ time_t estart = time(NULL);
+ //convert name file to redundant -> unique. set unique name equal to index so we can use vectors, save name for later.
+ string newNameFile = m->getRootName(namefile) + ".name.temp";
+ string newGroupFile = m->getRootName(groupfile) + ".group.temp";
+ indexToName = processNameFile(newNameFile);
+ indexToGroup = getGroupNames(newGroupFile, namesOfGroups);
+
+ //sort file by first column so the names of sequences will be easier to find
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + newGroupFile + " -o " + outfile;
+ system(command.c_str());
+ command = "sort -n " + newNameFile + " -o " + outName;
+ system(command.c_str());
+ #else //sort using windows sort
+ string command = "sort " + newGroupFile + " /O " + outfile;
+ system(command.c_str());
+ command = "sort " + newNameFile + " /O " + outName;
+ system(command.c_str());
+ #endif
+ m->mothurRemove(newNameFile);
+ m->mothurRemove(newGroupFile);
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort and index the group and name files. "); m->mothurOutEndLine();
+ }else { outName = namefile; }
+
+ time_t estart = time(NULL);
+ //open input file
+ ifstream in;
+ m->openInputFile(outName, in);
+
+ //open input file
+ ifstream in2;
- if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+ int total = 0;
+ vector< vector<int> > nameMapCount;
+ if (groupfile != "") {
+ m->openInputFile(outfile, in2);
+ nameMapCount.resize(indexToName.size());
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ nameMapCount[i].resize(indexToGroup.size(), 0);
+ }
+ }
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol;
+ in >> firstCol; m->gobble(in);
+
+ if (groupfile != "") {
+ int uniqueIndex;
+ in >> uniqueIndex; m->gobble(in);
+
+ string name; int groupIndex;
+ in2 >> name >> groupIndex; m->gobble(in2);
+
+ if (name != firstCol) { m->mothurOut("[ERROR]: found " + name + " in your groupfile, but " + firstCol + " was in your namefile, please correct.\n"); m->control_pressed = true; }
+
+ nameMapCount[uniqueIndex][groupIndex]++;
+ total++;
+ }else {
+ string secondCol;
+ in >> secondCol; m->gobble(in);
+ int num = m->getNumNames(secondCol);
+ out << firstCol << '\t' << num << endl;
+ total += num;
+ }
+ }
+ in.close();
+
+ if (groupfile != "") {
+ m->mothurRemove(outfile);
+ m->mothurRemove(outName);
+ in2.close();
+ for (map<int, string>::iterator it = indexToGroup.begin(); it != indexToGroup.end(); it++) { out << it->second << '\t'; }
+ out << endl;
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ string totalsLine = "";
+ int seqTotal = 0;
+ for (int j = 0; j < nameMapCount[i].size(); j++) {
+ seqTotal += nameMapCount[i][j];
+ totalsLine += toString(nameMapCount[i][j]) + '\t';
+ }
+ out << indexToName[i] << '\t' << seqTotal << '\t' << totalsLine << endl;
+ }
+ }
+
+ out.close();
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to create the count table file. "); m->mothurOutEndLine();
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processLarge");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<int, string> CountSeqsCommand::processNameFile(string name) {
+ try {
+ map<int, string> indexToNames;
+
+ ofstream out;
+ m->openOutputFile(name, out);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+ int count = 0;
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ //parse names into vector
+ vector<string> theseNames;
+ m->splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { out << theseNames[i] << '\t' << count << endl; }
+ indexToNames[count] = firstCol;
+ pairDone = false;
+ count++;
+ }
+ }
+ }
+ in.close();
+ out.close();
- m->mothurOutEndLine();
- m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
- m->mothurOutEndLine();
+ return indexToNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processNameFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<int, string> CountSeqsCommand::getGroupNames(string filename, set<string>& namesOfGroups) {
+ try {
+ map<int, string> indexToGroups;
+ map<string, int> groupIndex;
+ map<string, int>::iterator it;
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(groupfile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+ int count = 0;
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ it = groupIndex.find(secondCol);
+ if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
+ groupIndex[secondCol] = count;
+ count++;
+ }
+ out << firstCol << '\t' << groupIndex[secondCol] << endl;
+ namesOfGroups.insert(secondCol);
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+ out.close();
- return 0;
+ for (it = groupIndex.begin(); it != groupIndex.end(); it++) { indexToGroups[it->second] = it->first; }
+
+ return indexToGroups;
}
-
catch(exception& e) {
- m->errorOut(e, "CountSeqsCommand", "execute");
+ m->errorOut(e, "CountSeqsCommand", "getGroupNames");
exit(1);
}
}
//**********************************************************************************************************************
+
+
+
private:
string namefile, groupfile, outputDir, groups;
- bool abort;
- vector<string> Groups;
+ bool abort, large;
+ vector<string> Groups, outputNames;
+
+ int processSmall(string);
+ int processLarge(string);
+ map<int, string> processNameFile(string);
+ map<int, string> getGroupNames(string, set<string>&);
+
};
#endif
m->setFlowFile("");
}else if (types[i] == "biom") {
m->setBiomFile("");
+ }else if (types[i] == "counttable") {
+ m->setCountTableFile("");
}else if (types[i] == "processors") {
m->setProcessors("1");
}else if (types[i] == "all") {
types.insert("tree");
types.insert("flow");
types.insert("biom");
+ types.insert("counttable");
types.insert("processors");
return types;
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
+ if (counttablefile != "") { mothurOut("counttable=" + counttablefile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
if (biomfile != "") { return true; }
+ if (counttablefile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
taxonomyfile = "";
flowfile = "";
biomfile = "";
+ counttablefile = "";
processors = "1";
}
catch(exception& e) {
positions.push_back(0);
while(!in.eof()){
- //unsigned long long lastpos = in.tellg();
- //input = getline(in);
- //if (input.length() != 0) {
- //unsigned long long pos = in.tellg();
- //if (pos != -1) { positions.push_back(pos - input.length() - 1); }
- //else { positions.push_back(lastpos); }
- //}
- //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
-
-
//getline counting reads
char d = in.get(); count++;
while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) {
for (int i = 0; i < size; i++) {
if (!isspace(buffer[i])) { rest += buffer[i]; }
else {
- pieces.push_back(rest); rest = "";
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
while (i < size) { //gobble white space
if (isspace(buffer[i])) { i++; }
else { rest = buffer[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
for (int i = 0; i < input.length(); i++) {
if (!isspace(input[i])) { rest += input[i]; }
else {
- pieces.push_back(rest); rest = "";
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
while (i < input.length()) { //gobble white space
if (isspace(input[i])) { i++; }
else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
string getTaxonomyFile() { return taxonomyfile; }
string getFlowFile() { return flowfile; }
string getBiomFile() { return biomfile; }
+ string getCountTableFile() { return counttablefile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setBiomFile(string f) { biomfile = getFullPathName(f); }
+ void setCountTableFile(string f) { counttablefile = getFullPathName(f); }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
void printCurrentFiles();
processors = "1";
flowfile = "";
biomfile = "";
+ counttablefile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
vector<string> Groups;
vector<string> namesOfGroups;
it->second = m->getTaxonomyFile();
}else if (it->first == "biom") {
it->second = m->getBiomFile();
+ }else if (it->first == "counttable") {
+ it->second = m->getCountTableFile();
}else {
m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
}
#include "sharedsobs.h"
#include "sharednseqs.h"
#include "sharedutilities.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> RareFactSharedCommand::setParameters(){
CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter psubsampleiters("subsampleiters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(psubsampleiters);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
helpString += "Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n";
helpString += "The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n";
+ helpString += "The subsampleiters parameter allows you to choose the number of times you would like to run the subsample.\n";
+ helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
helpString += "The default value for groups is all the groups in your groupfile, and jumble is true.\n";
helpString += validCalculator.printCalc("sharedrarefaction");
helpString += "The label parameter is used to analyze specific labels in your input.\n";
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "subsampleiters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
+ if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
+ else {
+ if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
+ else { subsample = false; }
+ }
+
+ if (subsample == false) { iters = 1; }
}
}
}
}
-
+
+ /******************************************************/
+ if (subsample) {
+ if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
+ subsampleSize = subset[0]->getNumSeqs();
+ for (int i = 1; i < subset.size(); i++) {
+ int thisSize = subset[i]->getNumSeqs();
+
+ if (thisSize < subsampleSize) { subsampleSize = thisSize; }
+ }
+ }else {
+ newGroups.clear();
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < subset.size(); i++) {
+ if (subset[i]->getNumSeqs() < subsampleSize) {
+ m->mothurOut(subset[i]->getGroup() + " contains " + toString(subset[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete subset[i];
+ }else {
+ newGroups.push_back(subset[i]->getGroup());
+ temp.push_back(subset[i]);
+ }
+ }
+ subset = temp;
+ }
+
+ if (subset.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+ }
+ /******************************************************/
+
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+ if (subsample) { subsampleLookup(subset, fileNameRoot); }
+
processedLabels.insert(subset[0]->getLabel());
userLabels.erase(subset[0]->getLabel());
}
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+ if (subsample) { subsampleLookup(subset, fileNameRoot); }
+
processedLabels.insert(subset[0]->getLabel());
userLabels.erase(subset[0]->getLabel());
rCurve = new Rarefact(subset, rDisplays);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+
+ if (subsample) { subsampleLookup(subset, fileNameRoot); }
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
}
}
//**********************************************************************************************************************
+int RareFactSharedCommand::subsampleLookup(vector<SharedRAbundVector*>& thisLookup, string fileNameRoot) {
+ try {
+
+ map<string, vector<string> > filenames;
+ for (int thisIter = 0; thisIter < iters; thisIter++) {
+
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
+
+ //we want the summary results for the whole dataset, then the subsampling
+ SubSample sample;
+ vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thisItersLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisItersLookup[k]->getLabel());
+ temp->setGroup(thisItersLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
+ }
+
+ tempLabels = sample.getSample(newLookup, subsampleSize);
+ thisItersLookup = newLookup;
+
+
+ Rarefact* rCurve;
+ vector<Display*> rDisplays;
+
+ string thisfileNameRoot = fileNameRoot + toString(thisIter);
+
+ ValidCalculators validCalculator;
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedobserved") {
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(thisfileNameRoot+getOutputFileNameTag("sharedrarefaction"), "")));
+ filenames["sharedrarefaction"].push_back(thisfileNameRoot+getOutputFileNameTag("sharedrarefaction"));
+ }else if (Estimators[i] == "sharednseqs") {
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(thisfileNameRoot+getOutputFileNameTag("sharedr_nseqs"), "")));
+ filenames["sharedr_nseqs"].push_back(thisfileNameRoot+getOutputFileNameTag("sharedr_nseqs"));
+ }
+ }
+ }
+
+ rCurve = new Rarefact(thisItersLookup, rDisplays);
+ rCurve->getSharedCurve(freq, nIters);
+ delete rCurve;
+
+ //clean up memory
+ for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
+ thisItersLookup.clear();
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ }
+
+ //create std and ave outputs
+ vector< vector< vector< double > > > results; //iter -> numSampled -> data
+ for (map<string, vector<string> >::iterator it = filenames.begin(); it != filenames.end(); it++) {
+ vector<string> thisTypesFiles = it->second;
+ vector<string> columnHeaders;
+ for (int i = 0; i < thisTypesFiles.size(); i++) {
+ ifstream in;
+ m->openInputFile(thisTypesFiles[i], in);
+
+ string headers = m->getline(in); m->gobble(in);
+ columnHeaders = m->splitWhiteSpace(headers);
+ int numCols = columnHeaders.size();
+
+ vector<vector<double> > thisFilesLines;
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+ vector<double> data; data.resize(numCols, 0);
+ //read numSampled line
+ for (int j = 0; j < numCols; j++) { in >> data[j]; m->gobble(in); }
+ thisFilesLines.push_back(data);
+ }
+ in.close();
+ results.push_back(thisFilesLines);
+ m->mothurRemove(thisTypesFiles[i]);
+ }
+
+ if (!m->control_pressed) {
+ //process results
+ string outputFile = fileNameRoot + "ave-std." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag(it->first);
+ ofstream out;
+ m->openOutputFile(outputFile, out);
+ outputNames.push_back(outputFile); outputTypes[it->first].push_back(outputFile);
+
+ out << columnHeaders[0] << '\t' << "method\t";
+ for (int i = 1; i < columnHeaders.size(); i++) { out << columnHeaders[i] << '\t'; }
+ out << endl;
+
+ vector< vector<double> > aveResults; aveResults.resize(results[0].size());
+ for (int i = 0; i < aveResults.size(); i++) { aveResults[i].resize(results[0][i].size(), 0.0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < aveResults.size(); i++) { //initialize sums to zero.
+ aveResults[i][0] = results[thisIter][i][0];
+ for (int j = 1; j < aveResults[i].size(); j++) {
+ aveResults[i][j] += results[thisIter][i][j];
+ }
+ }
+ }
+
+ for (int i = 0; i < aveResults.size(); i++) { //finds average.
+ for (int j = 1; j < aveResults[i].size(); j++) {
+ aveResults[i][j] /= (float) iters;
+ }
+ }
+
+ //standard deviation
+ vector< vector<double> > stdResults; stdResults.resize(results[0].size());
+ for (int i = 0; i < stdResults.size(); i++) { stdResults[i].resize(results[0][i].size(), 0.0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int i = 0; i < stdResults.size(); i++) {
+ stdResults[i][0] = aveResults[i][0];
+ for (int j = 1; j < stdResults[i].size(); j++) {
+ stdResults[i][j] += ((results[thisIter][i][j] - aveResults[i][j]) * (results[thisIter][i][j] - aveResults[i][j]));
+ }
+ }
+ }
+
+ for (int i = 0; i < stdResults.size(); i++) { //finds average.
+ out << aveResults[i][0] << '\t' << "ave\t";
+ for (int j = 1; j < aveResults[i].size(); j++) { out << aveResults[i][j] << '\t'; }
+ out << endl;
+ out << stdResults[i][0] << '\t' << "std\t";
+ for (int j = 1; j < stdResults[i].size(); j++) {
+ stdResults[i][j] /= (float) iters;
+ stdResults[i][j] = sqrt(stdResults[i][j]);
+ out << stdResults[i][j] << '\t';
+ }
+ out << endl;
+ }
+ out.close();
+ }
+ }
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "subsample");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector<string> RareFactSharedCommand::createGroupFile(vector<string>& outputNames) {
try {
private:
vector<SharedRAbundVector*> lookup;
- int nIters;
+ int nIters, subsampleSize, iters;
string format;
float freq;
map<int, string> file2Group; //index in outputNames[i] -> group
- bool abort, allLines, jumble, groupMode;
+ bool abort, allLines, jumble, groupMode, subsample;
set<string> labels; //holds labels to be used
string label, calc, groups, outputDir, sharedfile, designfile;
vector<string> Estimators, Groups, outputNames, Sets;
int process(GroupMap&, string);
vector<string> createGroupFile(vector<string>&);
+ int subsampleLookup(vector<SharedRAbundVector*>&, string);
};
projects / mothur.git / commitdiff