#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
#include "npshannon.h"
#include "shannon.h"
+#include "heip.h"
+#include "smithwilson.h"
+#include "shannoneven.h"
#include "jackknife.h"
#include "geom.h"
#include "logsd.h"
#include "solow.h"
#include "shen.h"
+//**********************************************************************************************************************
+vector<string> SummaryCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","calc","abund","size","outputdir","groupmode","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SummaryCommand::SummaryCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "SummaryCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SummaryCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SummaryCommand::getRequiredFiles(){
+ try {
+ string AlignArray[] = {"shared","list","rabund","sabund","or"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SummaryCommand::SummaryCommand(string option) {
else {
//valid paramters for this command
- string Array[] = {"label","calc","abund","size","outputdir","inputdir"};
+ string Array[] = {"label","calc","abund","size","outputdir","groupmode","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
//make sure the user has already run the read.otu command
if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); m->mothurOutEndLine(); abort = true; }
//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 = "";
- outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
convert(temp, size);
+
+ temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
+ groupMode = m->isTrue(temp);
+
}
}
try {
m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
m->mothurOut("The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
- m->mothurOut("The summary.single command parameters are label, calc, abund. No parameters are required.\n");
+ m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode. No parameters are required.\n");
m->mothurOut("The summary.single command should be in the following format: \n");
m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
validCalculator->printCalc("summary", cout);
m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
+ m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n");
m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
}
if (abort == true) { return 0; }
- vector<string> outputNames;
-
string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+ int numLines = 0;
+ int numCols = 0;
+
for (int p = 0; p < inputFileNames.size(); p++) {
- string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary";
+ numLines = 0;
+ numCols = 0;
+
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
globaldata->inputFileName = inputFileNames[p];
- outputNames.push_back(fileNameRoot);
+ outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
sumCalculators.push_back(new Jackknife());
}else if(Estimators[i] == "shannon"){
sumCalculators.push_back(new Shannon());
+ }else if(Estimators[i] == "shannoneven"){
+ sumCalculators.push_back(new ShannonEven());
}else if(Estimators[i] == "npshannon"){
sumCalculators.push_back(new NPShannon());
+ }else if(Estimators[i] == "heip"){
+ sumCalculators.push_back(new Heip());
+ }else if(Estimators[i] == "smithwilson"){
+ sumCalculators.push_back(new SmithWilson());
}else if(Estimators[i] == "simpson"){
sumCalculators.push_back(new Simpson());
+ }else if(Estimators[i] == "simpsoneven"){
+ sumCalculators.push_back(new SimpsonEven());
+ }else if(Estimators[i] == "invsimpson"){
+ sumCalculators.push_back(new InvSimpson());
}else if(Estimators[i] == "bootstrap"){
sumCalculators.push_back(new Bootstrap());
}else if (Estimators[i] == "nseqs") {
if (sumCalculators.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
ofstream outputFileHandle;
- openOutputFile(fileNameRoot, outputFileHandle);
+ m->openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
read = new ReadOTUFile(globaldata->inputFileName);
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
outputFileHandle << '\t' << sumCalculators[i]->getName();
+ numCols++;
}
else{
outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+ numCols += 3;
}
}
outputFileHandle << endl;
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ numLines++;
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ numLines++;
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ numLines++;
delete sabund;
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
+ if ((hadShared != "") && (groupMode)) { outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames)); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
input = globaldata->ginput;
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
- string sharedFileRoot = getRootName(filename);
+ string sharedFileRoot = m->getRootName(filename);
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
for (int i = 0; i < lookup.size(); i++) {
RAbundVector rav = lookup[i]->getRAbundVector();
- openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+ m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
rav.print(*(filehandles[lookup[i]->getGroup()]));
(*(filehandles[lookup[i]->getGroup()])).close();
}
}
}
//**********************************************************************************************************************
+string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
+ try {
+
+ ofstream out;
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
+
+ //open combined file
+ m->openOutputFile(combineFileName, out);
+
+ //open each groups summary file
+ string newLabel = "";
+ map<string, vector<string> > files;
+ for (int i=0; i<outputNames.size(); i++) {
+ vector<string> thisFilesLines;
+
+ ifstream temp;
+ m->openInputFile(outputNames[i], temp);
+
+ //read through first line - labels
+ string tempLabel;
+ if (i == 0) { //we want to save the labels to output below
+ for (int j = 0; j < numCols+1; j++) {
+ temp >> tempLabel;
+
+ if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
+ }else{ newLabel += tempLabel + '\t'; }
+ }
+ }else{ for (int j = 0; j < numCols+1; j++) { temp >> tempLabel; } }
+
+ m->gobble(temp);
+
+ //for each label
+ for (int k = 0; k < numLines; k++) {
+
+ string thisLine = "";
+ string tempLabel;
+
+ for (int j = 0; j < numCols+1; j++) {
+ temp >> tempLabel;
+
+ //save for later
+ if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; }
+ else{ thisLine += tempLabel + "\t"; }
+ }
+
+ thisLine += "\n";
+
+ thisFilesLines.push_back(thisLine);
+
+ m->gobble(temp);
+ }
+
+ files[outputNames[i]] = thisFilesLines;
+
+ temp.close();
+ remove(outputNames[i].c_str());
+ }
+
+ //output label line to new file
+ out << newLabel << endl;
+
+ //for each label
+ for (int k = 0; k < numLines; k++) {
+
+ //grab summary data for each group
+ for (int i=0; i<outputNames.size(); i++) {
+ out << files[outputNames[i]][k];
+ }
+ }
+
+ outputNames.clear();
+
+ out.close();
+
+ //return combine file name
+ return combineFileName;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff