#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) {
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; }
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 = "F"; }
+ temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
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=False).\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"); }
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();
}
}
//**********************************************************************************************************************
-string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string> outputNames) {
+string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
try {
ofstream out;
//open each groups summary file
string newLabel = "";
- ifstream* temp;
- map<string, ifstream*> filehandles;
+ map<string, vector<string> > files;
for (int i=0; i<outputNames.size(); i++) {
- temp = new ifstream;
- filehandles[outputNames[i]] = temp;
- m->openInputFile(outputNames[i], *(temp));
+ 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;
+ 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; } }
+ }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;
- m->gobble(*(temp));
+ temp.close();
+ remove(outputNames[i].c_str());
}
//output label line to new file
out << newLabel << endl;
//for each label
- for (int i = 0; i < numLines; i++) {
+ for (int k = 0; k < numLines; k++) {
//grab summary data for each group
for (int i=0; i<outputNames.size(); i++) {
- string tempLabel;
-
- for (int j = 0; j < numCols+1; j++) {
- *(filehandles[outputNames[i]]) >> tempLabel;
-
- //print to combined file
- if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t'; }
- else{ out << tempLabel << '\t'; }
- }
-
- out << endl;
- m->gobble(*(filehandles[outputNames[i]]));
+ out << files[outputNames[i]][k];
}
}
- //close each groups summary file
- for (int i=0; i<outputNames.size(); i++) { (*(filehandles[outputNames[i]])).close(); }
+ outputNames.clear();
+
out.close();
//return combine file name
projects / mothur.git / blobdiff