#include "catchallcommand.h"
#include "globaldata.hpp"
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"sabund","label","inputdir","outputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CatchAllCommand::CatchAllCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["csv"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"sabund"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**************************************************************************************/
CatchAllCommand::CatchAllCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
- allLines = 0;
+ allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; }
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["csv"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
//check for required parameters
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
- else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide either a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
+ else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
string label = validParameter.validFile(parameters, "label", false);
//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 = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sabundfile); }
}
}
void CatchAllCommand::help(){
try {
- m->mothurOut("The catchall command interfaces mothur with the catchall program written by ...citation goes here...\n");
- m->mothurOut("For more information about clearcut refer to http://catchall.cac.cornell.edu/ \n");
- m->mothurOut("The catchall executable must be in a folder called catchall in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
+ m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
+ m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
+ m->mothurOut("The catchall executable must be in the same folder as your mothur executable. \n");
+ m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
m->mothurOut("The catchall command should be in the following format: \n");
if (abort == true) { return 0; }
- vector<string> outputNames;
-
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
//get location of catchall
GlobalData* globaldata = GlobalData::getInstance();
- string path = globaldata->argv;
+ path = globaldata->argv;
path = path.substr(0, (path.find_last_of('m')));
path = m->getFullPathName(path);
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
+ catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
#else
- catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
+ catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
#endif
read = new ReadOTUFile(sabundfile);
set<string> processedLabels;
set<string> userLabels = labels;
+ string summaryfilename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + "catchall.summary";
+ summaryfilename = m->getFullPathName(summaryfilename);
+ outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
+
+ ofstream out;
+ m->openOutputFile(summaryfilename, out);
+
+ out << "label\tmodel\testimate\tlci\tuci" << endl;
+
//for each label the user selected
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- //create list of output files catchall will make
- //datasetname_Analysis.csv
- //datasetname_BestModelsAnalysis.csv
- //datasetname_BestModelsFits.csv
- //datasetname_BubblePlot.csv
- //datasetname_Poisson_fits.csv
- //datasetname_SingleExp_fits.csv
- //datasetname_ThreeMixedExp_fits.csv
- //datasetname_TwoMixedExp_fits.csv
-
//create catchall input file from mothur's inputfile
string filename = process(sabund);
- sabund->print(cout);
+ string outputPath = m->getPathName(filename);
+
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
- //run catchall
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ //wrap entire string in ""
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+ //run catchall
system(catchAllCommand.c_str());
+
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
+ outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
+ outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- //create list of output files catchall will make
- //datasetname_Analysis.csv
- //datasetname_BestModelsAnalysis.csv
- //datasetname_BestModelsFits.csv
- //datasetname_BubblePlot.csv
- //datasetname_Poisson_fits.csv
- //datasetname_SingleExp_fits.csv
- //datasetname_ThreeMixedExp_fits.csv
- //datasetname_TwoMixedExp_fits.csv
-
//create catchall input file from mothur's inputfile
string filename = process(sabund);
-
+ string outputPath = m->getPathName(filename);
+
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
//run catchall
system(catchAllCommand.c_str());
-
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
+
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
+ outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
+ outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
sabund = (input->getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- //create list of output files catchall will make
- //datasetname_Analysis.csv
- //datasetname_BestModelsAnalysis.csv
- //datasetname_BestModelsFits.csv
- //datasetname_BubblePlot.csv
- //datasetname_Poisson_fits.csv
- //datasetname_SingleExp_fits.csv
- //datasetname_ThreeMixedExp_fits.csv
- //datasetname_TwoMixedExp_fits.csv
-
+
//create catchall input file from mothur's inputfile
string filename = process(sabund);
-
+ string outputPath = m->getPathName(filename);
+
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
//run catchall
system(catchAllCommand.c_str());
-
+
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
+ outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
+ outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
+ outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
delete sabund;
}
-
+
+ out.close();
delete read;
delete input; globaldata->ginput = NULL;
+ 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(); }
//**********************************************************************************************************************
string CatchAllCommand::process(SAbundVector* sabund) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".catchall";
+ string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
filename = m->getFullPathName(filename);
ofstream out;
exit(1);
}
}
+//**********************************************************************************************************************
+int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
+ try {
+
+ ifstream in;
+ m->openInputFile(file1, in);
+
+ if (!in.eof()) {
+
+ string header = m->getline(in); m->gobble(in);
+
+ int pos = header.find("Total Number of Observed Species =");
+ string numString = "";
+
+
+ if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
+ else {
+ //pos will be the position of the T in total, so we want to count to the position of =
+ pos += 34;
+ char c=header[pos];
+ while (c != ','){
+ if (c != ' ') {
+ numString += c;
+ }
+ pos++;
+ c=header[pos];
+
+ //sanity check
+ if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
+ }
+ }
+
+ string firstline = m->getline(in); m->gobble(in);
+ vector<string> values;
+ m->splitAtComma(firstline, values);
+
+ values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
+
+ if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
+ string secondline = m->getline(in); m->gobble(in);
+ values.clear();
+ m->splitAtComma(secondline, values);
+
+ values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
+ }
+
+ if (values.size() == 1) { //still not what we wanted fill values with numOTUs
+ values.resize(8, "");
+ values[1] = "Sobs";
+ values[4] = numString;
+ values[6] = numString;
+ values[7] = numString;
+ }
+
+ if (values.size() < 8) { values.resize(8, ""); }
+
+ out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "createSummaryFile");
+ exit(1);
+ }
+}
/**************************************************************************************/
-
-
-
projects / mothur.git / blobdiff