try {
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 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 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");
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))) {
string outputPath = m->getPathName(filename);
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
-
- //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());
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());
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } 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());
string outputPath = m->getPathName(filename);
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+ 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());
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());
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } 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());
string outputPath = m->getPathName(filename);
//create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+ 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());
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());
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
delete sabund;
}
-
+
+ out.close();
delete read;
delete input; globaldata->ginput = NULL;
}
}
//**********************************************************************************************************************
-string CatchAllCommand::createSummaryFile(string file1, string label) {
+int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + label + ".catchall.summary";
- filename = m->getFullPathName(filename);
- outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
-
- ofstream out;
- m->openOutputFile(filename, out);
-
- out << "group\tmodel\testimate\tlci\tuci" << endl;
ifstream in;
m->openInputFile(file1, in);
string header = m->getline(in); m->gobble(in);
int pos = header.find("Total Number of Observed Species =");
- cout << pos << '\t' << header.length() << endl; exit(1);
+ 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];
- string numString = "";
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);
- int numOtus; convert(numString, numOtus);
- cout << numOtus << endl;
+ 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();
- out.close();
- return filename;
+ return 0;
}
catch(exception& e) {
}
}
/**************************************************************************************/
-
-
-
projects / mothur.git / blobdiff