added summary output to catchall command

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index efe99b007d6cd37e823ccca91937f4c38cd26c1b..7b298ef87345ea7b9ce497ac6d0b2e6d2d94759d 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -179,6 +179,15 @@ int CatchAllCommand::execute() {
                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))) {
 
@@ -205,9 +214,9 @@ int CatchAllCommand::execute() {
                                        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());
@@ -241,9 +250,9 @@ int CatchAllCommand::execute() {
                                        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());
@@ -298,11 +307,12 @@ int CatchAllCommand::execute() {
                        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;
                
@@ -348,16 +358,8 @@ string CatchAllCommand::process(SAbundVector* sabund) {
        }
 }
 //**********************************************************************************************************************
-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);
@@ -367,28 +369,56 @@ string CatchAllCommand::createSummaryFile(string file1, string label) {
                        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) {

diff --git a/catchallcommand.h b/catchallcommand.h
index 8795cd7512284c32b96100d814e2febfecec9504..4406361a37230aced27bbaa4ca62c3f42bcd4db3 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -48,7 +48,7 @@ private:
        map< string, vector<string> > outputTypes;
        
        string process(SAbundVector*);
-       string createSummaryFile(string, string); 
+       int createSummaryFile(string, string, ofstream&); 
 };
 
 /****************************************************************************/

diff --git a/mothur b/mothur
index a9ab78c3274abb79502f022b4570f8fc522b8853..3f9ed5f3f197ceb119297445b75e58903a68710b 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/mothurout.cpp b/mothurout.cpp
index b30ee3ca630c91fea01343c9d873e709e027a4fb..e04158248ee6c9a0144cccda268d0efa2d703ada 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1221,17 +1221,6 @@ void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbo
                }
                container.push_back(individual);
 
-               /*
-               
-               while (estim.find_first_of(symbol) != -1) {
-                       individual = estim.substr(0,estim.find_first_of(symbol));
-                       if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-                               estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
-                               container.push_back(individual);
-                       }
-               }
-               //get last one
-               container.push_back(estim); */
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtChar");