fixed bug in sffinfo when ~ was used in the sff filename. fixed issue in shhh.flows...

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 82ff7faef0d8886d21fc6b642f34c88c1b143ea1..b3d359ca53aa31fa10fe209cf0cd52946c2fd79b 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -474,17 +474,38 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                
                //find different types of files
                map<string, map<string, string> > typesFiles;
+        map<string, vector< vector<string> > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci.
+        vector<string> groupNames;
                for (int i = 0; i < outputNames.size(); i++) {
+            
                        string extension = m->getExtension(outputNames[i]);
-                       
+            string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
+                       m->mothurRemove(combineFileName); //remove old file
+            
                        ifstream in;
                        m->openInputFile(outputNames[i], in);
                        
                        string labels = m->getline(in);
-                       string newLine = labels.substr(0, labels.find_first_of('\t'));
-                       
-                       newLine += "\tGroup" + labels.substr(labels.find_first_of('\t'));
             
+                       istringstream iss (labels,istringstream::in);
+            string newLabel = ""; vector<string> theseLabels;
+            while(!iss.eof()) {  iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); }
+            vector< vector<string> > allLabels;
+            vector<string> thisSet; thisSet.push_back(theseLabels[0]); allLabels.push_back(thisSet); thisSet.clear(); //makes "numSampled" its own grouping
+            for (int j = 1; j < theseLabels.size()-1; j++) {
+                if (theseLabels[j+1] == "lci") {
+                    thisSet.push_back(theseLabels[j]); 
+                    thisSet.push_back(theseLabels[j+1]); 
+                    thisSet.push_back(theseLabels[j+2]);
+                    j++; j++;
+                }else{ //no lci or hci for this calc.
+                    thisSet.push_back(theseLabels[j]); 
+                }
+                allLabels.push_back(thisSet); 
+                thisSet.clear();
+            }
+            fileLabels[combineFileName] = allLabels;
+                    
             map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
             if (itfind != typesFiles.end()) {
                 (itfind->second)[outputNames[i]] = file2Group[i];
@@ -493,62 +514,57 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                 temp[outputNames[i]] = file2Group[i];
                 typesFiles[extension] = temp;
             }
-                       
-                       string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
-                       
-                       //print headers
-                       ofstream out;
-                       m->openOutputFile(combineFileName, out);
-                       out << newLine << endl;
-                       out.close();
-                       
+            if (!(m->inUsersGroups(file2Group[i], groupNames))) {  groupNames.push_back(file2Group[i]); }
                }
                
                //for each type create a combo file
-               map<int, int> lineToNumber; 
+               
                for (map<string, map<string, string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
                        
                        ofstream out;
                        string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
                        m->openOutputFileAppend(combineFileName, out);
                        newFileNames.push_back(combineFileName);
-                       map<string, string> thisTypesFiles = it->second;
-               
+                       map<string, string> thisTypesFiles = it->second; //it->second maps filename to group
+            set<int> numSampledSet;
+            
                        //open each type summary file
-                       map<string, vector<string> > files; //maps file name to lines in file
+                       map<string, map<int, vector< vector<string> > > > files; //maps file name to lines in file
                        int maxLines = 0;
-                       int numColumns = 0;
                        for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
                 
                 string thisfilename = itFileNameGroup->first;
                 string group = itFileNameGroup->second;
-               
+                
                                ifstream temp;
                                m->openInputFile(thisfilename, temp);
                                
                                //read through first line - labels
                                m->getline(temp);       m->gobble(temp);
                                
-                               vector<string> thisFilesLines;
-                               
-                               thisFilesLines.push_back(group);
-                               int count = 1;
+                               map<int, vector< vector<string> > > thisFilesLines;
                                while (!temp.eof()){
-                               
-                                       string thisLine = m->getline(temp);
-                                       
-                                       string numSampled = thisLine.substr(0, thisLine.find_first_of('\t'));
-                                       int num = 0;
-                                       convert(numSampled, num);
-                                       numColumns = m->getNumChar(thisLine, '\t');
-                                       lineToNumber[count] = num;
-                                       count++;
-                                                                       
-                                       thisFilesLines.push_back(thisLine);
-                                       m->gobble(temp);
+                    int numSampled = 0;
+                    temp >> numSampled; m->gobble(temp);
+                
+                    vector< vector<string> > theseReads;
+                    vector<string> thisSet; thisSet.push_back(toString(numSampled)); theseReads.push_back(thisSet); thisSet.clear();
+                    for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
+                        vector<string> reads;
+                        string next = "";
+                        for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
+                            temp >> next; m->gobble(temp);
+                            reads.push_back(next);
+                        }
+                        theseReads.push_back(reads);
+                    }
+                    thisFilesLines[numSampled] = theseReads;
+                    m->gobble(temp);
+                   
+                    numSampledSet.insert(numSampled);
                                }
                                
-                               files[thisfilename] = thisFilesLines;
+                               files[group] = thisFilesLines;
                                
                                //save longest file for below
                                if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
@@ -557,34 +573,46 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                                m->mothurRemove(thisfilename);
                        }
                        
-                       
+            //output new labels line
+            out << fileLabels[combineFileName][0][0] << '\t';
+            for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
+                for (int n = 0; n < groupNames.size(); n++) { // for each group
+                    for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
+                        out << fileLabels[combineFileName][k][l] << '-' << groupNames[n] << '\t';
+                    }
+                }
+            }
+                       out << endl;
+            
                        //for each label
-                       for (int k = 1; k < maxLines; k++) {
+                       for (set<int>::iterator itNumSampled = numSampledSet.begin(); itNumSampled != numSampledSet.end(); itNumSampled++) {
                                
-                               //grab data for each group
-                               for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
-                    
-                                       string thisfilename = itFileNameGroup->first;
-                                       map<int, int>::iterator itLine = lineToNumber.find(k);
-                                       if (itLine != lineToNumber.end()) {
-                                               string output = toString(itLine->second);
-                                               if (k < files[thisfilename].size()) {
-                                                       string line = files[thisfilename][k];
-                                                       output = line.substr(0, line.find_first_of('\t'));
-                                                       output += '\t' + files[thisfilename][0] + '\t' + line.substr(line.find_first_of('\t'));
-                                               }else{
-                                                       output += '\t' + files[thisfilename][0] + '\t';
-                                                       for (int h = 0; h < numColumns; h++) {
-                                                               output += "NA\t";
-                                                       }
-                                               }
-                                               out << output << endl;
-                                       }else { m->mothurOut("[ERROR]: parsing results, cant find " + toString(k)); m->mothurOutEndLine(); }
-                               }
+                out << (*itNumSampled) << '\t';
+                               
+                if (m->control_pressed) { break; }
+                
+                for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk
+                                   //grab data for each group
+                    for (map<string, map<int, vector< vector<string> > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) {
+                        
+                        string group = itFileNameGroup->first;
+                       
+                        map<int, vector< vector<string> > >::iterator itLine = files[group].find(*itNumSampled);
+                        if (itLine != files[group].end()) { 
+                            for (int l = 0; l < (itLine->second)[k].size(); l++) { 
+                                out << (itLine->second)[k][l] << '\t';
+                               
+                            }                             
+                        }else { 
+                            for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { 
+                                out << "NA" << '\t';
+                            } 
+                        }
+                    }
+                }
+                out << endl;
                        }       
-                       
                        out.close();
-                       
                }
                
                //return combine file name

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 20caead668196fc75d10de1275956b7955bdd3b6..f267ba4b7859ed091f749456cb5495799ffc9ec0 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -306,6 +306,7 @@ int SffInfoCommand::execute(){
                        
                        int start = time(NULL);
                        
+            filenames[s] = m->getFullPathName(filenames[s]);
                        m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
                        
                        string accnos = "";

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 5bcd7d843a18829793afcc9660af7b7667385c4b..be410d9d9f4ecec2fc885a239c9ba57b5f409e89 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -150,14 +150,21 @@ ShhherCommand::ShhherCommand(string option) {
                        else{
                                ofstream temp;
                 
-                string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+                string thisoutputDir = outputDir;
+                if (outputDir == "") {  thisoutputDir =  m->hasPath(flowFilesFileName); } //if user entered a file with a path then preserve it
                 
-                               //flow.files = 9 character offset
-                               compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
+                               //we want to rip off .files, and also .flow if its there
+                string fileroot = m->getRootName(m->getSimpleName(flowFilesFileName));
+                if (fileroot[fileroot.length()-1] == '.') {  fileroot = fileroot.substr(0, fileroot.length()-1); } //rip off dot
+                string extension = m->getExtension(fileroot);
+                if (extension == ".flow") { fileroot = m->getRootName(fileroot);  }
+                else { fileroot += "."; } //add back if needed
+                
+                               compositeFASTAFileName = thisoutputDir + fileroot + "shhh.fasta";
                                m->openOutputFile(compositeFASTAFileName, temp);
                                temp.close();
                                
-                               compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
+                               compositeNamesFileName = thisoutputDir + fileroot + "shhh.names";
                                m->openOutputFile(compositeNamesFileName, temp);
                                temp.close();
                        }