changing command name classify.shared to classifyrf.shared

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index e48d50794d15b4b77dae6a15134d9bec54c8a911..5879241372dd3b60b34683683a0c1edbcbd64d57 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -23,7 +23,8 @@ vector<string> SeqErrorCommand::setParameters(){
                CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(preference);
                CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(pqfile);
                CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(preport);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+               CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
                CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pignorechimeras);
                CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pthreshold);
                CommandParameter paligned("aligned", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(paligned);
@@ -52,7 +53,8 @@ string SeqErrorCommand::getHelpString(){
                helpString += "The reference parameter...\n";
                helpString += "The qfile parameter...\n";
                helpString += "The report parameter...\n";
-               helpString += "The name parameter...\n";
+               helpString += "The name parameter allows you to provide a name file associated with the fasta file.\n";
+        helpString += "The count parameter allows you to provide a count file associated with the fasta file.\n";
                helpString += "The ignorechimeras parameter...\n";
                helpString += "The threshold parameter...\n";
                helpString += "The processors parameter...\n";
@@ -190,6 +192,14 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
+                
+                it = parameters.find("count");
+                               //user has given a names file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["count"] = inputDir + it->second;            }
+                               }
 
                                it = parameters.find("qfile");
                                //user has given a quality score file
@@ -227,6 +237,12 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        if(namesFileName == "not found"){       namesFileName = "";     }
                        else if (namesFileName == "not open") { namesFileName = ""; abort = true; }     
                        else { m->setNameFile(namesFileName); }
+            
+            //check for optional parameters
+                       countfile = validParameter.validFile(parameters, "count", true);
+                       if(countfile == "not found"){   countfile = ""; }
+                       else if (countfile == "not open") { countfile = ""; abort = true; }
+                       else { m->setCountTableFile(countfile); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if(qualFileName == "not found"){        qualFileName = "";      }
@@ -243,6 +259,8 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                outputDir += m->hasPath(queryFileName); //if user entered a file with a path then preserve it   
                        }
                        
+            if ((countfile != "") && (namesFileName != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+            
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
@@ -337,7 +355,12 @@ int SeqErrorCommand::execute(){
                
                getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 
-               if(namesFileName != ""){        weights = getWeights(); }
+               if(namesFileName != "")     {   weights = getWeights();         }
+        else if (countfile != "")   {
+            CountTable ct;
+            ct.readTable(countfile, false);
+            weights = ct.getNameMap();
+        }
                
                vector<unsigned long long> fastaFilePos;
                vector<unsigned long long> qFilePos;
@@ -407,6 +430,13 @@ int SeqErrorCommand::execute(){
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
                m->mothurOutEndLine();
                
+        //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("errorseq");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+        
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
@@ -636,7 +666,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        int misMatchSize;
                        in >> misMatchSize; m->gobble(in);
                        if (misMatchSize > misMatchCounts.size()) {     misMatchCounts.resize(misMatchSize, 0); }
-                       for (int j = 0; j < misMatchCounts.size(); j++) {
+                       for (int j = 0; j < misMatchSize; j++) {
                                in >> tempNum; misMatchCounts[j] += tempNum;
                        }
                        m->gobble(in);
@@ -778,7 +808,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
             
             getErrors(query, reference, minCompare);
                        
-                       if(namesFileName != ""){
+                       if((namesFileName != "") || (countfile != "")){
                                it = weights.find(query.getName());
                                minCompare.weight = it->second;
                        }
@@ -851,7 +881,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                                if (queryFile.eof()) { break; }
                        #endif
                        
-                       if(index % 100 == 0){   m->mothurOut(toString(index));  m->mothurOutEndLine(); }
+                       if(index % 100 == 0){   m->mothurOutJustToScreen(toString(index)+"\n");  }
                }
                queryFile.close();
                outChimeraReport.close();
@@ -862,7 +892,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                else if(qFileName != "" && aligned == false){   qualFile.close();                       }
         
                //report progress
-               m->mothurOut(toString(index));  m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(index)+"\n"); 
                
                return index;
        }
@@ -1382,9 +1412,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                        string sname = "";  nameStream >> sname;
                                        sname = sname.substr(1);
                     
-                    for (int i = 0; i < sname.length(); i++) {
-                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                    }
+                    m->checkName(sname);
                                        
                                        map<string, int>::iterator it = firstSeqNames.find(sname);
                                        
@@ -1445,9 +1473,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
-                    for (int i = 0; i < sname.length(); i++) {
-                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
-                    }
+                    m->checkName(sname);
                     
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);