added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 09ff9b5fea6a92ba4a45bb721cb33df9337e7ef6..6a9a61323b50a4ea688ba9faa7ea855a233bbab9 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -48,8 +48,8 @@ string ScreenSeqsCommand::getHelpString(){
                helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
                helpString += "The fasta parameter is required.\n";
                helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
-               helpString += "The start parameter .... The default is -1.\n";
-               helpString += "The end parameter .... The default is -1.\n";
+               helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n";
+               helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
                helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
                helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
                helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
@@ -70,6 +70,33 @@ string ScreenSeqsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ScreenSeqsCommand::getOutputFileNameTag(string type, string inputName=""){      
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta")            {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "taxonomy")    {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "name")        {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "group")       {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "accnos")      {   outputFileName =  "bad.accnos";   }
+            else if (type == "qfile")       {   outputFileName =  "good" + m->getExtension(inputName);   }
+            else if (type == "alignreport") {   outputFileName =  "good.align.report";                   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ScreenSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 ScreenSeqsCommand::ScreenSeqsCommand(){        
        try {
@@ -309,8 +336,8 @@ int ScreenSeqsCommand::execute(){
                        #endif
                }
                                        
-               string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
-               string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
+               string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+               string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
                
                int numFastaSeqs = 0;
                set<string> badSeqNames;
@@ -514,7 +541,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                string seqName, seqList, group;
                set<string>::iterator it;
 
-               string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
+               string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
                outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
                
                ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
@@ -560,7 +587,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                        ifstream inputGroups;
                        m->openInputFile(groupfile, inputGroups);
 
-                       string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+                       string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
                        outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
                        
                        ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
@@ -893,8 +920,8 @@ int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
                string seqName, group;
                set<string>::iterator it;
                
-               string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
-               outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
+               string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+        outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
                ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
                
                while(!inputGroups.eof()){
@@ -945,7 +972,7 @@ int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
                string seqName, group;
                set<string>::iterator it;
                
-               string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
+               string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + getOutputFileNameTag("alignreport");
                outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
                ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 
@@ -1009,7 +1036,7 @@ int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
                string seqName, tax;
                set<string>::iterator it;
                
-               string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy);
+               string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + getOutputFileNameTag("taxonomy", taxonomy);
                outputNames.push_back(goodTaxFile);  outputTypes["taxonomy"].push_back(goodTaxFile);
                ofstream goodTaxOut;    m->openOutputFile(goodTaxFile, goodTaxOut);
                                
@@ -1058,7 +1085,7 @@ int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
                m->openInputFile(qualfile, in);
                set<string>::iterator it;
                
-               string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
+               string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
                outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
                ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
                
@@ -1209,7 +1236,6 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
 
                        char* buf4 = new char[length];
-                       memcpy(buf4, outputString.c_str(), length);
 
                        MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
                        
@@ -1358,7 +1384,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
             
                        // Allocate memory for thread data.
-                       sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension, &badSeqNames);
+                       sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
                        pDataArray.push_back(tempSum);
                        
                        //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
@@ -1375,6 +1401,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) {        badSeqNames.insert(*it);       }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }