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

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 957f37a65bfb1c177f000c9c6d031ddfc3784c81..8d9a57a54ffd0db053956200602f3aa06fb4de5b 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -14,8 +14,8 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "qualityscores.h"
 #include "command.hpp"
 #include "sequence.hpp"
 #include "qualityscores.h"

-#include "groupmap.h"

 #include "trimoligos.h"
 #include "trimoligos.h"

+#include "counttable.h"

 
 
 class TrimSeqsCommand : public Command {
 
 
 class TrimSeqsCommand : public Command {


@@ -36,16 +36,13 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:

-       
-       GroupMap* groupMap;
-    

     struct linePair {
         unsigned long long start;
         unsigned long long end;
         linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
         linePair() {}
     };
     struct linePair {
         unsigned long long start;
         unsigned long long end;
         linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
         linePair() {}
     };

-
+    

        bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
        bool keepFirstTrim(Sequence&, QualityScores&);
        bool removeLastTrim(Sequence&, QualityScores&);
        bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
        bool keepFirstTrim(Sequence&, QualityScores&);
        bool removeLastTrim(Sequence&, QualityScores&);


@@ -55,7 +52,7 @@ private:
     string reverseOligo(string);
 
        bool abort, createGroup;
     string reverseOligo(string);
 
        bool abort, createGroup;

-       string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
+       string fastaFile, oligoFile, qFileName, groupfile, nameFile, countfile, outputDir;

        
        bool flip, allFiles, qtrim, keepforward;
        int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
        
        bool flip, allFiles, qtrim, keepforward;
        int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;


@@ -75,13 +72,15 @@ private:
        vector<string> barcodeNameVector;       //needed here?
        map<string, int> groupCounts;  
        map<string, string> nameMap;
        vector<string> barcodeNameVector;       //needed here?
        map<string, int> groupCounts;  
        map<string, string> nameMap;

+    map<string, int> nameCount; //for countfile name -> repCount
+    map<string, string> groupMap; //for countfile name -> group

 
        vector<int> processIDS;   //processid
        vector<linePair> lines;
        vector<linePair> qLines;
        
 
        vector<int> processIDS;   //processid
        vector<linePair> lines;
        vector<linePair> qLines;
        

-       int driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair, linePair);    
-       int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
+       int driverCreateTrim(string, string, string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair, linePair);    
+       int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);

        int setLines(string, string);
 };
 
        int setLines(string, string);
 };
 


@@ -92,7 +91,7 @@ private:
 struct trimData {
     unsigned long long start, end;
     MothurOut* m;
 struct trimData {
     unsigned long long start, end;
     MothurOut* m;

-    string filename, qFileName, trimFileName, scrapFileName, trimQFileName, scrapQFileName, trimNFileName, scrapNFileName, groupFileName, nameFile;
+    string filename, qFileName, trimFileName, scrapFileName, trimQFileName, scrapQFileName, trimNFileName, scrapNFileName, trimCFileName, scrapCFileName, groupFileName, nameFile, countfile;

        vector<vector<string> > fastaFileNames;
     vector<vector<string> > qualFileNames;
     vector<vector<string> > nameFileNames;
        vector<vector<string> > fastaFileNames;
     vector<vector<string> > qualFileNames;
     vector<vector<string> > nameFileNames;


@@ -105,6 +104,7 @@ struct trimData {
        map<string, int> barcodes;
     map<string, int> rbarcodes;
        map<string, int> primers;
        map<string, int> barcodes;
     map<string, int> rbarcodes;
        map<string, int> primers;

+    map<string, int> nameCount;

     vector<string>  linker;
     vector<string>  spacer;
        map<string, int> combos;
     vector<string>  linker;
     vector<string>  spacer;
        map<string, int> combos;


@@ -112,22 +112,26 @@ struct trimData {
        vector<string> barcodeNameVector;       
        map<string, int> groupCounts;  
        map<string, string> nameMap;
        vector<string> barcodeNameVector;       
        map<string, int> groupCounts;  
        map<string, string> nameMap;

+    map<string, string> groupMap;

     
        trimData(){}
     
        trimData(){}

-       trimData(string fn, string qn, string nf, string tn, string sn, string tqn, string sqn, string tnn, string snn, string gn, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<vector<string> > nfn, unsigned long long lstart, unsigned long long lend, unsigned long long qstart, unsigned long long qend,  MothurOut* mout,
+       trimData(string fn, string qn, string nf, string cf, string tn, string sn, string tqn, string sqn, string tnn, string snn, string tcn, string scn,string gn, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<vector<string> > nfn, unsigned long long lstart, unsigned long long lend, unsigned long long qstart, unsigned long long qend,  MothurOut* mout,

                       int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, map<string, int> rbar, vector<string> revP, vector<string> li, vector<string> spa, 
                       vector<string> priNameVector, vector<string> barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
                       int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage,
                       int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, map<string, int> rbar, vector<string> revP, vector<string> li, vector<string> spa, 
                       vector<string> priNameVector, vector<string> barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
                       int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage,

-                      int minL, int maxA, int maxH, int maxL, bool fli, map<string, string> nm) {
+                      int minL, int maxA, int maxH, int maxL, bool fli, map<string, string> nm, map<string, int> ncount) {

         filename = fn;
         qFileName = qn;
         nameFile = nf;
         filename = fn;
         qFileName = qn;
         nameFile = nf;

+        countfile = cf;

         trimFileName = tn;
         scrapFileName = sn;
         trimQFileName = tqn;
         scrapQFileName = sqn;
         trimNFileName = tnn;
         scrapNFileName = snn;
         trimFileName = tn;
         scrapFileName = sn;
         trimQFileName = tqn;
         scrapQFileName = sqn;
         trimNFileName = tnn;
         scrapNFileName = snn;

+        trimCFileName = tcn;
+        scrapCFileName = scn;

         groupFileName = gn;
         fastaFileNames = ffn;
         qualFileNames = qfn;
         groupFileName = gn;
         fastaFileNames = ffn;
         qualFileNames = qfn;


@@ -137,6 +141,7 @@ struct trimData {
         qlineStart = qstart;
         qlineEnd = qend;
                m = mout;
         qlineStart = qstart;
         qlineEnd = qend;
                m = mout;

+        nameCount = ncount;

         
         pdiffs = pd;
         bdiffs = bd;
         
         pdiffs = pd;
         bdiffs = bd;


@@ -203,7 +208,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                
                
                ofstream outGroupsFile;
                
                
                ofstream outGroupsFile;

-               if (pDataArray->createGroup){   pDataArray->m->openOutputFile(pDataArray->groupFileName, outGroupsFile);   }
+               if ((pDataArray->createGroup) && (pDataArray->countfile == "")){        pDataArray->m->openOutputFile(pDataArray->groupFileName, outGroupsFile);   }

                if(pDataArray->allFiles){
                        for (int i = 0; i < pDataArray->fastaFileNames.size(); i++) { //clears old file
                                for (int j = 0; j < pDataArray->fastaFileNames[i].size(); j++) { //clears old file
                if(pDataArray->allFiles){
                        for (int i = 0; i < pDataArray->fastaFileNames.size(); i++) { //clears old file
                                for (int j = 0; j < pDataArray->fastaFileNames[i].size(); j++) { //clears old file


@@ -222,6 +227,14 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                        }
                }
                
                        }
                }
                

+        ofstream trimCountFile;
+               ofstream scrapCountFile;
+               if(pDataArray->countfile != ""){
+                       pDataArray->m->openOutputFile(pDataArray->trimCFileName, trimCountFile);
+                       pDataArray->m->openOutputFile(pDataArray->scrapCFileName, scrapCountFile);
+            if ((pDataArray->lineStart == 0) || (pDataArray->lineStart == 1)) { trimCountFile << "Representative_Sequence\ttotal" << endl; scrapCountFile << "Representative_Sequence\ttotal" << endl; }
+               }
+        

                ifstream inFASTA;
                pDataArray->m->openInputFile(pDataArray->filename, inFASTA);
                if ((pDataArray->lineStart == 0) || (pDataArray->lineStart == 1)) {
                ifstream inFASTA;
                pDataArray->m->openInputFile(pDataArray->filename, inFASTA);
                if ((pDataArray->lineStart == 0) || (pDataArray->lineStart == 1)) {


@@ -248,7 +261,11 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                   
                        if (pDataArray->m->control_pressed) { 
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
                                   
                        if (pDataArray->m->control_pressed) { 
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();

-                               if (pDataArray->createGroup) {   outGroupsFile.close();   }
+                               if ((pDataArray->createGroup) && (pDataArray->countfile == "")) {        outGroupsFile.close();   }
+                if(pDataArray->qFileName != "")        {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
+                if(pDataArray->nameFile != "") {       scrapNameFile.close(); trimNameFile.close();    }
+                if(pDataArray->countfile != "")        {       scrapCountFile.close(); trimCountFile.close();  }
+

                                if(pDataArray->qFileName != ""){ qFile.close(); }
                                return 0;
                        }
                                if(pDataArray->qFileName != ""){ qFile.close(); }
                                return 0;
                        }


@@ -399,6 +416,15 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                                else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
                                        }
                                        
                                                else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
                                        }
                                        

+                    int numRedundants = 0;
+                    if (pDataArray->countfile != "") {
+                        map<string, int>::iterator itCount = pDataArray->nameCount.find(currSeq.getName());
+                        if (itCount != pDataArray->nameCount.end()) { 
+                            trimCountFile << itCount->first << '\t' << itCount->second << endl;
+                            numRedundants = itCount->second-1;
+                        }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
+                    }
+                                       

                                        if (pDataArray->createGroup) {
                                                if(pDataArray->barcodes.size() != 0){
                                                        string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
                                        if (pDataArray->createGroup) {
                                                if(pDataArray->barcodes.size() != 0){
                                                        string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];


@@ -412,9 +438,9 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                                                } 
                                                        }
                                                        
                                                                } 
                                                        }
                                                        

-                                                       outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+                                                       if (pDataArray->countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+                            else {   pDataArray->groupMap[currSeq.getName()] = thisGroup; }

                                                        
                                                        

-                            int numRedundants = 0;

                                                        if (pDataArray->nameFile != "") {
                                                                map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
                                                                if (itName != pDataArray->nameMap.end()) { 
                                                        if (pDataArray->nameFile != "") {
                                                                map<string, string>::iterator itName = pDataArray->nameMap.find(currSeq.getName());
                                                                if (itName != pDataArray->nameMap.end()) { 


@@ -462,6 +488,12 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                                if (itName != pDataArray->nameMap.end()) {  scrapNameFile << itName->first << '\t' << itName->second << endl; }
                                                else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
                                        }
                                                if (itName != pDataArray->nameMap.end()) {  scrapNameFile << itName->first << '\t' << itName->second << endl; }
                                                else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
                                        }

+                    if (pDataArray->countfile != "") {
+                        map<string, int>::iterator itCount = pDataArray->nameCount.find(currSeq.getName());
+                        if (itCount != pDataArray->nameCount.end()) { 
+                            trimCountFile << itCount->first << '\t' << itCount->second << endl;
+                        }else { pDataArray->m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
+                    }

                                        currSeq.setName(currSeq.getName() + '|' + trashCode);
                                        currSeq.setUnaligned(origSeq);
                                        currSeq.setAligned(origSeq);
                                        currSeq.setName(currSeq.getName() + '|' + trashCode);
                                        currSeq.setUnaligned(origSeq);
                                        currSeq.setAligned(origSeq);