added namefile to summary.seqs

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 78246b671e9d7f5b510565d0cb4650795fb4482f..54db537321479e37e03dae775a265b3206e13bdb 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1976,8 +1976,8 @@
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.17.2\\\"\"",
-                                       "RELEASE_DATE=\"\\\"3/02/2011\\\"\"",
+                                       "VERSION=\"\\\"1.17.3\\\"\"",
+                                       "RELEASE_DATE=\"\\\"3/07/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;

diff --git a/makefile b/makefile
index 7cc71f0e9a4064a2163707f3f7bc08da36af2b5e..df165b3e4195420a3543c352cd3d02c8df6b7dbc 100644 (file)
--- a/makefile
+++ b/makefile
@@ -14,7 +14,7 @@ USEMPI ?= no
 USEREADLINE ?= yes
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
-MOTHUR_FILES = "\"../release\""
+MOTHUR_FILES="\"../release\""
 RELEASE_DATE = "\"2/7/2011\""
 VERSION = "\"1.16.0\""
 

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 7da424c1ce0520fb8125915abb006126e93eeeec..8730997883ac5da6f8588e216f8311285303160d 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -13,7 +13,7 @@
 //**********************************************************************************************************************
 vector<string> SeqSummaryCommand::getValidParameters(){        
        try {
-               string Array[] =  {"fasta","processors","outputdir","inputdir"};
+               string Array[] =  {"fasta","name","processors","outputdir","inputdir"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -68,7 +68,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","processors","outputdir","inputdir"};
+                       string Array[] =  {"fasta","name","processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -94,6 +94,14 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("name");
+                               //user has given a template 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["name"] = inputDir + it->second;             }
+                               }
                        }
                        
                        //initialize outputTypes
@@ -105,6 +113,10 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true;  }       
                        
+                       namefile = validParameter.validFile(parameters, "name", true);
+                       if (namefile == "not open") { namefile = ""; abort = true; }
+                       else if (namefile == "not found") { namefile = "";  }   
+                       
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
@@ -127,7 +139,8 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
 void SeqSummaryCommand::help(){
        try {
                m->mothurOut("The summary.seqs command reads a fastafile and summarizes the sequences.\n");
-               m->mothurOut("The summary.seqs command parameters are fasta and processors, fasta is required.\n");
+               m->mothurOut("The summary.seqs command parameters are fasta, name and processors, fasta is required.\n");
+               m->mothurOut("The name parameter allows you to enter a name file associated with your fasta file. \n");
                m->mothurOut("The summary.seqs command should be in the following format: \n");
                m->mothurOut("summary.seqs(fasta=yourFastaFile, processors=2) \n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");     
@@ -158,6 +171,10 @@ int SeqSummaryCommand::execute(){
                vector<int> seqLength;
                vector<int> ambigBases;
                vector<int> longHomoPolymer;
+               
+               if (namefile != "") { readNames(); }
+               
+               if (m->control_pressed) { return 0; }
                        
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor; 
@@ -186,7 +203,7 @@ int SeqSummaryCommand::execute(){
                                
                                if (pid == 0) { //you are the root process
                                                //print header
-                                               string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\n"; 
+                                               string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";        
                                                int length = outputString.length();
                                                char* buf2 = new char[length];
                                                memcpy(buf2, outputString.c_str(), length);
@@ -334,7 +351,8 @@ int SeqSummaryCommand::execute(){
                m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); m->mothurOutEndLine();
                m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); m->mothurOutEndLine();
                m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); m->mothurOutEndLine();
-               m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
+               if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
+               else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
                
                if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
                
@@ -363,7 +381,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                
                //print header if you are process 0
                if (filePos->start == 0) {
-                       outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;   
+                       outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;  
                }
                                
                ifstream in;
@@ -381,17 +399,30 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                        Sequence current(in); m->gobble(in);
        
                        if (current.getName() != "") {
-                               startPosition.push_back(current.getStartPos());
-                               endPosition.push_back(current.getEndPos());
-                               seqLength.push_back(current.getNumBases());
-                               ambigBases.push_back(current.getAmbigBases());
-                               longHomoPolymer.push_back(current.getLongHomoPolymer());
                                
+                               int num = 1;
+                               if (namefile != "") {
+                                       //make sure this sequence is in the namefile, else error 
+                                       map<string, int>::iterator it = nameMap.find(current.getName());
+                                       
+                                       if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+                                       else { num = it->second; }
+                               }
+                               
+                               //for each sequence this sequence represents
+                               for (int i = 0; i < num; i++) {
+                                       startPosition.push_back(current.getStartPos());
+                                       endPosition.push_back(current.getEndPos());
+                                       seqLength.push_back(current.getNumBases());
+                                       ambigBases.push_back(current.getAmbigBases());
+                                       longHomoPolymer.push_back(current.getLongHomoPolymer());
+                               }
+                               
+                               count++;
                                outSummary << current.getName() << '\t';
                                outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
                                outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
-                               outSummary << current.getLongHomoPolymer() << endl;
-                               count++;
+                               outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -425,7 +456,6 @@ int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPo
                MPI_Status status; 
                MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 
-               
                for(int i=0;i<num;i++){
                        
                        if (m->control_pressed) { return 0; }
@@ -444,14 +474,27 @@ int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPo
                        Sequence current(iss);  
 
                        if (current.getName() != "") {
-                               startPosition.push_back(current.getStartPos());
-                               endPosition.push_back(current.getEndPos());
-                               seqLength.push_back(current.getNumBases());
-                               ambigBases.push_back(current.getAmbigBases());
-                               longHomoPolymer.push_back(current.getLongHomoPolymer());
+                               
+                               int num = 1;
+                               if (namefile != "") {
+                                       //make sure this sequence is in the namefile, else error 
+                                       map<string, int>::iterator it = nameMap.find(current.getName());
+                                       
+                                       if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+                                       else { num = it->second; }
+                               }
+                               
+                               //for each sequence this sequence represents
+                               for (int i = 0; i < num; i++) {
+                                       startPosition.push_back(current.getStartPos());
+                                       endPosition.push_back(current.getEndPos());
+                                       seqLength.push_back(current.getNumBases());
+                                       ambigBases.push_back(current.getAmbigBases());
+                                       longHomoPolymer.push_back(current.getLongHomoPolymer());
+                               }
                                
                                string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
-                               outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\n";
+                               outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
                                
                                //output to file
                                length = outputString.length();
@@ -495,6 +538,7 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                                m->openOutputFile(tempFile, out);
                                
                                out << num << endl;
+                               out << startPosition.size() << endl;
                                for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
                                for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
                                for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
@@ -525,6 +569,7 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                        
                        int temp, tempNum;
                        in >> tempNum; m->gobble(in); num += tempNum;
+                       in >> tempNum; m->gobble(in);
                        for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
                        for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
                        for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
@@ -543,6 +588,35 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                exit(1);
        }
 }
-//***************************************************************************************************************
+/**********************************************************************************************************************/
+int SeqSummaryCommand::readNames() { 
+       try {
+               //open input file
+               ifstream in;
+               m->openInputFile(namefile, in);
+               
+               while (!in.eof()) {
+                       if (m->control_pressed) { break; }
+                       
+                       string firstCol, secondCol;
+                       in >> firstCol >> secondCol; m->gobble(in);
+                       
+                       int num = m->getNumNames(secondCol);
+                       
+                       nameMap[firstCol] = num;
+               }
+               in.close();
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SeqSummaryCommand", "readNames");
+               exit(1);
+       }
+}
+
+/**********************************************************************************************************************/
+
 
 

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 305c6e34dd0fcf1a66e434b797ea3a5af991dfd0..fb24141f08a1314a386bc58899ec57ecf6c56e56 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -27,10 +27,11 @@ public:
        
 private:
        bool abort;
-       string fastafile, outputDir;
+       string fastafile, outputDir, namefile;
        int processors;
        vector<string> outputNames;
        map<string, vector<string> > outputTypes;
+       map<string, int> nameMap;
        
        struct linePair {
                unsigned long int start;
@@ -43,6 +44,7 @@ private:
        
        int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
        int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);       
+       int readNames();
 
        #ifdef USE_MPI
        int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);