filter.seqs can now accept multiple fasta files

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index d45d916296583824cbc260535a98f7ae850f882a..91d1181f3770b5010fcabd7e5c78e61b18186904 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -15,6 +15,7 @@
 FilterSeqsCommand::FilterSeqsCommand(string option)  {
        try {
                abort = false;
+               filterFileName = "";
                
                //allow user to run help
                if(option == "help") { help(); abort = true; }
@@ -58,16 +59,45 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        }
                        
                        //check for required parameters
-                       fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true; }
-                       else if (fastafile == "not open") { abort = true; }     
-                       
-                       //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 = ""; 
-                               outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it  
-                       }
+                       fasta = validParameter.validFile(parameters, "fasta", false);
+                       if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
+                       else { 
+                               splitAtDash(fasta, fastafileNames);
+                               
+                               //go through files and make sure they are good, if not, then disregard them
+                               for (int i = 0; i < fastafileNames.size(); i++) {
+                                       if (inputDir != "") {
+                                               string path = hasPath(fastafileNames[i]);
+                                               //if the user has not given a path then, add inputdir. else leave path alone.
+                                               if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
+                                       }
 
+                                       int ableToOpen;
+                                       ifstream in;
+                                       ableToOpen = openInputFile(fastafileNames[i], in);
+                                       if (ableToOpen == 1) { 
+                                               m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               //erase from file list
+                                               fastafileNames.erase(fastafileNames.begin()+i);
+                                               i--;
+                                       }else{  
+                                               string simpleName = getSimpleName(fastafileNames[i]);
+                                               filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+                                       }
+                                       in.close();
+                               }
+                               
+                               //make sure there is at least one valid file left
+                               if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+                       }
+                       
+                       if (!abort) {
+                               //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 = ""; 
+                                       outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it  
+                               }
+                       }
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        
@@ -107,7 +137,8 @@ void FilterSeqsCommand::help(){
        try {
                m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
                m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
-               m->mothurOut("The fasta parameter is required.\n");
+               m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
+               m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
                m->mothurOut("The trump parameter .... The default is ...\n");
                m->mothurOut("The soft parameter .... The default is ....\n");
                m->mothurOut("The hard parameter .... The default is ....\n");
@@ -130,13 +161,14 @@ int FilterSeqsCommand::execute() {
        try {
        
                if (abort == true) { return 0; }
+               vector<string> outputNames;
                
                ifstream inFASTA;
-               openInputFile(fastafile, inFASTA);
+               openInputFile(fastafileNames[0], inFASTA);
                
                Sequence testSeq(inFASTA);
                alignmentLength = testSeq.getAlignLength();
-               inFASTA.seekg(0);
+               inFASTA.close();
                
                F.setLength(alignmentLength);
                
@@ -148,18 +180,23 @@ int FilterSeqsCommand::execute() {
                else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 
                if(trump != '*' || isTrue(vertical) || soft != 0){
-                       while(!inFASTA.eof()){  //read through and create the filter...
-                               Sequence seq(inFASTA);
-                               if (seq.getName() != "") {
-                                       if(trump != '*'){       F.doTrump(seq); }
-                                       if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
-                                       numSeqs++;
-                                       cout.flush();
+                       for (int i = 0; i < fastafileNames.size(); i++) {
+                               ifstream in;
+                               openInputFile(fastafileNames[i], in);
+                               
+                               while(!in.eof()){       //read through and create the filter...
+                                       Sequence seq(in);
+                                       if (seq.getName() != "") {
+                                               if(trump != '*'){       F.doTrump(seq); }
+                                               if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
+                                               numSeqs++;
+                                               cout.flush();
+                                       }
                                }
+                               in.close();
                        }
                
                }
-               inFASTA.close();
                F.setNumSeqs(numSeqs);
                
                
@@ -169,38 +206,43 @@ int FilterSeqsCommand::execute() {
                filter = F.getFilter();
 
                ofstream outFilter;
-               string filterFile = outputDir + getRootName(getSimpleName(fastafile)) + "filter";
+               
+               string filterFile = outputDir + filterFileName + ".filter";
                openOutputFile(filterFile, outFilter);
                outFilter << filter << endl;
                outFilter.close();
+               outputNames.push_back(filterFile);
                
-               ifstream inFasta2;
-               openInputFile(fastafile, inFasta2);
-               string filteredFasta = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta";
-               ofstream outFASTA;
-               openOutputFile(filteredFasta, outFASTA);
-
                numSeqs = 0;
-               while(!inFasta2.eof()){
-                       Sequence seq(inFasta2);
-                       if (seq.getName() != "") {
-                               string align = seq.getAligned();
-                               string filterSeq = "";
-                               
-                               for(int j=0;j<alignmentLength;j++){
-                                       if(filter[j] == '1'){
-                                               filterSeq += align[j];
+               for (int i = 0; i < fastafileNames.size(); i++) {
+                       ifstream in;
+                       openInputFile(fastafileNames[i], in);
+                       string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta";
+                       ofstream outFASTA;
+                       openOutputFile(filteredFasta, outFASTA);
+                       outputNames.push_back(filteredFasta);
+                       
+                       
+                       while(!in.eof()){
+                               Sequence seq(in);
+                               if (seq.getName() != "") {
+                                       string align = seq.getAligned();
+                                       string filterSeq = "";
+                                       
+                                       for(int j=0;j<alignmentLength;j++){
+                                               if(filter[j] == '1'){
+                                                       filterSeq += align[j];
+                                               }
                                        }
+                                       
+                                       outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+                                       numSeqs++;
                                }
-                               
-                               outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
-                               numSeqs++;
+                               gobble(in);
                        }
-                       gobble(inFasta2);
+                       outFASTA.close();
+                       in.close();
                }
-               outFASTA.close();
-               inFasta2.close();
-               
                
                int filteredLength = 0;
                for(int i=0;i<alignmentLength;i++){
@@ -216,8 +258,7 @@ int FilterSeqsCommand::execute() {
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(filterFile); m->mothurOutEndLine();        
-               m->mothurOut(filteredFasta); m->mothurOutEndLine();
+               for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
                m->mothurOutEndLine();
 
                return 0;

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 0946396e3a0fe6623f3501feed5fc6e7b4ba239a..e8af5ec35c505d4b73875cee2fd1b3b78fb22b68 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -23,7 +23,8 @@ public:
        void help();
        
 private:
-       string vertical, filter, fastafile, hard, outputDir;    
+       string vertical, filter, fasta, hard, outputDir, filterFileName;
+       vector<string> fastafileNames;  
        int alignmentLength;
 
        char trump;