chimeracode

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 68450fb15a7b140803aab2d54d8c5bc84e7ce688..8c61ab221d14b27e0f158b93189148817c72b057 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -21,23 +21,52 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "trump", "soft", "hard", "vertical"};
+                       string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
                        ValidParameters validParameter;
+                       map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
-                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //if the user changes the input directory command factory will send this info to us in the output parameter 
+                       string inputDir = validParameter.validFile(parameters, "inputdir", false);              
+                       if (inputDir == "not found"){   inputDir = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("fasta");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //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("hard");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["hard"] = inputDir + it->second;             }
+                               }
+                       }
+                       
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { mothurOut("fasta is a required parameter for the filter.seqs command."); 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  
+                       }
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -121,10 +150,12 @@ int FilterSeqsCommand::execute() {
                if(trump != '*' || isTrue(vertical) || soft != 0){
                        while(!inFASTA.eof()){  //read through and create the filter...
                                Sequence seq(inFASTA);
-                               if(trump != '*'){       F.doTrump(seq); }
-                               if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
-                               numSeqs++;
-                               cout.flush();
+                               if (seq.getName() != "") {
+                                       if(trump != '*'){       F.doTrump(seq); }
+                                       if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
+                                       numSeqs++;
+                                       cout.flush();
+                               }
                        }
                
                }
@@ -138,31 +169,33 @@ int FilterSeqsCommand::execute() {
                filter = F.getFilter();
 
                ofstream outFilter;
-               string filterFile = getRootName(fastafile) + "filter";
+               string filterFile = outputDir + getRootName(getSimpleName(fastafile)) + "filter";
                openOutputFile(filterFile, outFilter);
                outFilter << filter << endl;
                outFilter.close();
                
                ifstream inFasta2;
                openInputFile(fastafile, inFasta2);
-               string filteredFasta = getRootName(fastafile) + "filter.fasta";
+               string filteredFasta = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta";
                ofstream outFASTA;
                openOutputFile(filteredFasta, outFASTA);
 
                numSeqs = 0;
                while(!inFasta2.eof()){
                        Sequence seq(inFasta2);
-                       string align = seq.getAligned();
-                       string filterSeq = "";
-       
-                       for(int j=0;j<alignmentLength;j++){
-                               if(filter[j] == '1'){
-                                       filterSeq += align[j];
+                       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(inFasta2);
                }
                outFASTA.close();