added taxonomy file to list of files list.seqs, get.seqs and remove.seqs can process

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 23c71ecdcf2ac06f522f034cbea813d4a1f2cd22..3200137343e8691e2e8df3f70fcd1940f933b88c 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -22,7 +22,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport","list","outputdir","inputdir"};
+                       string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -83,6 +83,14 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("taxonomy");
+                               //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["taxonomy"] = inputDir + it->second;         }
+                               }
                        }
 
                        //check for required parameters
@@ -106,8 +114,11 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
 
+                       taxfile = validParameter.validFile(parameters, "taxonomy", true);
+                       if (taxfile == "not open") { abort = true; }
+                       else if (taxfile == "not found") {  taxfile = "";  }
                        
-                       if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
+                       if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        
                        int okay = 1;
                        if (outputDir != "") { okay++; }
@@ -126,8 +137,8 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 
 void ListSeqsCommand::help(){
        try {
-               m->mothurOut("The list.seqs command reads a fasta, name, group, list or alignreport file and outputs a .accnos file containing sequence names.\n");
-               m->mothurOut("The list.seqs command parameters are fasta, name, group and alignreport.  You must provide one of these parameters.\n");
+               m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
+               m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n");
                m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
                m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
@@ -151,6 +162,7 @@ int ListSeqsCommand::execute(){
                else if (groupfile != "")       {       inputFileName = groupfile;      readGroup();    }
                else if (alignfile != "")       {       inputFileName = alignfile;      readAlign();    }
                else if (listfile != "")        {       inputFileName = listfile;       readList();             }
+               else if (taxfile != "")         {       inputFileName = taxfile;        readTax();              }
                
                if (m->control_pressed) { return 0; }
                
@@ -364,3 +376,32 @@ int ListSeqsCommand::readAlign(){
        }
 }
 //**********************************************************************************************************************
+int ListSeqsCommand::readTax(){
+       try {
+               
+               ifstream in;
+               openInputFile(taxfile, in);
+               string name, firstCol, secondCol;
+               
+               while(!in.eof()){
+               
+                       if (m->control_pressed) { in.close(); return 0; }
+
+                       in >> firstCol;                         
+                       in >> secondCol;                        
+                       
+                       names.push_back(firstCol);
+                       
+                       gobble(in);
+               }
+               in.close();
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "readTax");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************