]> git.donarmstrong.com Git - mothur.git/blobdiff - makegroupcommand.cpp
Revert to previous commit
[mothur.git] / makegroupcommand.cpp
diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
new file mode 100644 (file)
index 0000000..0add62e
--- /dev/null
@@ -0,0 +1,247 @@
+/*
+ *  makegroupcommand.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 5/7/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "makegroupcommand.h"
+#include "sequence.hpp"
+
+
+//**********************************************************************************************************************
+vector<string> MakeGroupCommand::setParameters(){      
+       try {
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+               CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeGroupCommand", "setParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+string MakeGroupCommand::getHelpString(){      
+       try {
+               string helpString = "";
+               helpString += "The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n";
+               helpString += "The make.group command parameters are fasta, groups and output. Fasta and group are required.\n";
+               helpString += "The output parameter allows you to specify the name of groupfile created. \n";
+               helpString += "The make.group command should be in the following format: \n";
+               helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
+               helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n";
+               return helpString;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeGroupCommand", "getHelpString");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+MakeGroupCommand::MakeGroupCommand(){  
+       try {
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["group"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
+MakeGroupCommand::MakeGroupCommand(string option)  {
+       try {
+               
+               abort = false; calledHelp = false;   
+       
+               //allow user to run help
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+               
+               else {
+                       vector<string> myArray = setParameters();
+                       
+                       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 (it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["group"] = tempOutNames;
+               
+                       //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 = "";          }
+
+                       fastaFileName = validParameter.validFile(parameters, "fasta", false);
+                       if (fastaFileName == "not found") {                             //if there is a current fasta file, use it
+                               string filename = m->getFastaFile(); 
+                               if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }else { 
+                               m->splitAtDash(fastaFileName, fastaFileNames);
+                               
+                               //go through files and make sure they are good, if not, then disregard them
+                               for (int i = 0; i < fastaFileNames.size(); i++) {
+                                       
+                                       bool ignore = false;
+                                       if (fastaFileNames[i] == "current") { 
+                                               fastaFileNames[i] = m->getFastaFile(); 
+                                               if (fastaFileNames[i] != "") {  
+                                                       m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); 
+                                                       filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));
+                                               }
+                                               else {  
+                                                       m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; 
+                                                       //erase from file list
+                                                       fastaFileNames.erase(fastaFileNames.begin()+i);
+                                                       i--;
+                                               }
+                                       }
+                                       
+                                       if (!ignore) {
+                                               if (inputDir != "") {
+                                                       string path = m->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];               }
+                                               }
+               
+                                               ifstream in;
+                                               int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
+                                       
+                                               //if you can't open it, try default location
+                                               if (ableToOpen == 1) {
+                                                       if (m->getDefaultPath() != "") { //default path is set
+                                                               string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+                                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                               ifstream in2;
+                                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                               in2.close();
+                                                               fastaFileNames[i] = tryPath;
+                                                       }
+                                               }
+                                               
+                                               //if you can't open it, try default location
+                                               if (ableToOpen == 1) {
+                                                       if (m->getOutputDir() != "") { //default path is set
+                                                               string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+                                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                               ifstream in2;
+                                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                               in2.close();
+                                                               fastaFileNames[i] = tryPath;
+                                                       }
+                                               }
+                                               in.close();
+                                               
+                                               if (ableToOpen == 1) { 
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+                                                       //erase from file list
+                                                       fastaFileNames.erase(fastaFileNames.begin()+i);
+                                                       i--;
+                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  m->setFastaFile(fastaFileNames[i]); }
+                                       }
+                               }
+                               
+                               //prevent giantic file name
+                               if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
+                               else {  filename += "groups";  }
+                               
+                               //make sure there is at least one valid file left
+                               if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); 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 = "";         }
+                       
+                       output = validParameter.validFile(parameters, "output", false);                 
+                       if (output == "not found") { output = "";  }
+                       else{ filename = output; }
+                       
+                       groups = validParameter.validFile(parameters, "groups", false);                 
+                       if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
+                       else { m->splitAtDash(groups, groupsNames);     }
+
+                       if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups.  This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true;  }
+               }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+
+int MakeGroupCommand::execute(){
+       try {
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
+               
+               if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
+                       
+               filename = outputDir + filename;
+               
+               ofstream out;
+               m->openOutputFile(filename, out);
+               
+               for (int i = 0; i < fastaFileNames.size(); i++) {
+               
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
+                       
+                       ifstream in;
+                       m->openInputFile(fastaFileNames[i], in);
+                       
+                       while (!in.eof()) {
+                               
+                               Sequence seq(in, "no align"); m->gobble(in);
+                               
+                               if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); m->mothurRemove(filename); return 0; }
+                               
+                               if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
+                       }
+                       in.close();
+               }
+               
+               out.close();
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); 
+               m->mothurOutEndLine();
+               
+               //set group file as new current groupfile
+               string current = "";
+               itTypes = outputTypes.find("group");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+               }
+               
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeGroupCommand", "execute");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+
+