sffmultiplecommand.cpp

   1 //
   2 //  sffmultiplecommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 8/14/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "sffmultiplecommand.h"
  10
  11
  12 //**********************************************************************************************************************
  13 vector<string> SffMultipleCommand::setParameters(){
  14         try {
  15                 CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfile);
  16
  17         //sffinfo
  18                 CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
  19
  20         //trim.flows
  21                 CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
  22                 CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
  23                 CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
  24                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
  25                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
  26         CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
  27                 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
  28         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
  29                 CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
  30                 CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
  31                 CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
  32                 CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
  33
  34         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  35                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  36                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  37
  38                 vector<string> myArray;
  39                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "SffMultipleCommand", "setParameters");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 string SffMultipleCommand::getHelpString(){
  49         try {
  50                 string helpString = "";
  51                 helpString += "The sff.multiple command reads a file containing sff filenames and optional oligos filenames. It runs the files through sffinfo, trim.flows, shhh.flows and trim.seqs combining the results.\n";
  52                 helpString += "The sff.multiple command parameters are file, trim, maxhomop, maxflows, minflows, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, signal, noise, allfiles, order. file is required. \n";
  53                 helpString += "The file parameter allows you to enter the a file containing the list of sff files and optional oligos files.\n";
  54         helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores generated by sffinfo trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n";
  55                 helpString += "Example sff.multiple(file=mySffOligosFile.txt, trim=F).\n";
  56                 helpString += "Note: No spaces between parameter labels (i.e. file), '=' and parameters (i.e.mySffOligosFile.txt).\n";
  57                 return helpString;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "SffMultipleCommand", "getHelpString");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 string SffMultipleCommand::getOutputFileNameTag(string type, string inputName=""){
  66         try {
  67         string outputFileName = "";
  68                 map<string, vector<string> >::iterator it;
  69
  70         //is this a type this command creates
  71         it = outputTypes.find(type);
  72         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  73         else {
  74             //if (type == "fasta")            {   outputFileName =  "fasta";   }
  75             //else if (type == "flow")    {   outputFileName =  "flow";   }
  76            // else if (type == "sfftxt")        {   outputFileName =  "sff.txt";   }
  77             //else if (type == "qfile")       {   outputFileName =  "qual";   }
  78             //else {
  79                 m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;
  80         //}
  81         }
  82         return outputFileName;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "SffMultipleCommand", "getOutputFileNameTag");
  86                 exit(1);
  87         }
  88 }
  89
  90
  91 //**********************************************************************************************************************
  92 SffMultipleCommand::SffMultipleCommand(){
  93         try {
  94                 abort = true; calledHelp = true;
  95                 setParameters();
  96                 vector<string> tempOutNames;
  97                 outputTypes["fasta"] = tempOutNames;
  98                 outputTypes["flow"] = tempOutNames;
  99                 outputTypes["qfile"] = tempOutNames;
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "SffMultipleCommand", "SffMultipleCommand");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107
 108 SffMultipleCommand::SffMultipleCommand(string option)  {
 109         try {
 110                 abort = false; calledHelp = false;
 111
 112                 //allow user to run help
 113                 if(option == "help") { help(); abort = true; calledHelp = true; }
 114                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 115
 116                 else {
 117                         //valid paramters for this command
 118                         vector<string> myArray = setParameters();
 119
 120                         OptionParser parser(option);
 121                         map<string, string> parameters = parser.getParameters();
 122
 123                         ValidParameters validParameter;
 124             map<string,string>::iterator it;
 125
 126                         //check to make sure all parameters are valid for command
 127                         for (it = parameters.begin(); it != parameters.end(); it++) {
 128                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 129                         }
 130
 131                         //initialize outputTypes
 132                         vector<string> tempOutNames;
 133                         outputTypes["fasta"] = tempOutNames;
 134                         outputTypes["flow"] = tempOutNames;
 135                         outputTypes["qfile"] = tempOutNames;
 136
 137                         //if the user changes the output directory command factory will send this info to us in the output parameter
 138                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 139
 140                         //if the user changes the input directory command factory will send this info to us in the output parameter
 141                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 142                         if (inputDir == "not found"){   inputDir = "";          }
 143                         else {
 144                                 string path;
 145                 it = parameters.find("file");
 146                                 //user has given a template file
 147                                 if(it != parameters.end()){
 148                                         path = m->hasPath(it->second);
 149                                         //if the user has not given a path then, add inputdir. else leave path alone.
 150                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 151                                 }
 152                         }
 153
 154                         filename = validParameter.validFile(parameters, "file", true);
 155             if (filename == "not open") { filename = ""; abort = true; }
 156             else if (filename == "not found") { filename = "";  }
 157
 158                         string temp;
 159                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 160                         trim = m->isTrue(temp);
 161                 }
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "SffMultipleCommand", "SffMultipleCommand");
 165                 exit(1);
 166         }
 167 }
 168 //**********************************************************************************************************************
 169 int SffMultipleCommand::execute(){
 170         try {
 171                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 172
 173                 vector<string> sffFiles, oligosFiles;
 174         readFile(sffFiles, oligosFiles);
 175
 176         if (m->control_pressed) { return 0; }
 177
 178
 179                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 180
 181                 //set fasta file as new current fastafile
 182                 string current = "";
 183                 itTypes = outputTypes.find("fasta");
 184                 if (itTypes != outputTypes.end()) {
 185                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 186                 }
 187
 188                 itTypes = outputTypes.find("qfile");
 189                 if (itTypes != outputTypes.end()) {
 190                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 191                 }
 192
 193                 itTypes = outputTypes.find("flow");
 194                 if (itTypes != outputTypes.end()) {
 195                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
 196                 }
 197
 198                 //report output filenames
 199                 m->mothurOutEndLine();
 200                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 201                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 202                 m->mothurOutEndLine();
 203
 204                 return 0;
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "SffMultipleCommand", "execute");
 208                 exit(1);
 209         }
 210 }
 211 //**********************************************************************************************************************
 212 int SffMultipleCommand::readFile(vector<string>& sffFiles, vector<string>& oligosFiles){
 213         try {
 214
 215         ifstream in;
 216         m->openInputFile(filename, in);
 217
 218         string oligos, sff;
 219         while (!in.eof()) {
 220
 221             if (m->control_pressed) { break; }
 222
 223             in >> sff;
 224
 225             //ignore file pairing
 226             if(sff[0] == '#'){ while (!in.eof())        {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } m->gobble(in); }
 227             else { //check for oligos file
 228                 oligos = "";
 229
 230                 // get rest of line in case there is a oligos filename
 231                 while (!in.eof())       {
 232                     char c = in.get();
 233                     if (c == 10 || c == 13){    break;  }
 234                     else if (c == 32 || c == 9){;} //space or tab
 235                     else {      oligos += c;  }
 236                 }
 237             }
 238             m->gobble(in);
 239
 240             sffFiles.push_back(sff);
 241             oligosFiles.push_back(oligos); //will push a blank if there is not an oligos for this sff file
 242         }
 243         in.close();
 244
 245         return 0;
 246     }
 247         catch(exception& e) {
 248                 m->errorOut(e, "SffMultipleCommand", "readFile");
 249                 exit(1);
 250         }
 251 }
 252 //**********************************************************************************************************************
 253
 254
 255
 256