sracommand.cpp

   1 //
   2 //  sracommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by SarahsWork on 10/28/13.
   6 //  Copyright (c) 2013 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "sracommand.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> SRACommand::setParameters(){
  13         try {
  14         CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","sra",false,false); parameters.push_back(psff);
  15                 CommandParameter pfastqfile("fastqfile", "InputTypes", "", "", "none", "none", "none","sra",false,false); parameters.push_back(pfastqfile);
  16         //choose only one multiple options
  17         CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform);
  18          //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "SRACommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string SRACommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The sra command creates a sequence read archive from sff or fastq files.\n";
  36                 helpString += "The sra command parameters are: sff, fastqfiles, oligos, platform....\n";
  37                 helpString += "The sffiles parameter is used to provide a file containing a \n";
  38                 helpString += "The new command should be in the following format: \n";
  39                 helpString += "new(...)\n";
  40                 return helpString;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "SRACommand", "getHelpString");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 string SRACommand::getOutputPattern(string type) {
  49     try {
  50         string pattern = "";
  51
  52         if (type == "sra") {  pattern = "[filename],sra"; }
  53         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  54
  55         return pattern;
  56     }
  57     catch(exception& e) {
  58         m->errorOut(e, "SRACommand", "getOutputPattern");
  59         exit(1);
  60     }
  61 }
  62 //**********************************************************************************************************************
  63 SRACommand::SRACommand(){
  64         try {
  65                 abort = true; calledHelp = true;
  66                 setParameters();
  67         vector<string> tempOutNames;
  68                 outputTypes["sra"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "SRACommand", "SRACommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 SRACommand::SRACommand(string option)  {
  77         try {
  78                 abort = false; calledHelp = false;
  79
  80                 //allow user to run help
  81                 if(option == "help") { help(); abort = true; calledHelp = true; }
  82                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  83
  84                 else {
  85                         //valid paramters for this command
  86                         vector<string> myArray = setParameters();
  87
  88                         OptionParser parser(option);
  89                         map<string,string> parameters = parser.getParameters();
  90
  91                         ValidParameters validParameter;
  92                         map<string,string>::iterator it;
  93                         //check to make sure all parameters are valid for command
  94                         for (it = parameters.begin(); it != parameters.end(); it++) {
  95                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  96                         }
  97
  98
  99                         //if the user changes the input directory command factory will send this info to us in the output parameter
 100                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 101                         if (inputDir == "not found"){   inputDir = "";          }
 102                         else {
 103
 104                 string path;
 105                                 it = parameters.find("sfffiles");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["sfffiles"] = inputDir + it->second;         }
 111                                 }
 112
 113                                 it = parameters.find("fastqfiles");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["fastqfiles"] = inputDir + it->second;               }
 119                                 }
 120             }
 121
 122                         //check for parameters
 123             fastqfiles = validParameter.validFile(parameters, "fastqfiles", true);
 124                         if (fastqfiles == "not open") { fastqfiles = "";  abort = true; }
 125                         else if (fastqfiles == "not found") { fastqfiles = ""; }
 126
 127                         sfffiles = validParameter.validFile(parameters, "sfffiles", true);
 128                         if (sfffiles == "not open") {  sfffiles = "";  abort = true; }
 129                         else if (sfffiles == "not found") { sfffiles = ""; }
 130
 131                         if ((fastqfiles == "") && (sfffiles == "")) {
 132                 m->mothurOut("No valid current files. You must provide a sfffiles or fastqfiles file before you can use the sra command."); m->mothurOutEndLine(); abort = true;
 133             }
 134
 135             //use only one Mutliple type
 136                         platform = validParameter.validFile(parameters, "platform", false);
 137                         if (platform == "not found") { platform = "454"; }
 138
 139                         if ((platform == "454") || (platform == "????") || (platform == "????") || (platform == "????")) { }
 140                         else { m->mothurOut("Not a valid platform option.  Valid platform options are 454, ...."); m->mothurOutEndLine(); abort = true; }
 141
 142
 143                 }
 144
 145         }
 146         catch(exception& e) {
 147                 m->errorOut(e, "SRACommand", "SRACommand");
 148                 exit(1);
 149         }
 150 }
 151 //**********************************************************************************************************************
 152
 153 int SRACommand::execute(){
 154         try {
 155
 156                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 157
 158
 159
 160         //output files created by command
 161                 m->mothurOutEndLine();
 162                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 163                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 164                 m->mothurOutEndLine();
 165         return 0;
 166
 167     }
 168         catch(exception& e) {
 169                 m->errorOut(e, "SRACommand", "SRACommand");
 170                 exit(1);
 171         }
 172 }
 173 //**********************************************************************************************************************
 174
 175