parsefastaqcommand.cpp

   1 /*
   2  *  parsefastaqcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/30/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "parsefastaqcommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 ParseFastaQCommand::ParseFastaQCommand(string option){
  15         try {
  16                 abort = false;
  17
  18                 if(option == "help") {  help(); abort = true; }
  19
  20                 else {
  21                         //valid paramters for this command
  22                         string Array[] =  {"fastaq", "outputdir", "inputdir"};
  23                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  24
  25                         OptionParser parser(option);
  26                         map<string,string> parameters = parser.getParameters();
  27
  28                         ValidParameters validParameter;
  29                         map<string,string>::iterator it;
  30
  31                         //check to make sure all parameters are valid for command
  32                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  33                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  34                         }
  35
  36                         //if the user changes the input directory command factory will send this info to us in the output parameter
  37                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  38                         if (inputDir == "not found"){   inputDir = "";          }
  39                         else {
  40                                 string path;
  41                                 it = parameters.find("fastaq");
  42                                 //user has given a template file
  43                                 if(it != parameters.end()){
  44                                         path = m->hasPath(it->second);
  45                                         //if the user has not given a path then, add inputdir. else leave path alone.
  46                                         if (path == "") {       parameters["fastaq"] = inputDir + it->second;           }
  47                                 }
  48                         }
  49
  50                         //check for required parameters
  51                         fastaQFile = validParameter.validFile(parameters, "fastaq", true);
  52                         if (fastaQFile == "not found") {        m->mothurOut("fastaq is a required parameter for the parse.fastaq command.");   m->mothurOutEndLine();  abort = true;   }
  53                         else if (fastaQFile == "not open")      {       fastaQFile = ""; abort = true;  }
  54
  55                         //if the user changes the output directory command factory will send this info to us in the output parameter
  56                         outputDir = validParameter.validFile(parameters, "outputdir", false);   if (outputDir == "not found"){  outputDir = m->hasPath(fastaQFile);     }
  57
  58                 }
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
  62                 exit(1);
  63         }
  64 }
  65 //**********************************************************************************************************************
  66
  67 void ParseFastaQCommand::help(){
  68         try {
  69                 m->mothurOut("The parse.fastaq command reads a fastaQ file and creates a fasta and quality file.\n");
  70                 m->mothurOut("The parse.fastaq command parameter is fastaq, and it is required.\n");
  71                 m->mothurOut("The parse.fastaq command should be in the following format: parse.fastaq(fastaq=yourFastaQFile).\n");
  72                 m->mothurOut("Example parse.fastaq(fastaq=test.fastaq).\n");
  73                 m->mothurOut("Note: No spaces between parameter labels (i.e. fastaq), '=' and yourFastaQFile.\n");
  74                 m->mothurOutEndLine();
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "ParseFastaQCommand", "help");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82
  83 ParseFastaQCommand::~ParseFastaQCommand()       {       /*      do nothing      */      }
  84
  85 //**********************************************************************************************************************
  86
  87 int ParseFastaQCommand::execute(){
  88         try {
  89                 if (abort == true) {    return 0;       }
  90
  91                 //open Output Files
  92                 string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
  93                 string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
  94                 ofstream outFasta, outQual;
  95                 m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile);
  96                 m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);
  97
  98                 ifstream in;
  99                 m->openInputFile(fastaQFile, in);
 100
 101                 while (!in.eof()) {
 102
 103                         //read sequence name
 104                         string name = m->getline(in); m->gobble(in);
 105                         if (name == "") {  m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 106                         else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 107                         else { name = name.substr(1); }
 108
 109                         //read sequence
 110                         string sequence = m->getline(in); m->gobble(in);
 111                         if (sequence == "") {  m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; break; }
 112
 113                         //read sequence name
 114                         string name2 = m->getline(in); m->gobble(in);
 115                         if (name2 == "") {  m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 116                         else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 117                         else { name2 = name2.substr(1);  }
 118
 119                         //read quality scores
 120                         string qual = m->getline(in); m->gobble(in);
 121                         if (qual == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
 122
 123                         //sanity check sequence length and number of quality scores match
 124                         if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 125                         if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
 126
 127                         //convert quality scores
 128                         vector<int> qualScores = convertQual(qual);
 129
 130                         //print sequence info to files
 131                         outFasta << ">" << name << endl << sequence << endl;
 132
 133                         outQual << ">" << name << endl;
 134                         for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
 135                         outQual << endl;
 136                 }
 137
 138                 in.close();
 139                 outFasta.close();
 140                 outQual.close();
 141
 142                 if (m->control_pressed) { remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
 143
 144                 m->mothurOutEndLine();
 145                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 146                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 147                 m->mothurOutEndLine();
 148
 149                 return 0;
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "ParseFastaQCommand", "execute");
 153                 exit(1);
 154         }
 155 }
 156 //**********************************************************************************************************************
 157 vector<int> ParseFastaQCommand::convertQual(string qual) {
 158         try {
 159                 vector<int> qualScores;
 160
 161                 int controlChar = int('!');
 162
 163                 for (int i = 0; i < qual.length(); i++) {
 164                         int temp = int(qual[i]);
 165                         temp -= controlChar;
 166
 167                         qualScores.push_back(temp);
 168                 }
 169
 170                 return qualScores;
 171         }
 172         catch(exception& e) {
 173                 m->errorOut(e, "ParseFastaQCommand", "convertQual");
 174                 exit(1);
 175         }
 176 }
 177 //**********************************************************************************************************************
 178
 179
 180