secondarystructurecommand.cpp

   1 /*
   2  *  secondarystructurecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/18/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "secondarystructurecommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14
  15 AlignCheckCommand::AlignCheckCommand(string option){
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta","map", "outputdir","inputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //if the user changes the input directory command factory will send this info to us in the output parameter
  39                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  40                         if (inputDir == "not found"){   inputDir = "";          }
  41                         else {
  42                                 string path;
  43                                 it = parameters.find("fasta");
  44                                 //user has given a template file
  45                                 if(it != parameters.end()){
  46                                         path = hasPath(it->second);
  47                                         //if the user has not given a path then, add inputdir. else leave path alone.
  48                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  49                                 }
  50
  51                                 it = parameters.find("map");
  52                                 //user has given a template file
  53                                 if(it != parameters.end()){
  54                                         path = hasPath(it->second);
  55                                         //if the user has not given a path then, add inputdir. else leave path alone.
  56                                         if (path == "") {       parameters["map"] = inputDir + it->second;              }
  57                                 }
  58                         }
  59
  60                         //check for required parameters
  61                         mapfile = validParameter.validFile(parameters, "map", true);
  62                         if (mapfile == "not open") { abort = true; }
  63                         else if (mapfile == "not found") {  mapfile = "";  mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; }
  64
  65                         fastafile = validParameter.validFile(parameters, "fasta", true);
  66                         if (fastafile == "not open") { abort = true; }
  67                         else if (fastafile == "not found") {  fastafile = "";  mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true;  }
  68
  69                         //if the user changes the output directory command factory will send this info to us in the output parameter
  70                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  71                                 outputDir = "";
  72                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  73                         }
  74
  75                 }
  76
  77         }
  78         catch(exception& e) {
  79                 errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84
  85 void AlignCheckCommand::help(){
  86         try {
  87                 mothurOut("The align.check command reads a fasta file and map file.\n");
  88                 mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
  89                 mothurOut("The align.check command parameters are fasta and map, both are required.\n");
  90                 mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
  91                 mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
  92                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
  93         }
  94         catch(exception& e) {
  95                 errorOut(e, "AlignCheckCommand", "help");
  96                 exit(1);
  97         }
  98 }
  99
 100 //**********************************************************************************************************************
 101
 102 int AlignCheckCommand::execute(){
 103         try {
 104
 105                 if (abort == true) { return 0; }
 106
 107                 //get secondary structure info.
 108                 readMap();
 109
 110                 ifstream in;
 111                 openInputFile(fastafile, in);
 112
 113                 ofstream out;
 114                 string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
 115                 openOutputFile(outfile, out);
 116
 117                 out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
 118                 out << "loop" << '\t' << "tilde" << '\t' << "total" << endl;
 119
 120
 121                 while(!in.eof()){
 122
 123                         Sequence seq(in);  gobble(in);
 124                         if (seq.getName() != "") {
 125                                 statData data = getStats(seq.getAligned());
 126
 127                                 out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
 128                                 out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
 129                         }
 130                 }
 131
 132                 in.close();
 133                 out.close();
 134
 135                 return 0;
 136         }
 137
 138         catch(exception& e) {
 139                 errorOut(e, "AlignCheckCommand", "execute");
 140                 exit(1);
 141         }
 142 }
 143 //**********************************************************************************************************************
 144 void AlignCheckCommand::readMap(){
 145         try {
 146
 147                 structMap.resize(1, 0);
 148                 ifstream in;
 149
 150                 openInputFile(mapfile, in);
 151
 152                 while(!in.eof()){
 153                         int position;
 154                         in >> position;
 155                         structMap.push_back(position);
 156                         gobble(in);
 157                 }
 158                 in.close();
 159
 160                 seqLength = structMap.size();
 161
 162
 163                 //check you make sure is structMap[10] = 380 then structMap[380] = 10.
 164                 for(int i=0;i<seqLength;i++){
 165                         if(structMap[i] != 0){
 166                                 if(structMap[structMap[i]] != i){
 167                                         mothurOut("Your map file contains an error:  line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); mothurOutEndLine();
 168                                 }
 169                         }
 170                 }
 171
 172
 173         }
 174         catch(exception& e) {
 175                 errorOut(e, "AlignCheckCommand", "readMap");
 176                 exit(1);
 177         }
 178 }
 179 /**************************************************************************************************/
 180
 181 statData AlignCheckCommand::getStats(string sequence){
 182         try {
 183
 184                 statData data;
 185                 sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
 186
 187                 int seqLength = sequence.length();
 188                 for(int i=1;i<seqLength;i++){
 189                         if(structMap[i] != 0){
 190                                 if(sequence[i] == 'A'){
 191                                         if(sequence[structMap[i]] == 'T')               {       data.tilde++;   }
 192                                         else if(sequence[structMap[i]] == 'A')  {       data.pound++;   }
 193                                         else if(sequence[structMap[i]] == 'G')  {       data.equal++;   }
 194                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   }
 195                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 196                                         data.total++;
 197                                 }
 198                                 else if(sequence[i] == 'T'){
 199                                         if(sequence[structMap[i]] == 'T')               {       data.plus++;    }
 200                                         else if(sequence[structMap[i]] == 'A')  {       data.tilde++;   }
 201                                         else if(sequence[structMap[i]] == 'G')  {       data.dash++;    }
 202                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   }
 203                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 204                                         data.total++;
 205                                 }
 206                                 else if(sequence[i] == 'G'){
 207                                         if(sequence[structMap[i]] == 'T')               {       data.dash++;    }
 208                                         else if(sequence[structMap[i]] == 'A')  {       data.equal++;   }
 209                                         else if(sequence[structMap[i]] == 'G')  {       data.pound++;   }
 210                                         else if(sequence[structMap[i]] == 'C')  {       data.tilde++;   }
 211                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 212                                         data.total++;
 213                                 }
 214                                 else if(sequence[i] == 'C'){
 215                                         if(sequence[structMap[i]] == 'T')               {       data.pound++;   }
 216                                         else if(sequence[structMap[i]] == 'A')  {       data.pound++;   }
 217                                         else if(sequence[structMap[i]] == 'G')  {       data.tilde++;   }
 218                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   }
 219                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 220                                         data.total++;
 221                                 }
 222                                 else if(sequence[i] == '-'){
 223                                         if(sequence[structMap[i]] == 'T')               {       data.pound++;   data.total++;   }
 224                                         else if(sequence[structMap[i]] == 'A')  {       data.pound++;   data.total++;   }
 225                                         else if(sequence[structMap[i]] == 'G')  {       data.pound++;   data.total++;   }
 226                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   data.total++;   }
 227                                         else if(sequence[structMap[i]] == '-')  {               /*donothing*/                           }
 228                                 }
 229                         }
 230                         else if(isalnum(sequence[i])){
 231                                 data.loop++;
 232                                 data.total++;
 233                         }
 234                 }
 235                 return data;
 236
 237         }
 238         catch(exception& e) {
 239                 errorOut(e, "AlignCheckCommand", "getStats");
 240                 exit(1);
 241         }
 242 }
 243
 244
 245 //**********************************************************************************************************************