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 vector<string> AlignCheckCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta","map", "outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "AlignCheckCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 AlignCheckCommand::AlignCheckCommand(){
  27         try {
  28                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["aligncheck"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> AlignCheckCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta","map"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> AlignCheckCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62
  63 AlignCheckCommand::AlignCheckCommand(string option)  {
  64         try {
  65                 abort = false;
  66                 haderror = 0;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"fasta","map", "outputdir","inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string,string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //initialize outputTypes
  88                         vector<string> tempOutNames;
  89                         outputTypes["aligncheck"] = tempOutNames;
  90
  91                         //if the user changes the input directory command factory will send this info to us in the output parameter
  92                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  93                         if (inputDir == "not found"){   inputDir = "";          }
  94                         else {
  95                                 string path;
  96                                 it = parameters.find("fasta");
  97                                 //user has given a template file
  98                                 if(it != parameters.end()){
  99                                         path = m->hasPath(it->second);
 100                                         //if the user has not given a path then, add inputdir. else leave path alone.
 101                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 102                                 }
 103
 104                                 it = parameters.find("map");
 105                                 //user has given a template file
 106                                 if(it != parameters.end()){
 107                                         path = m->hasPath(it->second);
 108                                         //if the user has not given a path then, add inputdir. else leave path alone.
 109                                         if (path == "") {       parameters["map"] = inputDir + it->second;              }
 110                                 }
 111                         }
 112
 113                         //check for required parameters
 114                         mapfile = validParameter.validFile(parameters, "map", true);
 115                         if (mapfile == "not open") { abort = true; }
 116                         else if (mapfile == "not found") {  mapfile = "";  m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
 117
 118                         fastafile = validParameter.validFile(parameters, "fasta", true);
 119                         if (fastafile == "not open") { abort = true; }
 120                         else if (fastafile == "not found") {  fastafile = "";  m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true;  }
 121
 122                         //if the user changes the output directory command factory will send this info to us in the output parameter
 123                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 124                                 outputDir = "";
 125                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 126                         }
 127
 128                 }
 129
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
 133                 exit(1);
 134         }
 135 }
 136 //**********************************************************************************************************************
 137
 138 void AlignCheckCommand::help(){
 139         try {
 140                 m->mothurOut("The align.check command reads a fasta file and map file.\n");
 141                 m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
 142                 m->mothurOut("The align.check command parameters are fasta and map, both are required.\n");
 143                 m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
 144                 m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
 145                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 146         }
 147         catch(exception& e) {
 148                 m->errorOut(e, "AlignCheckCommand", "help");
 149                 exit(1);
 150         }
 151 }
 152
 153 //**********************************************************************************************************************
 154
 155 int AlignCheckCommand::execute(){
 156         try {
 157
 158                 if (abort == true) { return 0; }
 159
 160                 //get secondary structure info.
 161                 readMap();
 162
 163                 ifstream in;
 164                 m->openInputFile(fastafile, in);
 165
 166                 ofstream out;
 167                 string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
 168                 m->openOutputFile(outfile, out);
 169
 170                 out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
 171                 out << "loop" << '\t' << "tilde" << '\t' << "total" << endl;
 172
 173
 174                 while(!in.eof()){
 175                         if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
 176
 177                         Sequence seq(in);  m->gobble(in);
 178                         if (seq.getName() != "") {
 179                                 statData data = getStats(seq.getAligned());
 180
 181                                 if (haderror == 1) { break; }
 182
 183                                 out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
 184                                 out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
 185                         }
 186                 }
 187
 188                 in.close();
 189                 out.close();
 190
 191                 if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
 192
 193                 m->mothurOutEndLine();
 194                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 195                 m->mothurOut(outfile); m->mothurOutEndLine();   outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
 196                 m->mothurOutEndLine();
 197
 198                 return 0;
 199         }
 200
 201         catch(exception& e) {
 202                 m->errorOut(e, "AlignCheckCommand", "execute");
 203                 exit(1);
 204         }
 205 }
 206 //**********************************************************************************************************************
 207 void AlignCheckCommand::readMap(){
 208         try {
 209
 210                 structMap.resize(1, 0);
 211                 ifstream in;
 212
 213                 m->openInputFile(mapfile, in);
 214
 215                 while(!in.eof()){
 216                         int position;
 217                         in >> position;
 218                         structMap.push_back(position);
 219                         m->gobble(in);
 220                 }
 221                 in.close();
 222
 223                 seqLength = structMap.size();
 224
 225
 226                 //check you make sure is structMap[10] = 380 then structMap[380] = 10.
 227                 for(int i=0;i<seqLength;i++){
 228                         if(structMap[i] != 0){
 229                                 if(structMap[structMap[i]] != i){
 230                                         m->mothurOut("Your map file contains an error:  line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine();
 231                                 }
 232                         }
 233                 }
 234
 235
 236         }
 237         catch(exception& e) {
 238                 m->errorOut(e, "AlignCheckCommand", "readMap");
 239                 exit(1);
 240         }
 241 }
 242 /**************************************************************************************************/
 243
 244 statData AlignCheckCommand::getStats(string sequence){
 245         try {
 246
 247                 statData data;
 248                 sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
 249
 250                 int length = sequence.length();
 251
 252                 if (length != seqLength) { m->mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); m->mothurOutEndLine(); haderror = 1; return data;  }
 253
 254                 for(int i=1;i<length;i++){
 255                         if(structMap[i] != 0){
 256                                 if(sequence[i] == 'A'){
 257                                         if(sequence[structMap[i]] == 'T')               {       data.tilde++;   }
 258                                         else if(sequence[structMap[i]] == 'A')  {       data.pound++;   }
 259                                         else if(sequence[structMap[i]] == 'G')  {       data.equal++;   }
 260                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   }
 261                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 262                                         data.total++;
 263                                 }
 264                                 else if(sequence[i] == 'T'){
 265                                         if(sequence[structMap[i]] == 'T')               {       data.plus++;    }
 266                                         else if(sequence[structMap[i]] == 'A')  {       data.tilde++;   }
 267                                         else if(sequence[structMap[i]] == 'G')  {       data.dash++;    }
 268                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   }
 269                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 270                                         data.total++;
 271                                 }
 272                                 else if(sequence[i] == 'G'){
 273                                         if(sequence[structMap[i]] == 'T')               {       data.dash++;    }
 274                                         else if(sequence[structMap[i]] == 'A')  {       data.equal++;   }
 275                                         else if(sequence[structMap[i]] == 'G')  {       data.pound++;   }
 276                                         else if(sequence[structMap[i]] == 'C')  {       data.tilde++;   }
 277                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 278                                         data.total++;
 279                                 }
 280                                 else if(sequence[i] == 'C'){
 281                                         if(sequence[structMap[i]] == 'T')               {       data.pound++;   }
 282                                         else if(sequence[structMap[i]] == 'A')  {       data.pound++;   }
 283                                         else if(sequence[structMap[i]] == 'G')  {       data.tilde++;   }
 284                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   }
 285                                         else if(sequence[structMap[i]] == '-')  {       data.pound++;   }
 286                                         data.total++;
 287                                 }
 288                                 else if(sequence[i] == '-'){
 289                                         if(sequence[structMap[i]] == 'T')               {       data.pound++;   data.total++;   }
 290                                         else if(sequence[structMap[i]] == 'A')  {       data.pound++;   data.total++;   }
 291                                         else if(sequence[structMap[i]] == 'G')  {       data.pound++;   data.total++;   }
 292                                         else if(sequence[structMap[i]] == 'C')  {       data.pound++;   data.total++;   }
 293                                         else if(sequence[structMap[i]] == '-')  {               /*donothing*/                           }
 294                                 }
 295                         }
 296                         else if(isalnum(sequence[i])){
 297                                 data.loop++;
 298                                 data.total++;
 299                         }
 300                 }
 301                 return data;
 302
 303         }
 304         catch(exception& e) {
 305                 m->errorOut(e, "AlignCheckCommand", "getStats");
 306                 exit(1);
 307         }
 308 }
 309
 310
 311 //**********************************************************************************************************************