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