chopseqscommand.cpp

   1 /*
   2  *  chopseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/10/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chopseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ChopSeqsCommand::getValidParameters(){
  15         try {
  16                 string AlignArray[] =  {"fasta","numbases","countgaps","keep","outputdir","inputdir"};
  17                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "ChopSeqsCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 ChopSeqsCommand::ChopSeqsCommand(){
  27         try {
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["fasta"] = tempOutNames;
  31                 outputTypes["accnos"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> ChopSeqsCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta","numbases"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> ChopSeqsCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "ChopSeqsCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 ChopSeqsCommand::ChopSeqsCommand(string option)  {
  63         try {
  64                 abort = false;
  65
  66                 //allow user to run help
  67                 if(option == "help") { help(); abort = true; }
  68
  69                 else {
  70                         //valid paramters for this command
  71                         string Array[] =  {"fasta","numbases","countgaps","keep","outputdir","inputdir"};
  72                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  73
  74                         OptionParser parser(option);
  75                         map<string,string> parameters = parser.getParameters();
  76
  77                         ValidParameters validParameter;
  78                         map<string,string>::iterator it;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //initialize outputTypes
  86                         vector<string> tempOutNames;
  87                         outputTypes["fasta"] = tempOutNames;
  88                         outputTypes["accnos"] = tempOutNames;
  89
  90                         //if the user changes the input directory command factory will send this info to us in the output parameter
  91                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  92                         if (inputDir == "not found"){   inputDir = "";          }
  93                         else {
  94                                 string path;
  95                                 it = parameters.find("fasta");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 101                                 }
 102                         }
 103
 104                         //check for required parameters
 105                         fastafile = validParameter.validFile(parameters, "fasta", true);
 106                         if (fastafile == "not open") { abort = true; }
 107                         else if (fastafile == "not found") {  m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
 108
 109                         //if the user changes the output directory command factory will send this info to us in the output parameter
 110                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
 111
 112                         string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; }
 113                         convert(temp, numbases);
 114
 115                         temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; }
 116                         countGaps = m->isTrue(temp);
 117
 118                         keep = validParameter.validFile(parameters, "keep", false);             if (keep == "not found") { keep = "front"; }
 119
 120                         if (numbases == 0)  { m->mothurOut("You must provide the number of bases you want to keep for the chops.seqs command."); m->mothurOutEndLine(); abort = true;  }
 121                 }
 122
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
 126                 exit(1);
 127         }
 128 }
 129 //**********************************************************************************************************************
 130
 131 void ChopSeqsCommand::help(){
 132         try {
 133                 m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences.\n");
 134                 m->mothurOut("The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta and numbases are required required.\n");
 135                 m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n");
 136                 m->mothurOut("The numbases parameter allows you to specify the number of bases you want to keep.\n");
 137                 m->mothurOut("The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n");
 138                 m->mothurOut("The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n");
 139                 m->mothurOut("Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n");
 140                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "ChopSeqsCommand", "help");
 144                 exit(1);
 145         }
 146 }
 147
 148 //**********************************************************************************************************************
 149
 150 int ChopSeqsCommand::execute(){
 151         try {
 152
 153                 if (abort == true) { return 0; }
 154
 155                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
 156                 string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
 157
 158                 ofstream out;
 159                 m->openOutputFile(outputFileName, out);
 160
 161                 ofstream outAcc;
 162                 m->openOutputFile(outputFileNameAccnos, outAcc);
 163
 164                 ifstream in;
 165                 m->openInputFile(fastafile, in);
 166
 167                 bool wroteAccnos = false;
 168
 169                 while (!in.eof()) {
 170
 171                         Sequence seq(in);
 172
 173                         if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
 174
 175                         if (seq.getName() != "") {
 176                                 string newSeqString = getChopped(seq);
 177
 178                                 //output trimmed sequence
 179                                 if (newSeqString != "") {
 180                                         out << ">" << seq.getName() << endl << newSeqString << endl;
 181                                 }else{
 182                                         outAcc << seq.getName() << endl;
 183                                         wroteAccnos = true;
 184                                 }
 185                         }
 186                 }
 187                 in.close();
 188                 out.close();
 189                 outAcc.close();
 190
 191                 m->mothurOutEndLine();
 192                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 193                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 194
 195                 if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
 196                 else {  remove(outputFileNameAccnos.c_str());  }
 197
 198                 m->mothurOutEndLine();
 199
 200                 return 0;
 201         }
 202
 203         catch(exception& e) {
 204                 m->errorOut(e, "ChopSeqsCommand", "execute");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209 string ChopSeqsCommand::getChopped(Sequence seq) {
 210         try {
 211                 string temp = seq.getAligned();
 212                 string tempUnaligned = seq.getUnaligned();
 213
 214                 if (countGaps) {
 215                         //if needed trim sequence
 216                         if (keep == "front") {//you want to keep the beginning
 217                                 int tempLength = temp.length();
 218
 219                                 if (tempLength > numbases) { //you have enough bases to remove some
 220
 221                                         int stopSpot = 0;
 222                                         int numBasesCounted = 0;
 223
 224                                         for (int i = 0; i < temp.length(); i++) {
 225                                                 //eliminate N's
 226                                                 if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
 227
 228                                                 numBasesCounted++;
 229
 230                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 231                                         }
 232
 233                                         if (stopSpot == 0) { temp = ""; }
 234                                         else {  temp = temp.substr(0, stopSpot);  }
 235
 236                                 }else { temp = ""; } //sequence too short
 237
 238                         }else { //you are keeping the back
 239                                 int tempLength = temp.length();
 240                                 if (tempLength > numbases) { //you have enough bases to remove some
 241
 242                                         int stopSpot = 0;
 243                                         int numBasesCounted = 0;
 244
 245                                         for (int i = (temp.length()-1); i >= 0; i--) {
 246                                                 //eliminate N's
 247                                                 if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
 248
 249                                                 numBasesCounted++;
 250
 251                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 252                                         }
 253
 254                                         if (stopSpot == 0) { temp = ""; }
 255                                         else {  temp = temp.substr(stopSpot+1);  }
 256                                 }
 257                                 else {  temp = ""; } //sequence too short
 258                         }
 259
 260                 }else{
 261
 262                         //if needed trim sequence
 263                         if (keep == "front") {//you want to keep the beginning
 264                                 int tempLength = tempUnaligned.length();
 265
 266                                 if (tempLength > numbases) { //you have enough bases to remove some
 267
 268                                         int stopSpot = 0;
 269                                         int numBasesCounted = 0;
 270
 271                                         for (int i = 0; i < temp.length(); i++) {
 272                                                 //eliminate N's
 273                                                 if (toupper(temp[i]) == 'N') {
 274                                                         temp[i] == '.';
 275                                                         tempLength--;
 276                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 277                                                 }
 278
 279                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 280
 281                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 282                                         }
 283
 284                                         if (stopSpot == 0) { temp = ""; }
 285                                         else {  temp = temp.substr(0, stopSpot);  }
 286
 287                                 }else { temp = ""; } //sequence too short
 288
 289                         }else { //you are keeping the back
 290                                 int tempLength = tempUnaligned.length();
 291                                 if (tempLength > numbases) { //you have enough bases to remove some
 292
 293                                         int stopSpot = 0;
 294                                         int numBasesCounted = 0;
 295
 296                                         for (int i = (temp.length()-1); i >= 0; i--) {
 297                                                 //eliminate N's
 298                                                 if (toupper(temp[i]) == 'N') {
 299                                                         temp[i] == '.';
 300                                                         tempLength--;
 301                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 302                                                 }
 303
 304                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 305
 306                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 307                                         }
 308
 309                                         if (stopSpot == 0) { temp = ""; }
 310                                         else {  temp = temp.substr(stopSpot+1);  }
 311                                 }
 312                                 else {  temp = ""; } //sequence too short
 313                         }
 314                 }
 315
 316                 return temp;
 317         }
 318         catch(exception& e) {
 319                 m->errorOut(e, "ChopSeqsCommand", "getChopped");
 320                 exit(1);
 321         }
 322 }
 323 //**********************************************************************************************************************
 324
 325