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","short","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                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["fasta"] = tempOutNames;
  32                 outputTypes["accnos"] = tempOutNames;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 vector<string> ChopSeqsCommand::getRequiredParameters(){
  41         try {
  42                 string Array[] =  {"fasta","numbases"};
  43                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 vector<string> ChopSeqsCommand::getRequiredFiles(){
  53         try {
  54                 vector<string> myArray;
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "ChopSeqsCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 ChopSeqsCommand::ChopSeqsCommand(string option)  {
  64         try {
  65                 abort = false;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"fasta","numbases","countgaps","keep","short","outputdir","inputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79                         map<string,string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //initialize outputTypes
  87                         vector<string> tempOutNames;
  88                         outputTypes["fasta"] = tempOutNames;
  89                         outputTypes["accnos"] = 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
 105                         //check for required parameters
 106                         fastafile = validParameter.validFile(parameters, "fasta", true);
 107                         if (fastafile == "not open") { abort = true; }
 108                         else if (fastafile == "not found") {  m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
 109
 110                         //if the user changes the output directory command factory will send this info to us in the output parameter
 111                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
 112
 113                         string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; }
 114                         convert(temp, numbases);
 115
 116                         temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; }
 117                         countGaps = m->isTrue(temp);
 118
 119                         temp = validParameter.validFile(parameters, "short", false);    if (temp == "not found") { temp = "f"; }
 120                         Short = m->isTrue(temp);
 121
 122                         keep = validParameter.validFile(parameters, "keep", false);             if (keep == "not found") { keep = "front"; }
 123
 124                         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;  }
 125                 }
 126
 127         }
 128         catch(exception& e) {
 129                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
 130                 exit(1);
 131         }
 132 }
 133 //**********************************************************************************************************************
 134
 135 void ChopSeqsCommand::help(){
 136         try {
 137                 m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences.\n");
 138                 m->mothurOut("The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta and numbases are required required.\n");
 139                 m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n");
 140                 m->mothurOut("The numbases parameter allows you to specify the number of bases you want to keep.\n");
 141                 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");
 142                 m->mothurOut("The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n");
 143                 m->mothurOut("The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n");
 144                 m->mothurOut("For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n");
 145                 m->mothurOut("Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n");
 146                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 147         }
 148         catch(exception& e) {
 149                 m->errorOut(e, "ChopSeqsCommand", "help");
 150                 exit(1);
 151         }
 152 }
 153
 154 //**********************************************************************************************************************
 155
 156 int ChopSeqsCommand::execute(){
 157         try {
 158
 159                 if (abort == true) { return 0; }
 160
 161                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
 162                 string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
 163
 164                 ofstream out;
 165                 m->openOutputFile(outputFileName, out);
 166
 167                 ofstream outAcc;
 168                 m->openOutputFile(outputFileNameAccnos, outAcc);
 169
 170                 ifstream in;
 171                 m->openInputFile(fastafile, in);
 172
 173                 bool wroteAccnos = false;
 174
 175                 while (!in.eof()) {
 176
 177                         Sequence seq(in);
 178
 179                         if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
 180
 181                         if (seq.getName() != "") {
 182                                 string newSeqString = getChopped(seq);
 183
 184                                 //output trimmed sequence
 185                                 if (newSeqString != "") {
 186                                         out << ">" << seq.getName() << endl << newSeqString << endl;
 187                                 }else{
 188                                         outAcc << seq.getName() << endl;
 189                                         wroteAccnos = true;
 190                                 }
 191                         }
 192                 }
 193                 in.close();
 194                 out.close();
 195                 outAcc.close();
 196
 197                 m->mothurOutEndLine();
 198                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 199                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 200
 201                 if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
 202                 else {  remove(outputFileNameAccnos.c_str());  }
 203
 204                 m->mothurOutEndLine();
 205
 206                 return 0;
 207         }
 208
 209         catch(exception& e) {
 210                 m->errorOut(e, "ChopSeqsCommand", "execute");
 211                 exit(1);
 212         }
 213 }
 214 //**********************************************************************************************************************
 215 string ChopSeqsCommand::getChopped(Sequence seq) {
 216         try {
 217                 string temp = seq.getAligned();
 218                 string tempUnaligned = seq.getUnaligned();
 219
 220                 if (countGaps) {
 221                         //if needed trim sequence
 222                         if (keep == "front") {//you want to keep the beginning
 223                                 int tempLength = temp.length();
 224
 225                                 if (tempLength > numbases) { //you have enough bases to remove some
 226
 227                                         int stopSpot = 0;
 228                                         int numBasesCounted = 0;
 229
 230                                         for (int i = 0; i < temp.length(); i++) {
 231                                                 //eliminate N's
 232                                                 if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
 233
 234                                                 numBasesCounted++;
 235
 236                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 237                                         }
 238
 239                                         if (stopSpot == 0) { temp = ""; }
 240                                         else {  temp = temp.substr(0, stopSpot);  }
 241
 242                                 }else {
 243                                         if (!Short) { temp = ""; } //sequence too short
 244                                 }
 245                         }else { //you are keeping the back
 246                                 int tempLength = temp.length();
 247                                 if (tempLength > numbases) { //you have enough bases to remove some
 248
 249                                         int stopSpot = 0;
 250                                         int numBasesCounted = 0;
 251
 252                                         for (int i = (temp.length()-1); i >= 0; i--) {
 253                                                 //eliminate N's
 254                                                 if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
 255
 256                                                 numBasesCounted++;
 257
 258                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 259                                         }
 260
 261                                         if (stopSpot == 0) { temp = ""; }
 262                                         else {  temp = temp.substr(stopSpot+1);  }
 263                                 }else {
 264                                         if (!Short) { temp = ""; } //sequence too short
 265                                 }
 266                         }
 267
 268                 }else{
 269
 270                         //if needed trim sequence
 271                         if (keep == "front") {//you want to keep the beginning
 272                                 int tempLength = tempUnaligned.length();
 273
 274                                 if (tempLength > numbases) { //you have enough bases to remove some
 275
 276                                         int stopSpot = 0;
 277                                         int numBasesCounted = 0;
 278
 279                                         for (int i = 0; i < temp.length(); i++) {
 280                                                 //eliminate N's
 281                                                 if (toupper(temp[i]) == 'N') {
 282                                                         temp[i] == '.';
 283                                                         tempLength--;
 284                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 285                                                 }
 286
 287                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 288
 289                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 290                                         }
 291
 292                                         if (stopSpot == 0) { temp = ""; }
 293                                         else {  temp = temp.substr(0, stopSpot);  }
 294
 295                                 }else {
 296                                         if (!Short) { temp = ""; } //sequence too short
 297                                 }
 298                         }else { //you are keeping the back
 299                                 int tempLength = tempUnaligned.length();
 300                                 if (tempLength > numbases) { //you have enough bases to remove some
 301
 302                                         int stopSpot = 0;
 303                                         int numBasesCounted = 0;
 304
 305                                         for (int i = (temp.length()-1); i >= 0; i--) {
 306                                                 //eliminate N's
 307                                                 if (toupper(temp[i]) == 'N') {
 308                                                         temp[i] == '.';
 309                                                         tempLength--;
 310                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 311                                                 }
 312
 313                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 314
 315                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 316                                         }
 317
 318                                         if (stopSpot == 0) { temp = ""; }
 319                                         else {  temp = temp.substr(stopSpot+1);  }
 320                                 }else {
 321                                         if (!Short) { temp = ""; } //sequence too short
 322                                 }
 323                         }
 324                 }
 325
 326                 return temp;
 327         }
 328         catch(exception& e) {
 329                 m->errorOut(e, "ChopSeqsCommand", "getChopped");
 330                 exit(1);
 331         }
 332 }
 333 //**********************************************************************************************************************
 334
 335