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::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnumbases);
  18                 CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcountgaps);
  19                 CommandParameter pshort("short", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshort);
  20                 CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "",false,false); parameters.push_back(pkeep);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "ChopSeqsCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string ChopSeqsCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
  38                 helpString += "The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
  39                 helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
  40                 helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
  41                 helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
  42                 helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
  43                 helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
  44                 helpString += "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";
  45                 helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
  46                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  47                 return helpString;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "ChopSeqsCommand", "getHelpString");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55 string ChopSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  56         try {
  57         string outputFileName = "";
  58                 map<string, vector<string> >::iterator it;
  59
  60         //is this a type this command creates
  61         it = outputTypes.find(type);
  62         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  63         else {
  64             if (type == "fasta") {  outputFileName =  "chop.fasta"; }
  65             else if (type == "accnos") {  outputFileName =  "chop.accnos"; }
  66             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  67         }
  68         return outputFileName;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "ChopSeqsCommand", "getOutputFileNameTag");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 ChopSeqsCommand::ChopSeqsCommand(){
  77         try {
  78                 abort = true; calledHelp = true;
  79                 setParameters();
  80                 vector<string> tempOutNames;
  81                 outputTypes["fasta"] = tempOutNames;
  82                 outputTypes["accnos"] = tempOutNames;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
  86                 exit(1);
  87         }
  88 }
  89 //**********************************************************************************************************************
  90 ChopSeqsCommand::ChopSeqsCommand(string option)  {
  91         try {
  92                 abort = false; calledHelp = false;
  93
  94                 //allow user to run help
  95                 if(option == "help") { help(); abort = true; calledHelp = true; }
  96                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  97
  98                 else {
  99                         vector<string> myArray = setParameters();
 100
 101                         OptionParser parser(option);
 102                         map<string,string> parameters = parser.getParameters();
 103
 104                         ValidParameters validParameter;
 105                         map<string,string>::iterator it;
 106
 107                         //check to make sure all parameters are valid for command
 108                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 109                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 110                         }
 111
 112                         //initialize outputTypes
 113                         vector<string> tempOutNames;
 114                         outputTypes["fasta"] = tempOutNames;
 115                         outputTypes["accnos"] = tempOutNames;
 116
 117                         //if the user changes the input directory command factory will send this info to us in the output parameter
 118                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 119                         if (inputDir == "not found"){   inputDir = "";          }
 120                         else {
 121                                 string path;
 122                                 it = parameters.find("fasta");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 128                                 }
 129                         }
 130
 131                         //check for required parameters
 132                         fastafile = validParameter.validFile(parameters, "fasta", true);
 133                         if (fastafile == "not open") { abort = true; }
 134                         else if (fastafile == "not found") {                            //if there is a current fasta file, use it
 135                                 fastafile = m->getFastaFile();
 136                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 137                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 138                         }else { m->setFastaFile(fastafile); }
 139
 140                         //if the user changes the output directory command factory will send this info to us in the output parameter
 141                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
 142
 143                         string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; }
 144                         m->mothurConvert(temp, numbases);
 145
 146                         temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; }
 147                         countGaps = m->isTrue(temp);
 148
 149                         temp = validParameter.validFile(parameters, "short", false);    if (temp == "not found") { temp = "f"; }
 150                         Short = m->isTrue(temp);
 151
 152                         keep = validParameter.validFile(parameters, "keep", false);             if (keep == "not found") { keep = "front"; }
 153
 154                         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;  }
 155                 }
 156
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
 160                 exit(1);
 161         }
 162 }
 163 //**********************************************************************************************************************
 164
 165 int ChopSeqsCommand::execute(){
 166         try {
 167
 168                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 169
 170                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
 171                 string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
 172
 173                 ofstream out;
 174                 m->openOutputFile(outputFileName, out);
 175
 176                 ofstream outAcc;
 177                 m->openOutputFile(outputFileNameAccnos, outAcc);
 178
 179                 ifstream in;
 180                 m->openInputFile(fastafile, in);
 181
 182                 bool wroteAccnos = false;
 183
 184                 while (!in.eof()) {
 185
 186                         Sequence seq(in);
 187
 188                         if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0;  }
 189
 190                         if (seq.getName() != "") {
 191                                 string newSeqString = getChopped(seq);
 192
 193                                 //output trimmed sequence
 194                                 if (newSeqString != "") {
 195                                         out << ">" << seq.getName() << endl << newSeqString << endl;
 196                                 }else{
 197                                         outAcc << seq.getName() << endl;
 198                                         wroteAccnos = true;
 199                                 }
 200                         }
 201                 }
 202                 in.close();
 203                 out.close();
 204                 outAcc.close();
 205
 206                 m->mothurOutEndLine();
 207                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 208                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 209
 210                 if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
 211                 else {  m->mothurRemove(outputFileNameAccnos);  }
 212
 213                 m->mothurOutEndLine();
 214
 215                 //set fasta file as new current fastafile
 216                 string current = "";
 217                 itTypes = outputTypes.find("fasta");
 218                 if (itTypes != outputTypes.end()) {
 219                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 220                 }
 221
 222                 if (wroteAccnos) { //set accnos file as new current accnosfile
 223                         itTypes = outputTypes.find("accnos");
 224                         if (itTypes != outputTypes.end()) {
 225                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 226                         }
 227                 }
 228
 229
 230                 return 0;
 231         }
 232
 233         catch(exception& e) {
 234                 m->errorOut(e, "ChopSeqsCommand", "execute");
 235                 exit(1);
 236         }
 237 }
 238 //**********************************************************************************************************************
 239 string ChopSeqsCommand::getChopped(Sequence seq) {
 240         try {
 241                 string temp = seq.getAligned();
 242                 string tempUnaligned = seq.getUnaligned();
 243
 244                 if (countGaps) {
 245                         //if needed trim sequence
 246                         if (keep == "front") {//you want to keep the beginning
 247                                 int tempLength = temp.length();
 248
 249                                 if (tempLength > numbases) { //you have enough bases to remove some
 250
 251                                         int stopSpot = 0;
 252                                         int numBasesCounted = 0;
 253
 254                                         for (int i = 0; i < temp.length(); i++) {
 255                                                 //eliminate N's
 256                                                 if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
 257
 258                                                 numBasesCounted++;
 259
 260                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 261                                         }
 262
 263                                         if (stopSpot == 0) { temp = ""; }
 264                                         else {  temp = temp.substr(0, stopSpot+1);  }
 265
 266                                 }else {
 267                                         if (!Short) { temp = ""; } //sequence too short
 268                                 }
 269                         }else { //you are keeping the back
 270                                 int tempLength = temp.length();
 271                                 if (tempLength > numbases) { //you have enough bases to remove some
 272
 273                                         int stopSpot = 0;
 274                                         int numBasesCounted = 0;
 275
 276                                         for (int i = (temp.length()-1); i >= 0; i--) {
 277                                                 //eliminate N's
 278                                                 if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
 279
 280                                                 numBasesCounted++;
 281
 282                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 283                                         }
 284
 285                                         if (stopSpot == 0) { temp = ""; }
 286                                         else {  temp = temp.substr(stopSpot+1);  }
 287                                 }else {
 288                                         if (!Short) { temp = ""; } //sequence too short
 289                                 }
 290                         }
 291
 292                 }else{
 293
 294                         //if needed trim sequence
 295                         if (keep == "front") {//you want to keep the beginning
 296                                 int tempLength = tempUnaligned.length();
 297
 298                                 if (tempLength > numbases) { //you have enough bases to remove some
 299
 300                                         int stopSpot = 0;
 301                                         int numBasesCounted = 0;
 302
 303                                         for (int i = 0; i < temp.length(); i++) {
 304                                                 //eliminate N's
 305                                                 if (toupper(temp[i]) == 'N') {
 306                                                         temp[i] = '.';
 307                                                         tempLength--;
 308                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 309                                                 }
 310
 311                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 312
 313                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 314                                         }
 315
 316                                         if (stopSpot == 0) { temp = ""; }
 317                                         else {  temp = temp.substr(0, stopSpot+1);  }
 318
 319                                 }else {
 320                                         if (!Short) { temp = ""; } //sequence too short
 321                                 }
 322                         }else { //you are keeping the back
 323                                 int tempLength = tempUnaligned.length();
 324                                 if (tempLength > numbases) { //you have enough bases to remove some
 325
 326                                         int stopSpot = 0;
 327                                         int numBasesCounted = 0;
 328
 329                                         for (int i = (temp.length()-1); i >= 0; i--) {
 330                                                 //eliminate N's
 331                                                 if (toupper(temp[i]) == 'N') {
 332                                                         temp[i] = '.';
 333                                                         tempLength--;
 334                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 335                                                 }
 336
 337                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 338
 339                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 340                                         }
 341
 342                                         if (stopSpot == 0) { temp = ""; }
 343                                         else {  temp = temp.substr(stopSpot);  }
 344                                 }else {
 345                                         if (!Short) { temp = ""; } //sequence too short
 346                                 }
 347                         }
 348                 }
 349
 350                 return temp;
 351         }
 352         catch(exception& e) {
 353                 m->errorOut(e, "ChopSeqsCommand", "getChopped");
 354                 exit(1);
 355         }
 356 }
 357 //**********************************************************************************************************************
 358
 359