screenseqscommand.cpp

   1 /*
   2  *  screenseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/3/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "screenseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 //***************************************************************************************************************
  14
  15 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string AlignArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
  25                                                                         "name", "group", "alignreport","outputdir","inputdir"};
  26                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/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("group");
  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["group"] = inputDir + it->second;            }
  58                                 }
  59
  60                                 it = parameters.find("name");
  61                                 //user has given a template file
  62                                 if(it != parameters.end()){
  63                                         path = hasPath(it->second);
  64                                         //if the user has not given a path then, add inputdir. else leave path alone.
  65                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  66                                 }
  67
  68                                 it = parameters.find("alignreport");
  69                                 //user has given a template file
  70                                 if(it != parameters.end()){
  71                                         path = hasPath(it->second);
  72                                         //if the user has not given a path then, add inputdir. else leave path alone.
  73                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
  74                                 }
  75                         }
  76
  77                         //check for required parameters
  78                         fastafile = validParameter.validFile(parameters, "fasta", true);
  79                         if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
  80                         else if (fastafile == "not open") { abort = true; }
  81
  82                         groupfile = validParameter.validFile(parameters, "group", true);
  83                         if (groupfile == "not open") { abort = true; }
  84                         else if (groupfile == "not found") { groupfile = ""; }
  85
  86                         namefile = validParameter.validFile(parameters, "name", true);
  87                         if (namefile == "not open") { abort = true; }
  88                         else if (namefile == "not found") { namefile = ""; }
  89
  90                         alignreport = validParameter.validFile(parameters, "alignreport", true);
  91                         if (alignreport == "not open") { abort = true; }
  92                         else if (alignreport == "not found") { alignreport = ""; }
  93
  94                         //if the user changes the output directory command factory will send this info to us in the output parameter
  95                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  96                                 outputDir = "";
  97                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  98                         }
  99
 100                         //check for optional parameter and set defaults
 101                         // ...at some point should added some additional type checking...
 102                         string temp;
 103                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 104                         convert(temp, startPos);
 105
 106                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 107                         convert(temp, endPos);
 108
 109                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 110                         convert(temp, maxAmbig);
 111
 112                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 113                         convert(temp, maxHomoP);
 114
 115                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 116                         convert(temp, minLength);
 117
 118                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 119                         convert(temp, maxLength);
 120                 }
 121
 122         }
 123         catch(exception& e) {
 124                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 125                 exit(1);
 126         }
 127 }
 128 //**********************************************************************************************************************
 129
 130 void ScreenSeqsCommand::help(){
 131         try {
 132                 m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
 133                 m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group.\n");
 134                 m->mothurOut("The fasta parameter is required.\n");
 135                 m->mothurOut("The start parameter .... The default is -1.\n");
 136                 m->mothurOut("The end parameter .... The default is -1.\n");
 137                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 138                 m->mothurOut("The maxhomop parameter .... The default is -1.\n");
 139                 m->mothurOut("The minlength parameter .... The default is -1.\n");
 140                 m->mothurOut("The maxlength parameter .... The default is -1.\n");
 141                 m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
 142                 m->mothurOut("The screen.seqs command should be in the following format: \n");
 143                 m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n");
 144                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 145                 m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 146                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 147
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "ScreenSeqsCommand", "help");
 151                 exit(1);
 152         }
 153 }
 154
 155 //***************************************************************************************************************
 156
 157 ScreenSeqsCommand::~ScreenSeqsCommand(){        /*      do nothing      */      }
 158
 159 //***************************************************************************************************************
 160
 161 int ScreenSeqsCommand::execute(){
 162         try{
 163
 164                 if (abort == true) { return 0; }
 165
 166                 ifstream inFASTA;
 167                 openInputFile(fastafile, inFASTA);
 168
 169                 set<string> badSeqNames;
 170
 171                 string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
 172                 string badSeqFile =  outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
 173
 174                 ofstream goodSeqOut;    openOutputFile(goodSeqFile, goodSeqOut);
 175                 ofstream badSeqOut;             openOutputFile(badSeqFile, badSeqOut);
 176
 177                 while(!inFASTA.eof()){
 178                         Sequence currSeq(inFASTA);
 179                         if (currSeq.getName() != "") {
 180                                 bool goodSeq = 1;               //      innocent until proven guilty
 181                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
 182                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
 183                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
 184                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
 185                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
 186                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
 187
 188                                 if(goodSeq == 1){
 189                                         currSeq.printSequence(goodSeqOut);
 190                                 }
 191                                 else{
 192                                         currSeq.printSequence(badSeqOut);
 193                                         badSeqNames.insert(currSeq.getName());
 194                                 }
 195                         }
 196                         gobble(inFASTA);
 197                 }
 198                 if(namefile != "" && groupfile != "")   {       screenNameGroupFile(badSeqNames);       }       // this screens both names and groups
 199                 else if(namefile != "")                                 {       screenNameGroupFile(badSeqNames);       }
 200                 else if(groupfile != "")                                {       screenGroupFile(badSeqNames);           }       // this screens just the groups
 201                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 202
 203                 goodSeqOut.close();
 204                 badSeqOut.close();
 205                 inFASTA.close();
 206
 207                 m->mothurOutEndLine();
 208                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 209                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();
 210                 m->mothurOut(badSeqFile); m->mothurOutEndLine();
 211                 m->mothurOutEndLine();
 212
 213
 214                 return 0;
 215         }
 216         catch(exception& e) {
 217                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 218                 exit(1);
 219         }
 220 }
 221
 222 //***************************************************************************************************************
 223
 224 void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 225
 226         ifstream inputNames;
 227         openInputFile(namefile, inputNames);
 228         set<string> badSeqGroups;
 229         string seqName, seqList, group;
 230         set<string>::iterator it;
 231
 232         string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
 233         string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
 234
 235         ofstream goodNameOut;   openOutputFile(goodNameFile, goodNameOut);
 236         ofstream badNameOut;    openOutputFile(badNameFile, badNameOut);
 237
 238         while(!inputNames.eof()){
 239                 inputNames >> seqName >> seqList;
 240                 it = badSeqNames.find(seqName);
 241
 242                 if(it != badSeqNames.end()){
 243                         badSeqNames.erase(it);
 244                         badNameOut << seqName << '\t' << seqList << endl;
 245                         if(namefile != ""){
 246                                 int start = 0;
 247                                 for(int i=0;i<seqList.length();i++){
 248                                         if(seqList[i] == ','){
 249                                                 badSeqGroups.insert(seqList.substr(start,i-start));
 250                                                 start = i+1;
 251                                         }
 252                                 }
 253                                 badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 254                         }
 255                 }
 256                 else{
 257                         goodNameOut << seqName << '\t' << seqList << endl;
 258                 }
 259                 gobble(inputNames);
 260         }
 261         inputNames.close();
 262         goodNameOut.close();
 263         badNameOut.close();
 264
 265         //we were unable to remove some of the bad sequences
 266         if (badSeqNames.size() != 0) {
 267                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 268                         m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 269                         m->mothurOutEndLine();
 270                 }
 271         }
 272
 273         if(groupfile != ""){
 274
 275                 ifstream inputGroups;
 276                 openInputFile(groupfile, inputGroups);
 277
 278                 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
 279                 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
 280
 281                 ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
 282                 ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);
 283
 284                 while(!inputGroups.eof()){
 285                         inputGroups >> seqName >> group;
 286
 287                         it = badSeqGroups.find(seqName);
 288
 289                         if(it != badSeqGroups.end()){
 290                                 badSeqGroups.erase(it);
 291                                 badGroupOut << seqName << '\t' << group << endl;
 292                         }
 293                         else{
 294                                 goodGroupOut << seqName << '\t' << group << endl;
 295                         }
 296                         gobble(inputGroups);
 297                 }
 298                 inputGroups.close();
 299                 goodGroupOut.close();
 300                 badGroupOut.close();
 301
 302                 //we were unable to remove some of the bad sequences
 303                 if (badSeqGroups.size() != 0) {
 304                         for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 305                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 306                                 m->mothurOutEndLine();
 307                         }
 308                 }
 309         }
 310 }
 311
 312 //***************************************************************************************************************
 313
 314 void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 315
 316         ifstream inputGroups;
 317         openInputFile(groupfile, inputGroups);
 318         string seqName, group;
 319         set<string>::iterator it;
 320
 321         string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
 322         string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
 323
 324         ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
 325         ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);
 326
 327         while(!inputGroups.eof()){
 328                 inputGroups >> seqName >> group;
 329                 it = badSeqNames.find(seqName);
 330
 331                 if(it != badSeqNames.end()){
 332                         badSeqNames.erase(it);
 333                         badGroupOut << seqName << '\t' << group << endl;
 334                 }
 335                 else{
 336                         goodGroupOut << seqName << '\t' << group << endl;
 337                 }
 338                 gobble(inputGroups);
 339         }
 340
 341         //we were unable to remove some of the bad sequences
 342         if (badSeqNames.size() != 0) {
 343                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 344                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 345                         m->mothurOutEndLine();
 346                 }
 347         }
 348
 349         inputGroups.close();
 350         goodGroupOut.close();
 351         badGroupOut.close();
 352
 353 }
 354
 355 //***************************************************************************************************************
 356
 357 void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 358
 359         ifstream inputAlignReport;
 360         openInputFile(alignreport, inputAlignReport);
 361         string seqName, group;
 362         set<string>::iterator it;
 363
 364         string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
 365         string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
 366
 367         ofstream goodAlignReportOut;    openOutputFile(goodAlignReportFile, goodAlignReportOut);
 368         ofstream badAlignReportOut;             openOutputFile(badAlignReportFile, badAlignReportOut);
 369
 370         while (!inputAlignReport.eof()) {               //      need to copy header
 371                 char c = inputAlignReport.get();
 372                 goodAlignReportOut << c;
 373                 badAlignReportOut << c;
 374                 if (c == 10 || c == 13){        break;  }
 375         }
 376
 377         while(!inputAlignReport.eof()){
 378                 inputAlignReport >> seqName;
 379                 it = badSeqNames.find(seqName);
 380                 string line;
 381                 while (!inputAlignReport.eof()) {               //      need to copy header
 382                         char c = inputAlignReport.get();
 383                         line += c;
 384                         if (c == 10 || c == 13){        break;  }
 385                 }
 386
 387                 if(it != badSeqNames.end()){
 388                         badSeqNames.erase(it);
 389                         badAlignReportOut << seqName << '\t' << line;;
 390                 }
 391                 else{
 392                         goodAlignReportOut << seqName << '\t' << line;
 393                 }
 394                 gobble(inputAlignReport);
 395         }
 396
 397         //we were unable to remove some of the bad sequences
 398         if (badSeqNames.size() != 0) {
 399                 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 400                         m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
 401                         m->mothurOutEndLine();
 402                 }
 403         }
 404
 405         inputAlignReport.close();
 406         goodAlignReportOut.close();
 407         badAlignReportOut.close();
 408
 409 }
 410
 411 //***************************************************************************************************************
 412
 413