binsequencecommand.cpp

   1 /*
   2  *  binsequencecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/3/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amhers. All rights reserved.
   7  *
   8  */
   9
  10 #include "binsequencecommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 vector<string> BinSeqCommand::setParameters(){
  15         try {
  16                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
  18         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
  19         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  21                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "BinSeqCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string BinSeqCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The bin.seqs command parameters are list, fasta, name, count, label and group.  The fasta and list are required, unless you have a valid current list and fasta file.\n";
  39                 helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
  40                 helpString += "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
  41                 helpString += "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n";
  42                 helpString += "The default value for label is all lines in your inputfile.\n";
  43                 helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
  44                 helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
  45                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  46                 return helpString;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "BinSeqCommand", "getHelpString");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 string BinSeqCommand::getOutputPattern(string type) {
  55     try {
  56         string pattern = "";
  57
  58         if (type == "fasta") {  pattern = "[filename],[distance],fasta"; } //makes file like: amazon.0.03.fasta
  59         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  60
  61         return pattern;
  62     }
  63     catch(exception& e) {
  64         m->errorOut(e, "BinSeqCommand", "getOutputPattern");
  65         exit(1);
  66     }
  67 }
  68 //**********************************************************************************************************************
  69 BinSeqCommand::BinSeqCommand(){
  70         try {
  71                 abort = true; calledHelp = true;
  72                 setParameters();
  73                 vector<string> tempOutNames;
  74                 outputTypes["fasta"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 BinSeqCommand::BinSeqCommand(string option) {
  83         try {
  84                 abort = false; calledHelp = false;
  85                 allLines = 1;
  86                 labels.clear();
  87
  88                 //allow user to run help
  89                 if(option == "help") { help(); abort = true; calledHelp = true; }
  90                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  91
  92                 else {
  93                         vector<string> myArray = setParameters();
  94
  95                         OptionParser parser(option);
  96                         map<string, string> parameters = parser.getParameters();
  97
  98                         ValidParameters validParameter;
  99                         map<string, string>::iterator it;
 100
 101                         //check to make sure all parameters are valid for command
 102                         for (it = parameters.begin(); it != parameters.end(); it++) {
 103                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 104                         }
 105
 106                         //initialize outputTypes
 107                         vector<string> tempOutNames;
 108                         outputTypes["fasta"] = tempOutNames;
 109
 110                         //if the user changes the input directory command factory will send this info to us in the output parameter
 111                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 112                         if (inputDir == "not found"){   inputDir = "";          }
 113                         else {
 114                                 string path;
 115                                 it = parameters.find("fasta");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 121                                 }
 122
 123                                 it = parameters.find("list");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 129                                 }
 130
 131                                 it = parameters.find("name");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 137                                 }
 138
 139                                 it = parameters.find("group");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 145                                 }
 146
 147                 it = parameters.find("count");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 153                                 }
 154                         }
 155
 156
 157                         //check for required parameters
 158                         fastafile = validParameter.validFile(parameters, "fasta", true);
 159                         if (fastafile == "not found") {                                 //if there is a current phylip file, use it
 160                                 fastafile = m->getFastaFile();
 161                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 162                                 else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 163                         }
 164                         else if (fastafile == "not open") { abort = true; }
 165                         else { m->setFastaFile(fastafile); }
 166
 167                         listfile = validParameter.validFile(parameters, "list", true);
 168                         if (listfile == "not found") {
 169                                 listfile = m->getListFile();
 170                                 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 171                                 else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 172                         }
 173                         else if (listfile == "not open") { listfile = ""; abort = true; }
 174                         else { m->setListFile(listfile); }
 175
 176                         //if the user changes the output directory command factory will send this info to us in the output parameter
 177                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 178                                 outputDir = "";
 179                                 outputDir += m->hasPath(listfile); //if user entered a file with a path then preserve it
 180                         }
 181
 182
 183                         //check for optional parameter and set defaults
 184                         // ...at some point should added some additional type checking...
 185
 186                         label = validParameter.validFile(parameters, "label", false);
 187                         if (label == "not found") { label = ""; }
 188                         else {
 189                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 190                                 else { allLines = 1;  }
 191                         }
 192
 193                         namesfile = validParameter.validFile(parameters, "name", true);
 194                         if (namesfile == "not open") { namesfile = ""; abort = true; }
 195                         else if (namesfile == "not found") { namesfile = ""; }
 196                         else {  m->setNameFile(namesfile); }
 197
 198                         groupfile = validParameter.validFile(parameters, "group", true);
 199                         if (groupfile == "not open") { abort = true; }
 200                         else if (groupfile == "not found") { groupfile = ""; }
 201                         else { m->setGroupFile(groupfile); }
 202
 203             countfile = validParameter.validFile(parameters, "count", true);
 204                         if (countfile == "not open") { countfile = ""; abort = true; }
 205                         else if (countfile == "not found") { countfile = "";  }
 206                         else { m->setCountTableFile(countfile); }
 207
 208             if ((namesfile != "") && (countfile != "")) {
 209                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 210             }
 211
 212             if ((groupfile != "") && (countfile != "")) {
 213                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 214             }
 215
 216             if (countfile == "") {
 217                 if (namesfile == ""){
 218                     vector<string> files; files.push_back(fastafile);
 219                     parser.getNameFile(files);
 220                 }
 221             }
 222
 223                 }
 224         }
 225         catch(exception& e) {
 226                 m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
 227                 exit(1);
 228         }
 229 }
 230 //**********************************************************************************************************************
 231
 232 BinSeqCommand::~BinSeqCommand(){}
 233 //**********************************************************************************************************************
 234
 235 int BinSeqCommand::execute(){
 236         try {
 237                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 238
 239                 int error = 0;
 240
 241                 fasta = new FastaMap();
 242                 if (groupfile != "") {
 243                         groupMap = new GroupMap(groupfile);
 244                         groupMap->readMap();
 245                 }
 246
 247                 //read fastafile
 248                 fasta->readFastaFile(fastafile);
 249
 250                 //if user gave a namesfile then use it
 251                 if (namesfile != "") {  readNamesFile();  }
 252         if (countfile != "") {  ct.readTable(countfile, true);  }
 253
 254                 input = new InputData(listfile, "list");
 255                 list = input->getListVector();
 256                 string lastLabel = list->getLabel();
 257
 258                 if (m->control_pressed) {  delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 259
 260                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 261                 set<string> processedLabels;
 262                 set<string> userLabels = labels;
 263
 264
 265                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 266
 267                         if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 268
 269                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 270
 271                                 error = process(list);
 272                                 if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 273
 274                                 processedLabels.insert(list->getLabel());
 275                                 userLabels.erase(list->getLabel());
 276                         }
 277
 278                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 279                                 string saveLabel = list->getLabel();
 280
 281                                 delete list;
 282                                 list = input->getListVector(lastLabel);
 283
 284                                 error = process(list);
 285                                 if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 286
 287                                 processedLabels.insert(list->getLabel());
 288                                 userLabels.erase(list->getLabel());
 289
 290                                 //restore real lastlabel to save below
 291                                 list->setLabel(saveLabel);
 292                         }
 293
 294                         lastLabel = list->getLabel();
 295
 296                         delete list;
 297                         list = input->getListVector();
 298                 }
 299
 300                 if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 301
 302                 //output error messages about any remaining user labels
 303                 set<string>::iterator it;
 304                 bool needToRun = false;
 305                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 306                         m->mothurOut("Your file does not include the label " + *it);
 307                         if (processedLabels.count(lastLabel) != 1) {
 308                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 309                                 needToRun = true;
 310                         }else {
 311                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 312                         }
 313                 }
 314
 315                 //run last label if you need to
 316                 if (needToRun == true)  {
 317                         if (list != NULL) {             delete list;    }
 318                         list = input->getListVector(lastLabel);
 319
 320                         error = process(list);
 321                         if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 322
 323                         delete list;
 324                 }
 325
 326                 delete input;
 327                 delete fasta;
 328                 if (groupfile != "") {  delete groupMap;   }
 329
 330                 if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                }  return 0; }
 331
 332         //set align file as new current fastafile
 333                 string currentFasta = "";
 334                 itTypes = outputTypes.find("fasta");
 335                 if (itTypes != outputTypes.end()) {
 336                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 337                 }
 338
 339                 m->mothurOutEndLine();
 340                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 341                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 342                 m->mothurOutEndLine();
 343
 344
 345                 return 0;
 346         }
 347         catch(exception& e) {
 348                 m->errorOut(e, "BinSeqCommand", "execute");
 349                 exit(1);
 350         }
 351 }
 352
 353 //**********************************************************************************************************************
 354 void BinSeqCommand::readNamesFile() {
 355         try {
 356                 vector<string> dupNames;
 357                 m->openInputFile(namesfile, inNames);
 358
 359                 string name, names, sequence;
 360
 361                 while(inNames){
 362                         inNames >> name;                        //read from first column  A
 363                         inNames >> names;               //read from second column  A,B,C,D
 364
 365                         dupNames.clear();
 366
 367                         //parse names into vector
 368                         m->splitAtComma(names, dupNames);
 369
 370                         //store names in fasta map
 371                         sequence = fasta->getSequence(name);
 372                         for (int i = 0; i < dupNames.size(); i++) {
 373                                 fasta->push_back(dupNames[i], sequence);
 374                         }
 375
 376                         m->gobble(inNames);
 377                 }
 378                 inNames.close();
 379
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "BinSeqCommand", "readNamesFile");
 383                 exit(1);
 384         }
 385 }
 386 //**********************************************************************************************************************
 387 //return 1 if error, 0 otherwise
 388 int BinSeqCommand::process(ListVector* list) {
 389         try {
 390         map<string, string> variables;
 391         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
 392         variables["[distance]"] = list->getLabel();
 393         string outputFileName = getOutputFileName("fasta", variables);
 394
 395         m->openOutputFile(outputFileName, out);
 396         outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 397
 398         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 399
 400         //for each bin in the list vector
 401         for (int i = 0; i < list->size(); i++) {
 402
 403             if (m->control_pressed) {  return 1; }
 404
 405             string binnames = list->get(i);
 406             vector<string> names;
 407             m->splitAtComma(binnames, names);
 408             for (int j = 0; j < names.size(); j++) {
 409                 string name = names[j];
 410
 411                 //do work for that name
 412                 string sequence = fasta->getSequence(name);
 413
 414                 if (countfile != "") {
 415                     if (sequence != "not found") {
 416                         if (ct.hasGroupInfo()) {
 417                             vector<string> groups = ct.getGroups(name);
 418                             string groupInfo = "";
 419                             for (int k = 0; k < groups.size()-1; k++) {
 420                                 groupInfo += groups[k] + "-";
 421                             }
 422                             if (groups.size() != 0) { groupInfo += groups[groups.size()-1]; }
 423                             else { groupInfo = "not found";  }
 424                             name = name + "\t" + groupInfo + "\t" + toString(i+1)+ "\tNumRep=" + toString(ct.getNumSeqs(name));
 425                             out << ">" << name << endl;
 426                             out << sequence << endl;
 427                         }else {
 428                             name = name + "\t" + toString(i+1) + "\tNumRep=" + toString(ct.getNumSeqs(name));
 429                             out << ">" << name << endl;
 430                             out << sequence << endl;
 431                         }
 432
 433                     }else { m->mothurOut(name + " is missing from your fasta. Does your list file contain all sequence names or just the uniques?"); m->mothurOutEndLine(); return 1; }
 434                 }else {
 435                     if (sequence != "not found") {
 436                         //if you don't have groups
 437                         if (groupfile == "") {
 438                             name = name + "\t" + toString(i+1);
 439                             out << ">" << name << endl;
 440                             out << sequence << endl;
 441                         }else {//if you do have groups
 442                             string group = groupMap->getGroup(name);
 443                             if (group == "not found") {
 444                                 m->mothurOut(name + " is missing from your group file. Please correct. ");  m->mothurOutEndLine();
 445                                 return 1;
 446                             }else{
 447                                 name = name + "\t" + group + "\t" + toString(i+1);
 448                                 out << ">" << name << endl;
 449                                 out << sequence << endl;
 450                             }
 451                         }
 452                     }else { m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine(); return 1; }
 453                 }
 454             }
 455         }
 456
 457         out.close();
 458         return 0;
 459
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "BinSeqCommand", "process");
 463                 exit(1);
 464         }
 465 }
 466 //**********************************************************************************************************************
 467
 468