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