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 BinSeqCommand::BinSeqCommand(string option){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 abort = false;
  17                 allLines = 1;
  18                 lines.clear();
  19                 labels.clear();
  20
  21                 //allow user to run help
  22                 if(option == "help") { help(); abort = true; }
  23
  24                 else {
  25                         //valid paramters for this command
  26                         string AlignArray[] =  {"fasta","line","label","name", "group"};
  27                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string, string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //make sure the user has already run the read.otu command
  40                         if (globaldata->getListFile() == "") {
  41                                 mothurOut("You must read a listfile before running the bin.seqs command.");
  42                                 mothurOutEndLine();
  43                                 abort = true;
  44                         }
  45
  46
  47                         //check for required parameters
  48                         fastafile = validParameter.validFile(parameters, "fasta", true);
  49                         if (fastafile == "not found") { mothurOut("fasta is a required parameter for the bin.seqs command.");  mothurOutEndLine(); abort = true; }
  50                         else if (fastafile == "not open") { abort = true; }
  51
  52                         //check for optional parameter and set defaults
  53                         // ...at some point should added some additional type checking...
  54                         line = validParameter.validFile(parameters, "line", false);
  55                         if (line == "not found") { line = "";  }
  56                         else {
  57                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  58                                 else { allLines = 1;  }
  59                         }
  60
  61                         label = validParameter.validFile(parameters, "label", false);
  62                         if (label == "not found") { label = ""; }
  63                         else {
  64                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  65                                 else { allLines = 1;  }
  66                         }
  67
  68                         //make sure user did not use both the line and label parameters
  69                         if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
  70                         //if the user has not specified any line or labels use the ones from read.otu
  71                         else if ((line == "") && (label == "")) {
  72                                 allLines = globaldata->allLines;
  73                                 labels = globaldata->labels;
  74                                 lines = globaldata->lines;
  75                         }
  76
  77                         namesfile = validParameter.validFile(parameters, "name", true);
  78                         if (namesfile == "not open") { abort = true; }
  79                         else if (namesfile == "not found") { namesfile = ""; }
  80
  81                         groupfile = validParameter.validFile(parameters, "group", true);
  82                         if (groupfile == "not open") { abort = true; }
  83                         else if (groupfile == "not found") { groupfile = ""; }
  84
  85                         if (abort == false) {
  86 //                              openInputFile(fastafile, in);
  87                                 fasta = new FastaMap();
  88                                 if (groupfile != "") {
  89                                         groupMap = new GroupMap(groupfile);
  90                                         groupMap->readMap();
  91                                 }
  92                         }
  93
  94                 }
  95         }
  96         catch(exception& e) {
  97                 errorOut(e, "BinSeqCommand", "BinSeqCommand");
  98                 exit(1);
  99         }
 100 }
 101 //**********************************************************************************************************************
 102
 103 void BinSeqCommand::help(){
 104         try {
 105                 mothurOut("The bin.seqs command can only be executed after a successful read.otu command of a listfile.\n");
 106                 mothurOut("The bin.seqs command parameters are fasta, name, line, label and group.  The fasta parameter is required, and you may not use line and label at the same time.\n");
 107                 mothurOut("The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
 108                 mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels).\n");
 109                 mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, line=1-3-5, name=amazon.names).\n");
 110                 mothurOut("The default value for line and label are all lines in your inputfile.\n");
 111                 mothurOut("The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n");
 112                 mothurOut("If you provide a groupfile, then it also appends the sequences group to the name.\n");
 113                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 114         }
 115         catch(exception& e) {
 116                 errorOut(e, "BinSeqCommand", "help");
 117                 exit(1);
 118         }
 119 }
 120
 121 //**********************************************************************************************************************
 122
 123 BinSeqCommand::~BinSeqCommand(){
 124         //made new in execute
 125         if (abort == false) {
 126                 delete input;  globaldata->ginput = NULL;
 127                 delete read;
 128                 globaldata->gListVector = NULL;
 129                 delete fasta;
 130                 if (groupfile != "") {  delete groupMap;  globaldata->gGroupmap = NULL; }
 131         }
 132 }
 133
 134 //**********************************************************************************************************************
 135
 136 int BinSeqCommand::execute(){
 137         try {
 138                 if (abort == true) {    return 0;       }
 139
 140                 int count = 1;
 141                 int error = 0;
 142
 143                 //read fastafile
 144                 fasta->readFastaFile(fastafile);
 145
 146
 147                 //set format to list so input can get listvector
 148 //              globaldata->setFormat("list");
 149
 150                 //if user gave a namesfile then use it
 151                 if (namesfile != "") {
 152                         readNamesFile();
 153                 }
 154
 155                 //read list file
 156                 read = new ReadOTUFile(globaldata->getListFile());
 157                 read->read(&*globaldata);
 158
 159                 input = globaldata->ginput;
 160                 list = globaldata->gListVector;
 161                 string lastLabel = list->getLabel();
 162
 163                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 164                 set<string> processedLabels;
 165                 set<string> userLabels = labels;
 166                 set<int> userLines = lines;
 167
 168
 169                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 170
 171                         if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
 172
 173                                 error = process(list, count);
 174                                 if (error == 1) { return 0; }
 175
 176                                 processedLabels.insert(list->getLabel());
 177                                 userLabels.erase(list->getLabel());
 178                                 userLines.erase(count);
 179                         }
 180
 181                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 182                                 delete list;
 183                                 list = input->getListVector(lastLabel);
 184
 185                                 error = process(list, count);
 186                                 if (error == 1) { return 0; }
 187
 188                                 processedLabels.insert(list->getLabel());
 189                                 userLabels.erase(list->getLabel());
 190
 191                         }
 192
 193                         lastLabel = list->getLabel();
 194
 195                         delete list;
 196                         list = input->getListVector();
 197                         count++;
 198                 }
 199
 200
 201                 //output error messages about any remaining user labels
 202                 set<string>::iterator it;
 203                 bool needToRun = false;
 204                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 205                         mothurOut("Your file does not include the label " + *it);
 206                         if (processedLabels.count(lastLabel) != 1) {
 207                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 208                                 needToRun = true;
 209                         }else {
 210                                 mothurOut(". Please refer to " + lastLabel + ".");  mothurOutEndLine();
 211                         }
 212                 }
 213
 214                 //run last line if you need to
 215                 if (needToRun == true)  {
 216                         delete list;
 217                         list = input->getListVector(lastLabel);
 218
 219                         error = process(list, count);
 220                         if (error == 1) { return 0; }
 221
 222                         delete list;
 223                 }
 224
 225                 return 0;
 226         }
 227         catch(exception& e) {
 228                 errorOut(e, "BinSeqCommand", "execute");
 229                 exit(1);
 230         }
 231 }
 232
 233 //**********************************************************************************************************************
 234 void BinSeqCommand::readNamesFile() {
 235         try {
 236                 vector<string> dupNames;
 237                 openInputFile(namesfile, inNames);
 238
 239                 string name, names, sequence;
 240
 241                 while(inNames){
 242                         inNames >> name;                        //read from first column  A
 243                         inNames >> names;               //read from second column  A,B,C,D
 244
 245                         dupNames.clear();
 246
 247                         //parse names into vector
 248                         splitAtComma(names, dupNames);
 249
 250                         //store names in fasta map
 251                         sequence = fasta->getSequence(name);
 252                         for (int i = 0; i < dupNames.size(); i++) {
 253                                 fasta->push_back(dupNames[i], sequence);
 254                         }
 255
 256                         gobble(inNames);
 257                 }
 258                 inNames.close();
 259
 260         }
 261         catch(exception& e) {
 262                 errorOut(e, "BinSeqCommand", "readNamesFile");
 263                 exit(1);
 264         }
 265 }
 266 //**********************************************************************************************************************
 267 //return 1 if error, 0 otherwise
 268 int BinSeqCommand::process(ListVector* list, int count) {
 269         try {
 270                                 string binnames, name, sequence;
 271                                 string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
 272                                 openOutputFile(outputFileName, out);
 273
 274                                 mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 275
 276                                 //for each bin in the list vector
 277                                 for (int i = 0; i < list->size(); i++) {
 278
 279                                         binnames = list->get(i);
 280                                         while (binnames.find_first_of(',') != -1) {
 281                                                 name = binnames.substr(0,binnames.find_first_of(','));
 282                                                 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 283
 284                                                 //do work for that name
 285                                                 sequence = fasta->getSequence(name);
 286                                                 if (sequence != "not found") {
 287                                                         //if you don't have groups
 288                                                         if (groupfile == "") {
 289                                                                 name = name + "|" + toString(i+1);
 290                                                                 out << ">" << name << endl;
 291                                                                 out << sequence << endl;
 292                                                         }else {//if you do have groups
 293                                                                 string group = groupMap->getGroup(name);
 294                                                                 if (group == "not found") {
 295                                                                         mothurOut(name + " is missing from your group file. Please correct. ");  mothurOutEndLine();
 296                                                                         remove(outputFileName.c_str());
 297                                                                         return 1;
 298                                                                 }else{
 299                                                                         name = name + "|" + group + "|" + toString(i+1);
 300                                                                         out << ">" << name << endl;
 301                                                                         out << sequence << endl;
 302                                                                 }
 303                                                         }
 304                                                 }else {
 305                                                         mothurOut(name + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
 306                                                         remove(outputFileName.c_str());
 307                                                         return 1;
 308                                                 }
 309
 310                                         }
 311
 312                                         //get last name
 313                                         sequence = fasta->getSequence(binnames);
 314                                         if (sequence != "not found") {
 315                                                 //if you don't have groups
 316                                                 if (groupfile == "") {
 317                                                         binnames = binnames + "|" + toString(i+1);
 318                                                         out << ">" << binnames << endl;
 319                                                         out << sequence << endl;
 320                                                 }else {//if you do have groups
 321                                                         string group = groupMap->getGroup(binnames);
 322                                                         if (group == "not found") {
 323                                                                 mothurOut(binnames + " is missing from your group file. Please correct. "); mothurOutEndLine();
 324                                                                 remove(outputFileName.c_str());
 325                                                                 return 1;
 326                                                         }else{
 327                                                                 binnames = binnames + "|" + group + "|" + toString(i+1);
 328                                                                 out << ">" << binnames << endl;
 329                                                                 out << sequence << endl;
 330                                                         }
 331                                                 }
 332                                         }else {
 333                                                 mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
 334                                                 remove(outputFileName.c_str());
 335                                                 return 1;
 336                                         }
 337                                 }
 338
 339                                 out.close();
 340                                 return 0;
 341
 342         }
 343         catch(exception& e) {
 344                 errorOut(e, "BinSeqCommand", "process");
 345                 exit(1);
 346         }
 347 }
 348 //**********************************************************************************************************************
 349
 350