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(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 fastafile = globaldata->getFastaFile();
  17                 namesfile = globaldata->getNameFile();
  18                 groupfile = globaldata->getGroupFile();
  19                 openInputFile(fastafile, in);
  20
  21                 if (groupfile != "") {
  22                         //read in group map info.
  23                         groupMap = new GroupMap(groupfile);
  24                         groupMap->readMap();
  25                 }
  26
  27                 fasta = new FastaMap();
  28         }
  29         catch(exception& e) {
  30                 cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  31                 exit(1);
  32         }
  33         catch(...) {
  34                 cout << "An unknown error has occurred in the BinSeqCommand class function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  35                 exit(1);
  36         }
  37 }
  38
  39 //**********************************************************************************************************************
  40
  41 BinSeqCommand::~BinSeqCommand(){
  42         delete input;
  43         delete read;
  44         delete fasta;
  45         delete list;
  46         if (groupfile != "") {
  47                 delete groupMap;
  48         }
  49 }
  50
  51 //**********************************************************************************************************************
  52
  53 int BinSeqCommand::execute(){
  54         try {
  55                 int count = 1;
  56                 int error = 0;
  57
  58                 //read fastafile
  59                 fasta->readFastaFile(in);
  60
  61                 //set format to list so input can get listvector
  62                 globaldata->setFormat("list");
  63
  64                 //if user gave a namesfile then use it
  65                 if (namesfile != "") {
  66                         readNamesFile();
  67                 }
  68
  69                 //read list file
  70                 read = new ReadOTUFile(globaldata->getListFile());
  71                 read->read(&*globaldata);
  72
  73                 input = globaldata->ginput;
  74                 list = globaldata->gListVector;
  75                 ListVector* lastList = list;
  76
  77                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
  78                 set<string> processedLabels;
  79                 set<string> userLabels = globaldata->labels;
  80                 set<int> userLines = globaldata->lines;
  81
  82
  83                 while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
  84
  85                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
  86
  87                                 error = process(list, count);
  88                                 if (error == 1) { return 0; }
  89
  90                                 processedLabels.insert(list->getLabel());
  91                                 userLabels.erase(list->getLabel());
  92                                 userLines.erase(count);
  93                         }
  94
  95                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
  96
  97                                 error = process(lastList, count);
  98                                 if (error == 1) { return 0; }
  99
 100                                 processedLabels.insert(lastList->getLabel());
 101                                 userLabels.erase(lastList->getLabel());
 102
 103                         }
 104
 105                         if (count != 1) { delete lastList; }
 106                         lastList = list;
 107
 108                         list = input->getListVector();
 109                         count++;
 110                 }
 111
 112
 113                 //output error messages about any remaining user labels
 114                 set<string>::iterator it;
 115                 bool needToRun = false;
 116                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 117                         cout << "Your file does not include the label "<< *it;
 118                         if (processedLabels.count(lastList->getLabel()) != 1) {
 119                                 cout << ". I will use " << lastList->getLabel() << "." << endl;
 120                                 needToRun = true;
 121                         }else {
 122                                 cout << ". Please refer to " << lastList->getLabel() << "." << endl;
 123                         }
 124                 }
 125
 126                 //run last line if you need to
 127                 if (needToRun == true)  {
 128                         error = process(lastList, count);
 129                         if (error == 1) { return 0; }
 130                 }
 131
 132                 delete lastList;
 133                 return 0;
 134         }
 135         catch(exception& e) {
 136                 cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 137                 exit(1);
 138         }
 139         catch(...) {
 140                 cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 141                 exit(1);
 142         }
 143 }
 144
 145 //**********************************************************************************************************************
 146 void BinSeqCommand::readNamesFile() {
 147         try {
 148                 vector<string> dupNames;
 149                 openInputFile(namesfile, inNames);
 150
 151                 string name, names, sequence;
 152
 153                 while(inNames){
 154                         inNames >> name;                        //read from first column  A
 155                         inNames >> names;               //read from second column  A,B,C,D
 156
 157                         dupNames.clear();
 158
 159                         //parse names into vector
 160                         splitAtComma(names, dupNames);
 161
 162                         //store names in fasta map
 163                         sequence = fasta->getSequence(name);
 164                         for (int i = 0; i < dupNames.size(); i++) {
 165                                 fasta->push_back(dupNames[i], sequence);
 166                         }
 167
 168                         gobble(inNames);
 169                 }
 170                 inNames.close();
 171
 172         }
 173         catch(exception& e) {
 174                 cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 175                 exit(1);
 176         }
 177         catch(...) {
 178                 cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 179                 exit(1);
 180         }
 181 }
 182 //**********************************************************************************************************************
 183 //return 1 if error, 0 otherwise
 184 int BinSeqCommand::process(ListVector* list, int count) {
 185         try {
 186                                 string binnames, name, sequence;
 187                                 string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
 188                                 openOutputFile(outputFileName, out);
 189
 190                                 cout << list->getLabel() << '\t' << count << endl;
 191
 192                                 //for each bin in the list vector
 193                                 for (int i = 0; i < list->size(); i++) {
 194
 195                                         binnames = list->get(i);
 196                                         while (binnames.find_first_of(',') != -1) {
 197                                                 name = binnames.substr(0,binnames.find_first_of(','));
 198                                                 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 199
 200                                                 //do work for that name
 201                                                 sequence = fasta->getSequence(name);
 202                                                 if (sequence != "not found") {
 203                                                         //if you don't have groups
 204                                                         if (groupfile == "") {
 205                                                                 name = name + "|" + toString(i+1);
 206                                                                 out << ">" << name << endl;
 207                                                                 out << sequence << endl;
 208                                                         }else {//if you do have groups
 209                                                                 string group = groupMap->getGroup(name);
 210                                                                 if (group == "not found") {
 211                                                                         cout << name << " is missing from your group file. Please correct. " << endl;
 212                                                                         remove(outputFileName.c_str());
 213                                                                         return 1;
 214                                                                 }else{
 215                                                                         name = name + "|" + group + "|" + toString(i+1);
 216                                                                         out << ">" << name << endl;
 217                                                                         out << sequence << endl;
 218                                                                 }
 219                                                         }
 220                                                 }else {
 221                                                         cout << name << " is missing from your fasta or name file. Please correct. " << endl;
 222                                                         remove(outputFileName.c_str());
 223                                                         return 1;
 224                                                 }
 225
 226                                         }
 227
 228                                         //get last name
 229                                         sequence = fasta->getSequence(binnames);
 230                                         if (sequence != "not found") {
 231                                                 //if you don't have groups
 232                                                 if (groupfile == "") {
 233                                                         binnames = binnames + "|" + toString(i+1);
 234                                                         out << ">" << binnames << endl;
 235                                                         out << sequence << endl;
 236                                                 }else {//if you do have groups
 237                                                         string group = groupMap->getGroup(binnames);
 238                                                         if (group == "not found") {
 239                                                                 cout << binnames << " is missing from your group file. Please correct. " << endl;
 240                                                                 remove(outputFileName.c_str());
 241                                                                 return 1;
 242                                                         }else{
 243                                                                 binnames = binnames + "|" + group + "|" + toString(i+1);
 244                                                                 out << ">" << binnames << endl;
 245                                                                 out << sequence << endl;
 246                                                         }
 247                                                 }
 248                                         }else {
 249                                                 cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
 250                                                 remove(outputFileName.c_str());
 251                                                 return 1;
 252                                         }
 253                                 }
 254
 255                                 out.close();
 256                                 return 0;
 257
 258         }
 259         catch(exception& e) {
 260                 cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 261                 exit(1);
 262         }
 263         catch(...) {
 264                 cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 265                 exit(1);
 266         }
 267 }
 268 //**********************************************************************************************************************
 269
 270