splitgroupscommand.cpp

   1 /*
   2  *  splitgroupscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/20/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "splitgroupscommand.h"
  11 #include "sharedutilities.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SplitGroupCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"name","group","groups","fasta","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "SplitGroupCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 vector<string> SplitGroupCommand::getRequiredParameters(){
  27         try {
  28                 string Array[] =  {"fasta","group"};
  29                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  30                 return myArray;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "SplitGroupCommand", "getRequiredParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> SplitGroupCommand::getRequiredFiles(){
  39         try {
  40                 vector<string> myArray;
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "SplitGroupCommand", "getRequiredFiles");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 SplitGroupCommand::SplitGroupCommand(){
  50         try {
  51                 abort = true; calledHelp = true;
  52                 vector<string> tempOutNames;
  53                 outputTypes["fasta"] = tempOutNames;
  54                 outputTypes["name"] = tempOutNames;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 SplitGroupCommand::SplitGroupCommand(string option)  {
  63         try {
  64                 abort = false; calledHelp = false;
  65
  66                 //allow user to run help
  67                 if(option == "help") { help(); abort = true; calledHelp = true; }
  68
  69                 else {
  70                         //valid paramters for this command
  71                         string Array[] =  {"name","group","groups","fasta","outputdir","inputdir"};
  72                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  73
  74                         OptionParser parser(option);
  75                         map<string, string> parameters = parser.getParameters();
  76
  77                         ValidParameters validParameter;
  78                         map<string, string>::iterator it;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //initialize outputTypes
  86                         vector<string> tempOutNames;
  87                         outputTypes["fasta"] = tempOutNames;
  88                         outputTypes["name"] = tempOutNames;
  89
  90                         //if the user changes the input directory command factory will send this info to us in the output parameter
  91                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  92                         if (inputDir == "not found"){   inputDir = "";          }
  93                         else {
  94                                 string path;
  95                                 it = parameters.find("group");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 101                                 }
 102
 103                                 it = parameters.find("fasta");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 109                                 }
 110
 111                                 it = parameters.find("name");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 117                                 }
 118
 119                         }
 120
 121
 122                         namefile = validParameter.validFile(parameters, "name", true);
 123                         if (namefile == "not open") { abort = true; }
 124                         else if (namefile == "not found") { namefile = ""; }
 125
 126                         fastafile = validParameter.validFile(parameters, "fasta", true);
 127                         if (fastafile == "not open") { abort = true; }
 128                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the split.group command. "); m->mothurOutEndLine(); abort = true;  }
 129
 130                         groupfile = validParameter.validFile(parameters, "group", true);
 131                         if (groupfile == "not open") {  groupfile = ""; abort = true; }
 132                         else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the split.group command. "); m->mothurOutEndLine(); abort = true; }
 133
 134                         groups = validParameter.validFile(parameters, "groups", false);
 135                         if (groups == "not found") { groups = ""; }
 136                         else { m->splitAtDash(groups, Groups);  }
 137
 138                         //if the user changes the output directory command factory will send this info to us in the output parameter
 139                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(groupfile);      }
 140                 }
 141
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "SplitGroupCommand", "SplitAbundCommand");
 145                 exit(1);
 146         }
 147 }
 148 //**********************************************************************************************************************
 149 void SplitGroupCommand::help(){
 150         try {
 151                 m->mothurOut("The split.group command reads a group file, and parses your fasta and names files by groups. \n");
 152                 m->mothurOut("The split.group command parameters are fasta, name, group and groups.\n");
 153                 m->mothurOut("The fasta and group parameters are required.\n");
 154                 m->mothurOut("The groups parameter allows you to select groups to create files for.  \n");
 155                 m->mothurOut("For example if you set groups=A-B-C, you will get a .A.fasta, .A.names, .B.fasta, .B.names, .C.fasta, .C.names files.  \n");
 156                 m->mothurOut("If you want .fasta and .names files for all groups, set groups=all.  \n");
 157                 m->mothurOut("The split.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n");
 158                 m->mothurOut("Example: split.group(fasta=abrecovery.fasta, group=abrecovery.groups).\n");
 159                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 160
 161         }
 162         catch(exception& e) {
 163                 m->errorOut(e, "SplitGroupCommand", "help");
 164                 exit(1);
 165         }
 166 }
 167 //**********************************************************************************************************************
 168 SplitGroupCommand::~SplitGroupCommand(){ }
 169 //**********************************************************************************************************************
 170 int SplitGroupCommand::execute(){
 171         try {
 172
 173                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 174
 175                 groupMap = new GroupMap(groupfile);
 176                 groupMap->readMap();
 177
 178                 SharedUtil util;  util.setGroups(Groups, groupMap->namesOfGroups);
 179
 180                 if (namefile != "") {  readNames();  }
 181                 splitFasta();
 182
 183                 delete groupMap;
 184
 185                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 186
 187                 m->mothurOutEndLine();
 188                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 189                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 190                 m->mothurOutEndLine();
 191
 192                 return 0;
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "SplitGroupCommand", "execute");
 196                 exit(1);
 197         }
 198 }
 199 /**********************************************************************************************************************/
 200 int SplitGroupCommand::readNames() {
 201         try {
 202                 //open input file
 203                 ifstream in;
 204                 m->openInputFile(namefile, in);
 205
 206                 while (!in.eof()) {
 207                         if (m->control_pressed) { break; }
 208
 209                         string firstCol, secondCol;
 210                         in >> firstCol >> secondCol; m->gobble(in);
 211
 212                         vector<string> names;
 213                         m->splitAtComma(secondCol, names);
 214
 215                         nameMap[firstCol] = names;
 216                 }
 217                 in.close();
 218
 219                 return 0;
 220
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "SplitGroupCommand", "readNames");
 224                 exit(1);
 225         }
 226 }
 227
 228 /**********************************************************************************************************************/
 229 int SplitGroupCommand::splitFasta() {
 230         try {
 231
 232                 string filerootFasta =  outputDir + m->getRootName(m->getSimpleName(fastafile));
 233                 string filerootName =  outputDir + m->getRootName(m->getSimpleName(namefile));
 234                 ofstream* temp;
 235                 ofstream* temp2;
 236                 map<string, ofstream*> filehandles;
 237                 map<string, ofstream*>::iterator it3;
 238
 239                 for (int i=0; i<Groups.size(); i++) {
 240                         temp = new ofstream;
 241                         filehandles[Groups[i]+"fasta"] = temp;
 242                         m->openOutputFile(filerootFasta + Groups[i] + ".fasta", *(filehandles[Groups[i]+"fasta"]));
 243                         outputNames.push_back(filerootFasta + Groups[i] + ".fasta"); outputTypes["fasta"].push_back(filerootFasta + Groups[i] + ".fasta");
 244
 245                         if (namefile != "") {
 246                                 temp2 = new ofstream;
 247                                 filehandles[Groups[i]+"name"] = temp2;
 248                                 m->openOutputFile(filerootName + Groups[i] + ".names", *(filehandles[Groups[i]+"name"]));
 249                                 outputNames.push_back(filerootName + Groups[i] + ".names"); outputTypes["name"].push_back(filerootFasta + Groups[i] + ".names");
 250                         }
 251                 }
 252
 253                 //open input file
 254                 ifstream in;
 255                 m->openInputFile(fastafile, in);
 256
 257                 while (!in.eof()) {
 258                         if (m->control_pressed) { break; }
 259
 260                         Sequence seq(in); m->gobble(in);
 261
 262                         if (seq.getName() != "") {
 263
 264                                 itNames = nameMap.find(seq.getName());
 265
 266                                 if (itNames == nameMap.end()) {
 267                                         if (namefile != "") {  m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();  }
 268                                         else { //no names file given
 269                                                 string group = groupMap->getGroup(seq.getName());
 270
 271                                                 if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 272                                                         seq.printSequence(*(filehandles[group+"fasta"]));
 273                                                 }else if(group == "not found") {
 274                                                         m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 275                                                 }
 276                                         }
 277                                 }else{
 278                                         vector<string> names = itNames->second;
 279                                         map<string, string> group2Names;
 280                                         map<string, string>::iterator it;
 281
 282                                         for (int i = 0; i < names.size(); i++) {  //build strings for new group names file, will select rep below
 283                                                 string group = groupMap->getGroup(names[i]);
 284
 285                                                 if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
 286                                                         it = group2Names.find(group);
 287                                                         if (it == group2Names.end()) {
 288                                                                 group2Names[group] = names[i] + ",";
 289                                                         }else{
 290                                                                 group2Names[group] += names[i] + ",";
 291                                                         }
 292                                                 }else if(group == "not found") {
 293                                                         m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
 294                                                 }
 295                                         }
 296
 297                                         for (map<string, string>::iterator itGroups = group2Names.begin(); itGroups != group2Names.end(); itGroups++) {
 298                                                 //edit names string, by grabbing the first guy as the rep and removing the last comma
 299                                                 string newNames = itGroups->second;
 300                                                 newNames = newNames.substr(0, newNames.length()-1);
 301                                                 string repName = "";
 302
 303                                                 int pos = newNames.find_first_of(',');
 304                                                 if (pos == newNames.npos) { //only one sequence so it represents itself
 305                                                         repName = newNames;
 306                                                 }else{
 307                                                         repName = newNames.substr(0, pos);
 308                                                 }
 309
 310                                                 *(filehandles[itGroups->first+"name"]) << repName << '\t' << newNames << endl;
 311                                                 *(filehandles[itGroups->first+"fasta"]) << ">" << repName << endl << seq.getAligned() << endl;
 312                                         }
 313                                 }
 314                         }
 315                 }
 316
 317                 in.close();
 318
 319                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 320                         (*(filehandles[it3->first])).close();
 321                         delete it3->second;
 322                 }
 323
 324                 vector<string> newOutputNames;
 325                 //remove blank files
 326                 for (int i = 0; i < outputNames.size(); i++) {
 327                         if (m->isBlank(outputNames[i])) {
 328                                 remove(outputNames[i].c_str());
 329                         }else { newOutputNames.push_back(outputNames[i]); }
 330                 }
 331                 outputNames = newOutputNames;
 332
 333                 return 0;
 334
 335         }
 336         catch(exception& e) {
 337                 m->errorOut(e, "SplitGroupCommand", "splitFasta");
 338                 exit(1);
 339         }
 340 }
 341 /**********************************************************************************************************************/
 342