phylotypecommand.cpp

   1 /*
   2  *  phylotypecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/20/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "phylotypecommand.h"
  11 #include "phylotree.h"
  12 #include "listvector.hpp"
  13 #include "rabundvector.hpp"
  14 #include "sabundvector.hpp"
  15
  16 /**********************************************************************************************************************/
  17 PhylotypeCommand::PhylotypeCommand(string option)  {
  18         try {
  19                 abort = false;
  20
  21                 //allow user to run help
  22                 if(option == "help") { help(); abort = true; }
  23
  24                 else {
  25
  26                         //valid paramters for this command
  27                         string AlignArray[] =  {"taxonomy","cutoff","label","name","outputdir","inputdir"};
  28                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  29
  30                         OptionParser parser(option);
  31                         map<string, string> parameters = parser.getParameters();
  32
  33                         ValidParameters validParameter;
  34                         map<string, string>::iterator it;
  35
  36                         //check to make sure all parameters are valid for command
  37                         for (it = parameters.begin(); it != parameters.end(); it++) {
  38                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  39                         }
  40
  41                         //if the user changes the input directory command factory will send this info to us in the output parameter
  42                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  43                         if (inputDir == "not found"){   inputDir = "";          }
  44                         else {
  45                                 string path;
  46                                 it = parameters.find("taxonomy");
  47                                 //user has given a template file
  48                                 if(it != parameters.end()){
  49                                         path = hasPath(it->second);
  50                                         //if the user has not given a path then, add inputdir. else leave path alone.
  51                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
  52                                 }
  53
  54                                 it = parameters.find("name");
  55                                 //user has given a template file
  56                                 if(it != parameters.end()){
  57                                         path = hasPath(it->second);
  58                                         //if the user has not given a path then, add inputdir. else leave path alone.
  59                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  60                                 }
  61                         }
  62
  63                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
  64                         if (taxonomyFileName == "not found") {
  65                                 m->mothurOut("taxonomy is a required parameter for the phylotype command.");
  66                                 m->mothurOutEndLine();
  67                                 abort = true;
  68                         }else if (taxonomyFileName == "not open") { abort = true; }
  69
  70                         namefile = validParameter.validFile(parameters, "name", true);
  71                         if (namefile == "not open") { abort = true; }
  72                         else if (namefile == "not found") { namefile = ""; }
  73                         else { readNamesFile(); }
  74
  75                         //if the user changes the output directory command factory will send this info to us in the output parameter
  76                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  77                                 outputDir = "";
  78                                 outputDir += hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
  79                         }
  80
  81                         string temp = validParameter.validFile(parameters, "cutoff", false);
  82                         if (temp == "not found") { temp = "-1"; }
  83                         convert(temp, cutoff);
  84
  85                         label = validParameter.validFile(parameters, "label", false);
  86                         if (label == "not found") { label = ""; allLines = 1; }
  87                         else {
  88                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  89                                 else { allLines = 1;  }
  90                         }
  91
  92                 }
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  96                 exit(1);
  97         }
  98 }
  99 /**********************************************************************************************************************/
 100
 101 void PhylotypeCommand::help(){
 102         try {
 103                 m->mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
 104                 m->mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
 105                 m->mothurOut("The cutoff parameter allows you to specify the level you want to stop at.  The default is the highest level in your taxonomy file. \n");
 106                 m->mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
 107                 m->mothurOut("For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n");
 108                 m->mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes.  The default all levels in your taxonomy file. \n");
 109                 m->mothurOut("For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n");
 110                 m->mothurOut("The phylotype command should be in the following format: \n");
 111                 m->mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
 112                 m->mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "PhylotypeCommand", "help");
 116                 exit(1);
 117         }
 118 }
 119 /**********************************************************************************************************************/
 120
 121 PhylotypeCommand::~PhylotypeCommand(){}
 122
 123 /**********************************************************************************************************************/
 124
 125 int PhylotypeCommand::execute(){
 126         try {
 127
 128                 if (abort == true) { return 0; }
 129
 130                 vector<string> outputNames;
 131
 132                 //reads in taxonomy file and makes all the taxonomies the same length
 133                 //by appending the last taxon to a given taxonomy as many times as needed to
 134                 //make it as long as the longest taxonomy in the file
 135                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
 136
 137                 if (m->control_pressed) { delete taxEqual; return 0; }
 138
 139                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 140
 141                 delete taxEqual;
 142
 143                 //build taxonomy tree from equalized file
 144                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 145                 vector<int> leaves = tree->getGenusNodes();
 146
 147                 //store leaf nodes in current map
 148                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 149
 150                 bool done = false;
 151                 if (tree->get(leaves[0]).parent == -1) {  m->mothurOut("Empty Tree"); m->mothurOutEndLine();    done = true;    }
 152
 153                 if (m->control_pressed) { delete tree; return 0; }
 154
 155                 string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
 156
 157                 ofstream outList;
 158                 string outputListFile = fileroot + "tx.list";
 159                 openOutputFile(outputListFile, outList);
 160                 ofstream outSabund;
 161                 string outputSabundFile = fileroot + "tx.sabund";
 162                 openOutputFile(outputSabundFile, outSabund);
 163                 ofstream outRabund;
 164                 string outputRabundFile = fileroot + "tx.rabund";
 165                 openOutputFile(outputRabundFile, outRabund);
 166
 167                 outputNames.push_back(outputListFile);
 168                 outputNames.push_back(outputSabundFile);
 169                 outputNames.push_back(outputRabundFile);
 170
 171                 int count = 1;
 172                 //start at leaves of tree and work towards root, processing the labels the user wants
 173                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 174
 175                         string level = toString(count);
 176                         count++;
 177
 178                         if (m->control_pressed) {
 179                                 outRabund.close(); outSabund.close(); outList.close();
 180                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 181                                 delete tree; return 0;
 182                         }
 183
 184                         //is this a level the user want output for
 185                         if(allLines == 1 || labels.count(level) == 1){
 186
 187                                 //output level
 188                                 m->mothurOut(level); m->mothurOutEndLine();
 189
 190                                 ListVector list;
 191                                 list.setLabel(level);
 192                                 //go through nodes and build listvector
 193                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 194
 195                                         //get parents
 196                                         TaxNode node = tree->get(itCurrent->first);
 197                                         parentNodes[node.parent] = node.parent;
 198
 199                                         vector<string> names = node.accessions;
 200
 201                                         //make the names compatable with listvector
 202                                         string name = "";
 203                                         for (int i = 0; i < names.size(); i++) {
 204                                                 if (namefile != "") {
 205                                                         map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
 206
 207                                                         if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
 208                                                         else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
 209
 210                                                 }else{   name += names[i] + ",";        }
 211                                         }
 212                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 213
 214                                         //add bin to list vector
 215                                         list.push_back(name);
 216                                 }
 217
 218                                 //print listvector
 219                                 list.print(outList);
 220                                 //print rabund
 221                                 list.getRAbundVector().print(outRabund);
 222                                 //print sabund
 223                                 list.getSAbundVector().print(outSabund);
 224
 225                                 labels.erase(level);
 226
 227                         }else {
 228
 229                                 //just get parents
 230                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 231                                         int parent = tree->get(itCurrent->first).parent;
 232                                         parentNodes[parent] = parent;
 233                                 }
 234                         }
 235
 236                         //move up a level
 237                         currentNodes = parentNodes;
 238                         parentNodes.clear();
 239
 240                         //have we reached the rootnode
 241                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 242                 }
 243
 244                 outList.close();
 245                 outSabund.close();
 246                 outRabund.close();
 247
 248                 delete tree;
 249
 250                 if (m->control_pressed) {
 251                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 252                         return 0;
 253                 }
 254
 255                 m->mothurOutEndLine();
 256                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 257                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 258                 m->mothurOutEndLine();
 259
 260                 return 0;
 261         }
 262
 263         catch(exception& e) {
 264                 m->errorOut(e, "PhylotypeCommand", "execute");
 265                 exit(1);
 266         }
 267 }
 268 /*****************************************************************/
 269 int PhylotypeCommand::readNamesFile() {
 270         try {
 271
 272                 ifstream in;
 273                 openInputFile(namefile, in);
 274
 275                 string first, second;
 276                 map<string, string>::iterator itNames;
 277
 278                 while(!in.eof()) {
 279                         in >> first >> second; gobble(in);
 280
 281                         itNames = namemap.find(first);
 282                         if (itNames == namemap.end()) {
 283                                 namemap[first] = second;
 284                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
 285                 }
 286                 in.close();
 287
 288                 return 0;
 289         }
 290         catch(exception& e) {
 291                 m->errorOut(e, "PhylotypeCommand", "readNamesFile");
 292                 exit(1);
 293         }
 294 }
 295
 296 /**********************************************************************************************************************/