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","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
  55                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
  56                         if (taxonomyFileName == "not found") {
  57                                 mothurOut("taxonomy is a required parameter for the phylotype command.");
  58                                 mothurOutEndLine();
  59                                 abort = true;
  60                         }else if (taxonomyFileName == "not open") { abort = true; }
  61
  62                         //if the user changes the output directory command factory will send this info to us in the output parameter
  63                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  64                                 outputDir = "";
  65                                 outputDir += hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
  66                         }
  67
  68                         string temp = validParameter.validFile(parameters, "cutoff", false);
  69                         if (temp == "not found") { temp = "-1"; }
  70                         convert(temp, cutoff);
  71
  72                         label = validParameter.validFile(parameters, "label", false);
  73                         if (label == "not found") { label = ""; allLines = 1; }
  74                         else {
  75                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  76                                 else { allLines = 1;  }
  77                         }
  78
  79                 }
  80         }
  81         catch(exception& e) {
  82                 errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  83                 exit(1);
  84         }
  85 }
  86 /**********************************************************************************************************************/
  87
  88 void PhylotypeCommand::help(){
  89         try {
  90                 mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
  91                 mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
  92                 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");
  93                 mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
  94                 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");
  95                 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");
  96                 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");
  97                 mothurOut("The phylotype command should be in the following format: \n");
  98                 mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
  99                 mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
 100         }
 101         catch(exception& e) {
 102                 errorOut(e, "PhylotypeCommand", "help");
 103                 exit(1);
 104         }
 105 }
 106 /**********************************************************************************************************************/
 107
 108 PhylotypeCommand::~PhylotypeCommand(){}
 109
 110 /**********************************************************************************************************************/
 111
 112 int PhylotypeCommand::execute(){
 113         try {
 114
 115                 if (abort == true) { return 0; }
 116
 117                 //reads in taxonomy file and makes all the taxonomies the same length
 118                 //by appending the last taxon to a given taxonomy as many times as needed to
 119                 //make it as long as the longest taxonomy in the file
 120                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff);
 121
 122                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 123
 124                 delete taxEqual;
 125
 126                 //build taxonomy tree from equalized file
 127                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 128                 vector<int> leaves = tree->getGenusNodes();
 129
 130                 //store leaf nodes in current map
 131                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 132
 133                 bool done = false;
 134                 if (tree->get(leaves[0]).parent == -1) {  mothurOut("Empty Tree"); mothurOutEndLine();  done = true;    }
 135
 136                 string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
 137
 138                 ofstream outList;
 139                 string outputListFile = fileroot + "tx.list";
 140                 openOutputFile(outputListFile, outList);
 141                 ofstream outSabund;
 142                 string outputSabundFile = fileroot + "tx.sabund";
 143                 openOutputFile(outputSabundFile, outSabund);
 144                 ofstream outRabund;
 145                 string outputRabundFile = fileroot + "tx.rabund";
 146                 openOutputFile(outputRabundFile, outRabund);
 147
 148                 int count = 1;
 149                 //start at leaves of tree and work towards root, processing the labels the user wants
 150                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 151
 152                         string level = toString(count);
 153                         count++;
 154
 155                         //is this a level the user want output for
 156                         if(allLines == 1 || labels.count(level) == 1){
 157
 158                                 //output level
 159                                 mothurOut(level); mothurOutEndLine();
 160
 161                                 ListVector list;
 162                                 list.setLabel(level);
 163                                 //go through nodes and build listvector
 164                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 165
 166                                         //get parents
 167                                         TaxNode node = tree->get(itCurrent->first);
 168                                         parentNodes[node.parent] = node.parent;
 169
 170                                         vector<string> names = node.accessions;
 171
 172                                         //make the names compatable with listvector
 173                                         string name = "";
 174                                         for (int i = 0; i < names.size(); i++) {  name += names[i] + ",";       }
 175                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 176
 177                                         //add bin to list vector
 178                                         list.push_back(name);
 179                                 }
 180
 181                                 //print listvector
 182                                 list.print(outList);
 183                                 //print rabund
 184                                 list.getRAbundVector().print(outRabund);
 185                                 //print sabund
 186                                 list.getSAbundVector().print(outSabund);
 187
 188                                 labels.erase(level);
 189
 190                         }else {
 191
 192                                 //just get parents
 193                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 194                                         int parent = tree->get(itCurrent->first).parent;
 195                                         parentNodes[parent] = parent;
 196                                 }
 197                         }
 198
 199                         //move up a level
 200                         currentNodes = parentNodes;
 201                         parentNodes.clear();
 202
 203                         //have we reached the rootnode
 204                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 205                 }
 206
 207                 outList.close();
 208                 outSabund.close();
 209                 outRabund.close();
 210
 211                 delete tree;
 212
 213                 return 0;
 214         }
 215
 216         catch(exception& e) {
 217                 errorOut(e, "PhylotypeCommand", "execute");
 218                 exit(1);
 219         }
 220 }
 221 /**********************************************************************************************************************/