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"};
  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
  35                         //check to make sure all parameters are valid for command
  36                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
  41                         if (taxonomyFileName == "not found") {
  42                                 mothurOut("taxonomy is a required parameter for the phylotype command.");
  43                                 mothurOutEndLine();
  44                                 abort = true;
  45                         }else if (taxonomyFileName == "not open") { abort = true; }
  46
  47                         string temp = validParameter.validFile(parameters, "cutoff", false);
  48                         if (temp == "not found") { temp = "-1"; }
  49                         convert(temp, cutoff);
  50
  51                         label = validParameter.validFile(parameters, "label", false);
  52                         if (label == "not found") { label = ""; allLines = 1; }
  53                         else {
  54                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  55                                 else { allLines = 1;  }
  56                         }
  57
  58                 }
  59         }
  60         catch(exception& e) {
  61                 errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  62                 exit(1);
  63         }
  64 }
  65 /**********************************************************************************************************************/
  66
  67 void PhylotypeCommand::help(){
  68         try {
  69                 mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
  70                 mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
  71                 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");
  72                 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");
  73                 mothurOut("The phylotype command should be in the following format: \n");
  74                 mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
  75                 mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
  76         }
  77         catch(exception& e) {
  78                 errorOut(e, "PhylotypeCommand", "help");
  79                 exit(1);
  80         }
  81 }
  82 /**********************************************************************************************************************/
  83
  84 PhylotypeCommand::~PhylotypeCommand(){}
  85
  86 /**********************************************************************************************************************/
  87
  88 int PhylotypeCommand::execute(){
  89         try {
  90
  91                 if (abort == true) { return 0; }
  92
  93                 //reads in taxonomy file and makes all the taxonomies the same length
  94                 //by appending the last taxon to a given taxonomy as many times as needed to
  95                 //make it as long as the longest taxonomy in the file
  96                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff);
  97
  98                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
  99
 100                 delete taxEqual;
 101
 102                 //build taxonomy tree from equalized file
 103                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 104                 vector<int> leaves = tree->getGenusNodes();
 105
 106                 //store leaf nodes in current map
 107                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 108
 109                 bool done = false;
 110                 if (tree->get(leaves[0]).parent == -1) {  mothurOut("Empty Tree"); mothurOutEndLine();  done = true;    }
 111
 112                 ofstream outList;
 113                 string outputListFile = getRootName(taxonomyFileName) + "tax.list";
 114                 openOutputFile(outputListFile, outList);
 115                 ofstream outSabund;
 116                 string outputSabundFile = getRootName(taxonomyFileName) + "tax.sabund";
 117                 openOutputFile(outputSabundFile, outSabund);
 118                 ofstream outRabund;
 119                 string outputRabundFile = getRootName(taxonomyFileName) + "tax.rabund";
 120                 openOutputFile(outputRabundFile, outRabund);
 121
 122
 123                 //start at leaves of tree and work towards root, processing the labels the user wants
 124                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 125
 126                         string level = toString(tree->get(currentNodes.begin()->first).level);
 127
 128                         //is this a level the user want output for
 129                         if(allLines == 1 || labels.count(level) == 1){
 130
 131                                 //output level
 132                                 mothurOut(level); mothurOutEndLine();
 133
 134                                 ListVector list;
 135                                 list.setLabel(level);
 136                                 //go through nodes and build listvector
 137                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 138
 139                                         //get parents
 140                                         TaxNode node = tree->get(itCurrent->first);
 141                                         parentNodes[node.parent] = node.parent;
 142
 143                                         vector<string> names = node.accessions;
 144
 145                                         //make the names compatable with listvector
 146                                         string name = "";
 147                                         for (int i = 0; i < names.size(); i++) {  name += names[i] + ",";       }
 148                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 149
 150                                         //add bin to list vector
 151                                         list.push_back(name);
 152                                 }
 153
 154                                 //print listvector
 155                                 list.print(outList);
 156                                 //print rabund
 157                                 list.getRAbundVector().print(outRabund);
 158                                 //print sabund
 159                                 list.getSAbundVector().print(outSabund);
 160
 161                                 labels.erase(level);
 162
 163                         }else {
 164
 165                                 //just get parents
 166                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 167                                         int parent = tree->get(itCurrent->first).parent;
 168                                         parentNodes[parent] = parent;
 169                                 }
 170                         }
 171
 172                         //move up a level
 173                         currentNodes = parentNodes;
 174                         parentNodes.clear();
 175
 176                         //have we reached the rootnode
 177                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 178                 }
 179
 180                 outList.close();
 181                 outSabund.close();
 182                 outRabund.close();
 183
 184                 delete tree;
 185
 186                 return 0;
 187         }
 188
 189         catch(exception& e) {
 190                 errorOut(e, "PhylotypeCommand", "execute");
 191                 exit(1);
 192         }
 193 }
 194 /**********************************************************************************************************************/