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("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
  73                 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");
  74                 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");
  75                 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");
  76                 mothurOut("The phylotype command should be in the following format: \n");
  77                 mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
  78                 mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
  79         }
  80         catch(exception& e) {
  81                 errorOut(e, "PhylotypeCommand", "help");
  82                 exit(1);
  83         }
  84 }
  85 /**********************************************************************************************************************/
  86
  87 PhylotypeCommand::~PhylotypeCommand(){}
  88
  89 /**********************************************************************************************************************/
  90
  91 int PhylotypeCommand::execute(){
  92         try {
  93
  94                 if (abort == true) { return 0; }
  95
  96                 //reads in taxonomy file and makes all the taxonomies the same length
  97                 //by appending the last taxon to a given taxonomy as many times as needed to
  98                 //make it as long as the longest taxonomy in the file
  99                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff);
 100
 101                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 102
 103                 delete taxEqual;
 104
 105                 //build taxonomy tree from equalized file
 106                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 107                 vector<int> leaves = tree->getGenusNodes();
 108
 109                 //store leaf nodes in current map
 110                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 111
 112                 bool done = false;
 113                 if (tree->get(leaves[0]).parent == -1) {  mothurOut("Empty Tree"); mothurOutEndLine();  done = true;    }
 114
 115                 ofstream outList;
 116                 string outputListFile = getRootName(taxonomyFileName) + "tax.list";
 117                 openOutputFile(outputListFile, outList);
 118                 ofstream outSabund;
 119                 string outputSabundFile = getRootName(taxonomyFileName) + "tax.sabund";
 120                 openOutputFile(outputSabundFile, outSabund);
 121                 ofstream outRabund;
 122                 string outputRabundFile = getRootName(taxonomyFileName) + "tax.rabund";
 123                 openOutputFile(outputRabundFile, outRabund);
 124
 125                 int count = 1;
 126                 //start at leaves of tree and work towards root, processing the labels the user wants
 127                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 128
 129                         string level = toString(count);
 130                         count++;
 131
 132                         //is this a level the user want output for
 133                         if(allLines == 1 || labels.count(level) == 1){
 134
 135                                 //output level
 136                                 mothurOut(level); mothurOutEndLine();
 137
 138                                 ListVector list;
 139                                 list.setLabel(level);
 140                                 //go through nodes and build listvector
 141                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 142
 143                                         //get parents
 144                                         TaxNode node = tree->get(itCurrent->first);
 145                                         parentNodes[node.parent] = node.parent;
 146
 147                                         vector<string> names = node.accessions;
 148
 149                                         //make the names compatable with listvector
 150                                         string name = "";
 151                                         for (int i = 0; i < names.size(); i++) {  name += names[i] + ",";       }
 152                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 153
 154                                         //add bin to list vector
 155                                         list.push_back(name);
 156                                 }
 157
 158                                 //print listvector
 159                                 list.print(outList);
 160                                 //print rabund
 161                                 list.getRAbundVector().print(outRabund);
 162                                 //print sabund
 163                                 list.getSAbundVector().print(outSabund);
 164
 165                                 labels.erase(level);
 166
 167                         }else {
 168
 169                                 //just get parents
 170                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 171                                         int parent = tree->get(itCurrent->first).parent;
 172                                         parentNodes[parent] = parent;
 173                                 }
 174                         }
 175
 176                         //move up a level
 177                         currentNodes = parentNodes;
 178                         parentNodes.clear();
 179
 180                         //have we reached the rootnode
 181                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 182                 }
 183
 184                 outList.close();
 185                 outSabund.close();
 186                 outRabund.close();
 187
 188                 delete tree;
 189
 190                 return 0;
 191         }
 192
 193         catch(exception& e) {
 194                 errorOut(e, "PhylotypeCommand", "execute");
 195                 exit(1);
 196         }
 197 }
 198 /**********************************************************************************************************************/