seqsummarycommand.cpp

   1 /*
   2  *  seqcoordcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 5/30/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "seqsummarycommand.h"
  11 #include "sequence.hpp"
  12
  13 //***************************************************************************************************************
  14
  15 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta","outputdir","inputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //if the user changes the input directory command factory will send this info to us in the output parameter
  39                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  40                         if (inputDir == "not found"){   inputDir = "";          }
  41                         else {
  42                                 string path;
  43                                 it = parameters.find("fasta");
  44                                 //user has given a template file
  45                                 if(it != parameters.end()){
  46                                         path = hasPath(it->second);
  47                                         //if the user has not given a path then, add inputdir. else leave path alone.
  48                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  49                                 }
  50                         }
  51
  52                         //check for required parameters
  53                         fastafile = validParameter.validFile(parameters, "fasta", true);
  54                         if (fastafile == "not open") { abort = true; }
  55                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true;  }
  56
  57                         //if the user changes the output directory command factory will send this info to us in the output parameter
  58                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  59                                 outputDir = "";
  60                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  61                         }
  62
  63                 }
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71
  72 void SeqSummaryCommand::help(){
  73         try {
  74                 m->mothurOut("The summary.seqs command reads a fastafile and ....\n");
  75                 m->mothurOut("The summary.seqs command parameter is fasta and it is required.\n");
  76                 m->mothurOut("The summary.seqs command should be in the following format: \n");
  77                 m->mothurOut("summary.seqs(fasta=yourFastaFile) \n");
  78                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "SeqSummaryCommand", "help");
  82                 exit(1);
  83         }
  84 }
  85
  86 //***************************************************************************************************************
  87
  88 SeqSummaryCommand::~SeqSummaryCommand(){        /*      do nothing      */      }
  89
  90 //***************************************************************************************************************
  91
  92 int SeqSummaryCommand::execute(){
  93         try{
  94
  95                 if (abort == true) { return 0; }
  96
  97                 ifstream inFASTA;
  98                 openInputFile(fastafile, inFASTA);
  99                 int numSeqs = 0;
 100
 101                 ofstream outSummary;
 102                 string summaryFile = outputDir + getSimpleName(fastafile) + ".summary";
 103                 openOutputFile(summaryFile, outSummary);
 104
 105                 vector<int> startPosition;
 106                 vector<int> endPosition;
 107                 vector<int> seqLength;
 108                 vector<int> ambigBases;
 109                 vector<int> longHomoPolymer;
 110
 111                 outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
 112
 113                 while(!inFASTA.eof()){
 114                         if (m->control_pressed) { inFASTA.close(); outSummary.close(); remove(summaryFile.c_str()); return 0; }
 115
 116                         Sequence current(inFASTA);
 117                         if (current.getName() != "") {
 118                                 startPosition.push_back(current.getStartPos());
 119                                 endPosition.push_back(current.getEndPos());
 120                                 seqLength.push_back(current.getNumBases());
 121                                 ambigBases.push_back(current.getAmbigBases());
 122                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 123
 124                                 outSummary << current.getName() << '\t';
 125                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 126                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 127                                 outSummary << current.getLongHomoPolymer() << endl;
 128
 129                                 numSeqs++;
 130                         }
 131                         gobble(inFASTA);
 132                 }
 133                 inFASTA.close();
 134
 135                 sort(startPosition.begin(), startPosition.end());
 136                 sort(endPosition.begin(), endPosition.end());
 137                 sort(seqLength.begin(), seqLength.end());
 138                 sort(ambigBases.begin(), ambigBases.end());
 139                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 140
 141                 int ptile0_25   = int(numSeqs * 0.025);
 142                 int ptile25             = int(numSeqs * 0.250);
 143                 int ptile50             = int(numSeqs * 0.500);
 144                 int ptile75             = int(numSeqs * 0.750);
 145                 int ptile97_5   = int(numSeqs * 0.975);
 146                 int ptile100    = numSeqs - 1;
 147
 148                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 149                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 150                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 151
 152                 if (m->control_pressed) {  outSummary.close(); remove(summaryFile.c_str()); return 0; }
 153
 154                 m->mothurOutEndLine();
 155                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
 156                 m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); m->mothurOutEndLine();
 157                 m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); m->mothurOutEndLine();
 158                 m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); m->mothurOutEndLine();
 159                 m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); m->mothurOutEndLine();
 160                 m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); m->mothurOutEndLine();
 161                 m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); m->mothurOutEndLine();
 162                 m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); m->mothurOutEndLine();
 163                 m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
 164
 165                 outSummary.close();
 166
 167                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 168
 169                 m->mothurOutEndLine();
 170                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 171                 m->mothurOut(summaryFile); m->mothurOutEndLine();
 172                 m->mothurOutEndLine();
 173
 174                 return 0;
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "SeqSummaryCommand", "execute");
 178                 exit(1);
 179         }
 180 }
 181
 182 //***************************************************************************************************************
 183
 184