chopseqscommand.cpp

   1 /*
   2  *  chopseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/10/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chopseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14
  15 ChopSeqsCommand::ChopSeqsCommand(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","end","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 (map<string,string>::iterator 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 output directory command factory will send this info to us in the output parameter
  39                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  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("fasta");
  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["fasta"] = inputDir + it->second;            }
  52                                 }
  53                         }
  54
  55                         //check for required parameters
  56                         fastafile = validParameter.validFile(parameters, "fasta", true);
  57                         if (fastafile == "not open") { abort = true; }
  58                         else if (fastafile == "not found") {  m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; }
  59
  60                         string temp = validParameter.validFile(parameters, "end", false);
  61                         if (temp == "not found") {  m->mothurOut("You must provide an end for the chops.seqs command."); m->mothurOutEndLine(); abort = true; }
  62                         else {
  63                                 convert(temp, end);
  64                                 if (end < 0) { m->mothurOut("End must be positive."); m->mothurOutEndLine(); abort = true;  }
  65                         }
  66
  67                 }
  68
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76
  77 void ChopSeqsCommand::help(){
  78         try {
  79                 m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta with sequences trimmed to the end position.\n");
  80                 m->mothurOut("The chop.seqs command parameters are fasta and end, both are required.\n");
  81                 m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, end=yourEnd).\n");
  82                 m->mothurOut("Example chop.seqs(fasta=amazon.fasta, end=200).\n");
  83                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "ChopSeqsCommand", "help");
  87                 exit(1);
  88         }
  89 }
  90
  91 //**********************************************************************************************************************
  92
  93 int ChopSeqsCommand::execute(){
  94         try {
  95
  96                 if (abort == true) { return 0; }
  97
  98                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
  99
 100                 ofstream out;
 101                 openOutputFile(outputFileName, out);
 102
 103                 ifstream in;
 104                 openInputFile(fastafile, in);
 105
 106                 while (!in.eof()) {
 107
 108                         Sequence seq(in, "no align");
 109
 110                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0;  }
 111
 112                         if (seq.getName() != "") {
 113                                 string temp = seq.getUnaligned();
 114
 115                                 //output sequence name
 116                                 out << ">" << seq.getName() << endl;
 117
 118                                 //if needed trim sequence
 119                                 if (temp.length() > end) {  temp = temp.substr(0, end);         }
 120
 121                                 //output trimmed sequence
 122                                 out << temp << endl;
 123                         }
 124                 }
 125                 in.close();
 126                 out.close();
 127
 128                 m->mothurOutEndLine();
 129                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 130                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 131                 m->mothurOutEndLine();
 132
 133                 return 0;
 134         }
 135
 136         catch(exception& e) {
 137                 m->errorOut(e, "ChopSeqsCommand", "execute");
 138                 exit(1);
 139         }
 140 }
 141
 142 //**********************************************************************************************************************
 143
 144