chimeraseqscommand.cpp

   1 /*
   2  *  chimeraseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/29/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraseqscommand.h"
  11 #include "bellerophon.h"
  12 #include "pintail.h"
  13 #include "ccode.h"
  14 #include "chimeracheckrdp.h"
  15 #include "chimeraslayer.h"
  16
  17
  18 //***************************************************************************************************************
  19
  20 ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
  21         try {
  22                 abort = false;
  23
  24                 //allow user to run help
  25                 if(option == "help") { help(); abort = true; }
  26
  27                 else {
  28                         //valid paramters for this command
  29                         string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters","outputdir","inputdir" };
  30                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  31
  32                         OptionParser parser(option);
  33                         map<string,string> parameters = parser.getParameters();
  34
  35                         ValidParameters validParameter;
  36                         map<string,string>::iterator it;
  37
  38                         //check to make sure all parameters are valid for command
  39                         for (it = parameters.begin(); it != parameters.end(); it++) {
  40                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  41                         }
  42
  43                         //if the user changes the input directory command factory will send this info to us in the output parameter
  44                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  45                         if (inputDir == "not found"){   inputDir = "";          }
  46                         else {
  47                                 string path;
  48                                 it = parameters.find("fasta");
  49                                 //user has given a template file
  50                                 if(it != parameters.end()){
  51                                         path = hasPath(it->second);
  52                                         //if the user has not given a path then, add inputdir. else leave path alone.
  53                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  54                                 }
  55
  56                                 it = parameters.find("template");
  57                                 //user has given a template file
  58                                 if(it != parameters.end()){
  59                                         path = hasPath(it->second);
  60                                         //if the user has not given a path then, add inputdir. else leave path alone.
  61                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  62                                 }
  63
  64                                 it = parameters.find("conservation");
  65                                 //user has given a template file
  66                                 if(it != parameters.end()){
  67                                         path = hasPath(it->second);
  68                                         //if the user has not given a path then, add inputdir. else leave path alone.
  69                                         if (path == "") {       parameters["conservation"] = inputDir + it->second;             }
  70                                 }
  71
  72                                 it = parameters.find("quantile");
  73                                 //user has given a template file
  74                                 if(it != parameters.end()){
  75                                         path = hasPath(it->second);
  76                                         //if the user has not given a path then, add inputdir. else leave path alone.
  77                                         if (path == "") {       parameters["quantile"] = inputDir + it->second;         }
  78                                 }
  79
  80                                 it = parameters.find("name");
  81                                 //user has given a template file
  82                                 if(it != parameters.end()){
  83                                         path = hasPath(it->second);
  84                                         //if the user has not given a path then, add inputdir. else leave path alone.
  85                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  86                                 }
  87                         }
  88
  89
  90                         //check for required parameters
  91                         fastafile = validParameter.validFile(parameters, "fasta", true);
  92                         if (fastafile == "not open") { abort = true; }
  93                         else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true;  }
  94
  95                         //if the user changes the output directory command factory will send this info to us in the output parameter
  96                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  97                                 outputDir = "";
  98                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  99                         }
 100
 101                         templatefile = validParameter.validFile(parameters, "template", true);
 102                         if (templatefile == "not open") { abort = true; }
 103                         else if (templatefile == "not found") { templatefile = "";  }
 104
 105                         consfile = validParameter.validFile(parameters, "conservation", true);
 106                         if (consfile == "not open") { abort = true; }
 107                         else if (consfile == "not found") { consfile = "";  }
 108
 109                         quanfile = validParameter.validFile(parameters, "quantile", true);
 110                         if (quanfile == "not open") { abort = true; }
 111                         else if (quanfile == "not found") { quanfile = "";  }
 112
 113                         namefile = validParameter.validFile(parameters, "name", true);
 114                         if (namefile == "not open") { abort = true; }
 115                         else if (namefile == "not found") { namefile = "";  }
 116
 117                         maskfile = validParameter.validFile(parameters, "mask", false);
 118                         if (maskfile == "not found") { maskfile = "";  }
 119                         else if (maskfile != "default")  {
 120                                 if (inputDir != "") {
 121                                         string path = hasPath(maskfile);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       maskfile = inputDir + maskfile;         }
 124                                 }
 125
 126                                 ifstream in;
 127                                 int     ableToOpen = openInputFile(maskfile, in);
 128                                 if (ableToOpen == 1) { abort = true; }
 129                                 in.close();
 130                         }
 131
 132                         method = validParameter.validFile(parameters, "method", false);                 if (method == "not found") { method = "pintail"; }
 133
 134                         string temp;
 135                         temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
 136                         filter = isTrue(temp);
 137
 138                         temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
 139                         correction = isTrue(temp);
 140
 141                         temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
 142                         convert(temp, processors);
 143
 144                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 145                         convert(temp, ksize);
 146
 147                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 148                         svg = isTrue(temp);
 149
 150                         temp = validParameter.validFile(parameters, "window", false);
 151                         if ((temp == "not found") && (method == "chimeraslayer")) { temp = "100"; }
 152                         else if (temp == "not found") { temp = "0"; }
 153                         convert(temp, window);
 154
 155                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 156                         convert(temp, match);
 157
 158                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 159                         convert(temp, mismatch);
 160
 161                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.0"; }
 162                         convert(temp, divR);
 163
 164                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 165                         convert(temp, minSimilarity);
 166
 167                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "5"; }
 168                         convert(temp, parents);
 169
 170                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 171                         convert(temp, iters);
 172
 173                         temp = validParameter.validFile(parameters, "increment", false);
 174                         if ((temp == "not found") && ((method == "chimeracheck") || (method == "chimeraslayer"))) { temp = "10"; }
 175                         else if (temp == "not found") { temp = "25"; }
 176                         convert(temp, increment);
 177
 178                         temp = validParameter.validFile(parameters, "numwanted", false);
 179                         if ((temp == "not found") && (method == "chimeraslayer")) { temp = "10"; }
 180                         else if (temp == "not found") { temp = "20"; }
 181                         convert(temp, numwanted);
 182
 183
 184
 185                         if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
 186
 187
 188                 }
 189         }
 190         catch(exception& e) {
 191                 errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
 192                 exit(1);
 193         }
 194 }
 195 //**********************************************************************************************************************
 196
 197 void ChimeraSeqsCommand::help(){
 198         try {
 199
 200                 //"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name"
 201                 //mothurOut("chimera.seqs ASSUMES that your sequences are ALIGNED and if using a template that the template file sequences are the same length as the fasta file sequences.\n\n");
 202                 mothurOut("The chimera.seqs command reads a fastafile and creates list of potentially chimeric sequences.\n");
 203                 mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters.\n");
 204                 mothurOut("The fasta parameter is always required and template is required if using pintail, ccode or chimeracheck.\n");
 205                 mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
 206                 mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n");
 207                 mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 208                 mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is pintail. Options include bellerophon, ccode and chimeracheck \n");
 209                 mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n");
 210                 mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n");
 211                 mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences.\n");
 212                 mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences. \n");
 213                 mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n");
 214                 mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences.\n");
 215                 mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
 216                 mothurOut("The ksize parameter allows you to input kmersize. \n");
 217                 mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\n");
 218                 mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
 219                 //mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
 220                 mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
 221                 mothurOut("Details for each method: \n");
 222                 mothurOut("\tpintail: \n");
 223                 mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=300, increment=25, conservation=not required, but will improve speed, quantile=not required, but will greatly improve speed. \n");
 224                 mothurOut("\t\tIf you have run chimera.seqs using pintail a .quan and .freq file will be created for your template, if you have not provided them for use in future command executions.\n");
 225                 mothurOut("\tbellerophon: \n");
 226                 mothurOut("\t\tparameters: fasta=required, filter=F, processors=1, window=1/4 length of seq, increment=25, correction=T. \n");
 227                 mothurOut("\tccode: \n");
 228                 mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n");
 229                 mothurOut("\tchimeracheck: \n");
 230                 mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n");
 231                 //mothurOut("\tchimeraslayer: \n");
 232                 //mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n");
 233                 mothurOut("The chimera.seqs command should be in the following format: \n");
 234                 mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
 235                 mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");
 236                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 237         }
 238         catch(exception& e) {
 239                 errorOut(e, "ChimeraSeqsCommand", "help");
 240                 exit(1);
 241         }
 242 }
 243
 244 //***************************************************************************************************************
 245
 246 ChimeraSeqsCommand::~ChimeraSeqsCommand(){      /*      do nothing      */      }
 247
 248 //***************************************************************************************************************
 249
 250 int ChimeraSeqsCommand::execute(){
 251         try{
 252
 253                 if (abort == true) { return 0; }
 254
 255                 if (method == "bellerophon")                    {               chimera = new Bellerophon(fastafile, outputDir);                        }
 256                 else if (method == "pintail")                   {               chimera = new Pintail(fastafile, templatefile, outputDir);      }
 257                 else if (method == "ccode")                             {               chimera = new Ccode(fastafile, templatefile);                           }
 258                 else if (method == "chimeracheck")              {               chimera = new ChimeraCheckRDP(fastafile, templatefile, outputDir);      }
 259                 else if (method == "chimeraslayer")             {               chimera = new ChimeraSlayer(fastafile, templatefile);           }
 260                 else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
 261
 262                 //set user options
 263                 if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
 264
 265                 //saves time to avoid generating it
 266                 chimera->setCons(consfile);
 267
 268                 //saves time to avoid generating it
 269                 chimera->setQuantiles(quanfile);
 270
 271                 chimera->setMask(maskfile);
 272                 chimera->setFilter(filter);
 273                 chimera->setCorrection(correction);
 274                 chimera->setProcessors(processors);
 275                 chimera->setWindow(window);
 276                 chimera->setIncrement(increment);
 277                 chimera->setNumWanted(numwanted);
 278                 chimera->setKmerSize(ksize);
 279                 chimera->setSVG(svg);
 280                 chimera->setName(namefile);
 281                 chimera->setMatch(match);
 282                 chimera->setMisMatch(mismatch);
 283                 chimera->setDivR(divR);
 284                 chimera->setParents(parents);
 285                 chimera->setMinSim(minSimilarity);
 286                 chimera->setIters(iters);
 287
 288
 289                 //find chimeras
 290                 int error = chimera->getChimeras();
 291
 292                 //there was a problem
 293                 if (error == 1) {  return 0;  }
 294
 295                 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".chimeras";
 296                 ofstream out;
 297                 openOutputFile(outputFileName, out);
 298
 299                 //print results
 300                 chimera->print(out);
 301
 302                 out.close();
 303
 304                 delete chimera;
 305
 306                 return 0;
 307
 308         }
 309         catch(exception& e) {
 310                 errorOut(e, "ChimeraSeqsCommand", "execute");
 311                 exit(1);
 312         }
 313 }
 314 /**************************************************************************************************/
 315