#include "chimeraccodecommand.h"
#include "ccode.h"
-
//**********************************************************************************************************************
-vector<string> ChimeraCcodeCommand::getValidParameters(){
+vector<string> ChimeraCcodeCommand::setParameters(){
try {
- string AlignArray[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" };
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
+ CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "",false,false); parameters.push_back(pnumwanted);
+ CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "getValidParameters");
+ m->errorOut(e, "ChimeraCcodeCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ChimeraCcodeCommand::ChimeraCcodeCommand(){
+string ChimeraCcodeCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["chimera"] = tempOutNames;
- outputTypes["mapinfo"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> ChimeraCcodeCommand::getRequiredParameters(){
- try {
- string AlignArray[] = {"template","fasta"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
+ helpString += "This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
+ helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
+ helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+ helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \n";
+ helpString += "The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+#ifdef USE_MPI
+ helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
+#endif
+ helpString += "The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n";
+ helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n";
+ helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n";
+ helpString += "The chimera.ccode command should be in the following format: \n";
+ helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n";
+ helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "getRequiredParameters");
+ m->errorOut(e, "ChimeraCcodeCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ChimeraCcodeCommand::getRequiredFiles(){
+ChimeraCcodeCommand::ChimeraCcodeCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["mapinfo"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "getRequiredFiles");
+ m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
- it = parameters.find("template");
+ it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["template"] = inputDir + it->second; }
+ if (path == "") { parameters["reference"] = inputDir + it->second; }
}
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", false);
- if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; }
- else {
+ if (fastafile == "not found") { //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else {
m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
- templatefile = validParameter.validFile(parameters, "template", true);
+ templatefile = validParameter.validFile(parameters, "reference", true);
if (templatefile == "not open") { abort = true; }
- else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; }
+ else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; }
maskfile = validParameter.validFile(parameters, "mask", false);
if (maskfile == "not found") { maskfile = ""; }
temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
filter = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
convert(temp, processors);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ChimeraCcodeCommand::help(){
- try {
-
- m->mothurOut("The chimera.ccode command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
- m->mothurOut("This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n");
- m->mothurOut("The chimera.ccode command parameters are fasta, template, filter, mask, processors, window and numwanted.\n");
- m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
- m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
- m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
- m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
- #ifdef USE_MPI
- m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
- #endif
- m->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");
- m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n");
- m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
- m->mothurOut("The chimera.ccode command should be in the following format: \n");
- m->mothurOut("chimera.ccode(fasta=yourFastaFile, template=yourTemplate) \n");
- m->mothurOut("Example: chimera.ccode(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "help");
- exit(1);
- }
-}
-
//***************************************************************************************************************
-
-ChimeraCcodeCommand::~ChimeraCcodeCommand(){ /* do nothing */ }
-
-//***************************************************************************************************************
-
int ChimeraCcodeCommand::execute(){
try{
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