#include "bellerophon.h"
//**********************************************************************************************************************
-vector<string> ChimeraBellerophonCommand::getValidParameters(){
+vector<string> ChimeraBellerophonCommand::setParameters(){
try {
- string AlignArray[] = {"fasta","filter","correction","processors","window","increment","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraBellerophonCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> ChimeraBellerophonCommand::getRequiredParameters(){
- try {
- string AlignArray[] = {"fasta"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ 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 pcorrection("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
+ CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
+ 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, "ChimeraBellerophonCommand", "getRequiredParameters");
+ m->errorOut(e, "ChimeraBellerophonCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ChimeraBellerophonCommand::getRequiredFiles(){
+string ChimeraBellerophonCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ helpString += "The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n";
+ helpString += "The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required, unless you have a valid current file.\n";
+ helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+ helpString += "The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n";
+ helpString += "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, default=true.\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 window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n";
+ helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n";
+ helpString += "chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n";
+ helpString += "Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \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, "ChimeraBellerophonCommand", "getRequiredFiles");
+ m->errorOut(e, "ChimeraBellerophonCommand", "getHelpString");
exit(1);
}
}
ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta","filter","correction","processors","window","increment","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 = ""; }
fastafile = validParameter.validFile(parameters, "fasta", false);
- if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon 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
temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
correction = 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 ChimeraBellerophonCommand::help(){
- try {
- m->mothurOut("The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n");
- m->mothurOut("The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required.\n");
- m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n");
- m->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, default=true.\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 window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n");
- m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n");
- m->mothurOut("chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n");
- m->mothurOut("Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \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, "ChimeraBellerophonCommand", "help");
- exit(1);
- }
-}
-
//***************************************************************************************************************
-
-ChimeraBellerophonCommand::~ChimeraBellerophonCommand(){ /* do nothing */ }
-
-//***************************************************************************************************************
-
int ChimeraBellerophonCommand::execute(){
try{
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