#include "chimerapintailcommand.h"
#include "pintail.h"
+
//**********************************************************************************************************************
vector<string> ChimeraPintailCommand::setParameters(){
try {
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);
-
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
#ifdef USE_MPI
helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
#endif
+ helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=300. \n";
helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=25.\n";
helpString += "The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n";
ChimeraPintailCommand::ChimeraPintailCommand(string option) {
try {
abort = false; calledHelp = false;
+ rdb = ReferenceDB::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
convert(temp, increment);
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ rdb->save = save;
+ if (save) { //clear out old references
+ rdb->clearMemory();
+ }
+
+ //this has to go after save so that if the user sets save=t and provides no reference we abort
+ templatefile = validParameter.validFile(parameters, "reference", true);
+ if (templatefile == "not found") {
+ //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templatefile = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (templatefile == "not open") { abort = true; }
+ else { if (save) { rdb->setSavedReference(templatefile); } }
+
+
maskfile = validParameter.validFile(parameters, "mask", false);
if (maskfile == "not found") { maskfile = ""; }
else if (maskfile != "default") {
//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, "reference", true);
- if (templatefile == "not open") { abort = true; }
- else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true; }
-
consfile = validParameter.validFile(parameters, "conservation", true);
if (consfile == "not open") { abort = true; }
else if (consfile == "not found") {
if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
//check for quantile to save the time
+ string baseName = templatefile;
+ if (templatefile == "saved") { baseName = rdb->getSavedReference(); }
+
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
- tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
- tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
- tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
- tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest(tempQuan.c_str());
string tryPath = m->getDefaultPath();
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
- tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
- tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
- tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
- tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest2(tempQuan.c_str());