#include "chimeraslayercommand.h"
#include "chimeraslayer.h"
#include "deconvolutecommand.h"
+#include "referencedb.h"
//**********************************************************************************************************************
vector<string> ChimeraSlayerCommand::setParameters(){
CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
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;
helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, and realign.\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 += "The name parameter allows you to provide a name file, if you are using template=self. \n";
+ helpString += "The name parameter allows you to provide a name file, if you are using reference=self. \n";
helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n";
helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n";
+ 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 chimera.slayer command should be in the following format: \n";
helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
try {
abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
//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 = ""; }
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
+ 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();
+ }
string path;
it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
- if (it->second == "self") { templatefile = "self"; }
+ if (it->second == "self") {
+ templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
+ }
+ }
else {
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
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.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true; }
+ else 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 (save) { rdb->setSavedReference(templatefile); } }
+ }
+ }else if (hasName) { templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
}
- }else if (hasName) { templatefile = "self"; }
- else { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
+ }
+ else {
+ 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();
+ templatefile = ""; abort = true;
+ }
+ }
+
- string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- convert(temp, processors);
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
convert(temp, ksize);
convert(temp, numwanted);
if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
+
+ if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
}
}
catch(exception& e) {
int ChimeraSlayerCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
for (int s = 0; s < fastaFileNames.size(); s++) {
m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
projects / mothur.git / blobdiff