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/*
* chimerabellerophoncommand.cpp
* Mothur
*
* Created by westcott on 4/1/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "chimerabellerophoncommand.h"
#include "bellerophon.h"
#include "removeseqscommand.h"
//**********************************************************************************************************************
vector<string> ChimeraBellerophonCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
CommandParameter pcorrection("correction", "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 premovechimeras("removechimeras", "Boolean", "", "t", "", "", "","fasta",false,false); parameters.push_back(premovechimeras);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
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", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ChimeraBellerophonCommand::getHelpString(){
try {
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 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 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 += "The removechimeras parameter allows you to indicate you would like to automatically remove the sequences that are flagged as chimeric. Default=t.\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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "ChimeraBellerophonCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string ChimeraBellerophonCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "chimera") { pattern = "[filename],bellerophon.chimeras"; }
else if (type == "accnos") { pattern = "[filename],bellerophon.accnos"; }
else if (type == "fasta") { pattern = "[filename],bellerophon.fasta"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ChimeraBellerophonCommand", "getOutputPattern");
exit(1);
}
}
//***************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) : Command() {
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fasta file and the fasta parameter is required.\n"); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
else { current->setFastaFile(fastafile); }
string temp;
temp = validParameter.valid(parameters, "filter"); if (temp == "not found") { temp = "F"; }
filter = util.isTrue(temp);
temp = validParameter.valid(parameters, "correction"); if (temp == "not found") { temp = "T"; }
correction = util.isTrue(temp);
temp = validParameter.valid(parameters, "window"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, window);
temp = validParameter.valid(parameters, "increment"); if (temp == "not found") { temp = "25"; }
util.mothurConvert(temp, increment);
temp = validParameter.valid(parameters, "removechimeras"); if (temp == "not found") { temp = "t"; }
removeChimeras = util.isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
exit(1);
}
}
//***************************************************************************************************************
int ChimeraBellerophonCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
m->mothurOut("Checking sequences from " + fastafile + " ...\n" );
long start = time(nullptr);
MothurChimera* chimera = new Bellerophon(fastafile, filter, correction, window, increment, outputdir);
chimera->getChimeras();
if (m->getControl_pressed()) { delete chimera; return 0; }
if (outputdir == "") { outputdir = util.hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string outputFileName = getOutputFileName("chimera", variables);
string accnosFileName = getOutputFileName("accnos", variables);
ofstream out; util.openOutputFile(outputFileName, out); outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
ofstream out2; util.openOutputFile(accnosFileName, out2); outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
//print results
numSeqs = chimera->print(out, out2, "");
out.close(); out2.close();
delete chimera;
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
m->mothurOut("\nIt took " + toString(time(nullptr) - start) + " secs to check " + toString(numSeqs) + " sequences.\n\n");
if (removeChimeras) {
if (!util.isBlank(accnosFileName)) {
m->mothurOut("\nRemoving chimeras from your input files:\n");
string inputString = "fasta=" + fastafile + ", accnos=" + accnosFileName;
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: remove.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* removeCommand = new RemoveSeqsCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string currentName = getOutputFileName("fasta", variables);
util.renameFile(filenames["fasta"][0], currentName);
util.mothurRemove(filenames["fasta"][0]);
outputNames.push_back(currentName); outputTypes["fasta"].push_back(currentName);
}else { m->mothurOut("\nNo chimeras found, skipping remove.seqs.\n"); }
}
//set accnos file as new current accnosfile
string currentName = "";
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setAccnosFile(currentName); }
}
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraBellerophonCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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