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/*
* chimeraccodecommand.cpp
* Mothur
*
* Created by westcott on 3/30/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "chimeraccodecommand.h"
#include "ccode.h"
#include "removeseqscommand.h"
//**********************************************************************************************************************
vector<string> ChimeraCcodeCommand::setParameters(){
try {
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-mapinfo-accnos",false,true,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 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["mapinfo"] = 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, "ChimeraCcodeCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ChimeraCcodeCommand::getHelpString(){
try {
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 algorithms 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 += "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 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 removechimeras parameter allows you to indicate you would like to automatically remove the sequences that are flagged as chimeric. Default=t.\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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string ChimeraCcodeCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "chimera") { pattern = "[filename],[tag],ccode.chimeras-[filename],ccode.chimeras"; }
else if (type == "accnos") { pattern = "[filename],[tag],ccode.accnos-[filename],ccode.accnos"; }
else if (type == "fasta") { pattern = "[filename],ccode.fasta-[filename],[tag],ccode.fasta"; }
else if (type == "mapinfo") { pattern = "[filename],mapinfo"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "getOutputPattern");
exit(1);
}
}
//***************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(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); }
maskfile = validParameter.validPath(parameters, "mask");
if (maskfile == "not found") { maskfile = ""; }
else if (maskfile != "default") {
ifstream in;
bool ableToOpen = util.openInputFile(maskfile, in);
if (!ableToOpen) { abort = true; }
in.close();
}else if (maskfile == "default") { m->mothurOut("[NOTE]: Using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.\n"); }
string temp;
temp = validParameter.valid(parameters, "filter"); if (temp == "not found") { temp = "F"; }
filter = util.isTrue(temp);
temp = validParameter.valid(parameters, "window"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, window);
temp = validParameter.valid(parameters, "numwanted"); if (temp == "not found") { temp = "20"; }
util.mothurConvert(temp, numwanted);
temp = validParameter.valid(parameters, "removechimeras"); if (temp == "not found") { temp = "t"; }
removeChimeras = util.isTrue(temp);
//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");
if (templatefile == "not found") { m->mothurOut("[ERROR]: The reference parameter is a required, aborting.\n"); abort = true;
}else if (templatefile == "not open") { abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
exit(1);
}
}
//***************************************************************************************************************
int ChimeraCcodeCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
m->mothurOut("Checking sequences from " + fastafile + " ...\n" );
long start = time(nullptr);
if (outputdir == "") { outputdir = util.hasPath(fastafile); }
string outputFileName, accnosFileName;
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string mapInfo = getOutputFileName("mapinfo", variables);
if (maskfile != "") { variables["[tag]"] = maskfile; }
outputFileName = getOutputFileName("chimera", variables);
accnosFileName = getOutputFileName("accnos", variables);
if (m->getControl_pressed()) { return 0; }
numSeqs = driver(outputFileName, fastafile, accnosFileName);
if (m->getControl_pressed()) { util.mothurRemove(outputFileName); util.mothurRemove(accnosFileName); return 0; }
ofstream outHeader;
string tempHeader = outputdir + util.getRootName(util.getSimpleName(fastafile)) + maskfile + "ccode.chimeras.tempHeader";
util.openOutputFile(tempHeader, outHeader); outHeader << "For full window mapping info refer to " << mapInfo << endl << endl; outHeader.close();
util.appendFiles(outputFileName, tempHeader);
util.mothurRemove(outputFileName);
rename(tempHeader.c_str(), outputFileName.c_str());
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
outputNames.push_back(mapInfo); outputTypes["mapinfo"].push_back(mapInfo);
outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
m->mothurOut("\nIt took " + toString(time(nullptr) - start) + " secs to check " + toString(numSeqs) + " sequences.\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]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int ChimeraCcodeCommand::driver(string outputFName, string filename, string accnos){
try {
MothurChimera* chimera = new Ccode(fastafile, templatefile, filter, maskfile, window, numwanted, outputdir);
//is your template aligned?
if (chimera->getUnaligned()) { m->mothurOut("[ERROR]: Your reference sequences are unaligned, please correct.\n"); delete chimera; return 0; }
templateSeqsLength = chimera->getLength();
ofstream out;
util.openOutputFile(outputFName, out);
ofstream out2;
util.openOutputFile(accnos, out2);
ifstream inFASTA;
util.openInputFile(filename, inFASTA);
int count = 0;
while (!inFASTA.eof()) {
if (m->getControl_pressed()) { count = 1; break; }
Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
if (candidateSeq->getAligned().length() != templateSeqsLength) {
m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping.\n");
}else{
//find chimeras
chimera->getChimeras(candidateSeq);
if (m->getControl_pressed()) { delete candidateSeq; return 1; }
//print results
chimera->print(out, out2);
}
count++;
}
delete candidateSeq;
//report progress
if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
}
//report progress
if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
out.close();
out2.close();
inFASTA.close();
delete chimera;
return count;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "driver");
exit(1);
}
}
//**********************************************************************************************************************
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