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/*
* chimeracheckcommand.cpp
* Mothur
*
* Created by westcott on 3/31/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "chimeracheckcommand.h"
//**********************************************************************************************************************
vector<string> ChimeraCheckCommand::setParameters(){
try {
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
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;
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, "ChimeraCheckCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ChimeraCheckCommand::getHelpString(){
try {
string helpString = "";
helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
helpString += "This command was created using the algorithms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\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 increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n";
helpString += "The ksize parameter allows you to input kmersize, default is 7. \n";
helpString += "The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n";
helpString += "The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n";
helpString += "The chimera.check command should be in the following format: \n";
helpString += "chimera.check(fasta=yourFastaFile, reference=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n";
helpString += "Example: chimera.check(fasta=AD.fasta, reference=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string ChimeraCheckCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "chimera") { pattern = "[filename],chimeracheck.chimeras"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern");
exit(1);
}
}
//***************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(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); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
//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; }
string temp = validParameter.valid(parameters, "ksize"); if (temp == "not found") { temp = "7"; }
util.mothurConvert(temp, ksize);
temp = validParameter.valid(parameters, "svg"); if (temp == "not found") { temp = "F"; }
svg = util.isTrue(temp);
if (namefile != "") { svg = true; }
temp = validParameter.valid(parameters, "increment"); if (temp == "not found") { temp = "10"; }
util.mothurConvert(temp, increment);
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
exit(1);
}
}
//***************************************************************************************************************
int ChimeraCheckCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
m->mothurOut("Checking sequences from " + fastafile + " ...\n" );
long start = time(nullptr);
numSeqs = checkChimeras();
if (m->getControl_pressed()) { for (int j = 0; j < outputNames.size(); j++) { util.mothurRemove(outputNames[j]); } outputTypes.clear(); return 0; }
m->mothurOut("\nThis method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values.\n");
m->mothurOut("\nIt took " + toString(time(nullptr) - start) + " secs to check " + toString(numSeqs) + " sequences.\n\n");
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, "ChimeraCheckCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int ChimeraCheckCommand::checkChimeras(){
try {
if (outputdir == "") { outputdir = util.hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string outputFileName = getOutputFileName("chimera", variables);
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
MothurChimera* chimera = new ChimeraCheckRDP(fastafile, templatefile, namefile, svg, increment, ksize, outputdir);
ofstream out;
util.openOutputFile(outputFileName, out);
ofstream out2;
ifstream inFASTA;
util.openInputFile(fastafile, inFASTA);
int count = 0;
while (!inFASTA.eof()) {
if (m->getControl_pressed()) { break; }
Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
//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();
inFASTA.close();
delete chimera;
return count;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckCommand", "checkChimeras");
exit(1);
}
}
/**************************************************************************************************/
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