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/*
* deuniqueseqscommand.cpp
* Mothur
*
* Created by westcott on 10/19/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "deuniqueseqscommand.h"
#include "sequence.hpp"
#include "counttable.h"
//**********************************************************************************************************************
vector<string> DeUniqueSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "namecount", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "namecount", "none","group",false,false,true); parameters.push_back(pcount);
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["fasta"] = tempOutNames;
outputTypes["group"] = 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, "DeUniqueSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string DeUniqueSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The deunique.seqs command reads a fastafile and namefile or countfile, and creates a fastafile containing all the sequences. It you provide a count file with group information a group file is also created.\n";
helpString += "The deunique.seqs command parameters are fasta, name and count. Fasta is required and you must provide either a name or count file.\n";
helpString += "The deunique.seqs command should be in the following format: \n";
helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n";
helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n";
;
return helpString;
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string DeUniqueSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],redundant.fasta"; }
else if (type == "group") { pattern = "[filename],redundant.groups"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "getOutputPattern");
exit(1);
}
}
/**************************************************************************************/
DeUniqueSeqsCommand::DeUniqueSeqsCommand(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 open") { abort = true; }
else if (fastaFile == "not found") {
fastaFile = current->getFastaFile();
if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required.\n"); abort = true; }
}else { current->setFastaFile(fastaFile); }
nameFile = validParameter.validFile(parameters, "name");
if (nameFile == "not open") { abort = true; }
else if (nameFile == "not found"){ nameFile = ""; }
else { current->setNameFile(nameFile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if ((countfile != "") && (nameFile != "")) { m->mothurOut("When executing a deunique.seqs command you must enter ONLY ONE of the following: count or name.\n"); abort = true; }
if ((countfile == "") && (nameFile == "")) { //look for currents
nameFile = current->getNameFile();
if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter.\n"); }
else {
countfile = current->getCountFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current name or count files one is required.\n"); abort = true; }
}
}
}
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "DeUniqueSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
int DeUniqueSeqsCommand::execute() {
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
//prepare filenames and open files
ofstream out;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastaFile); }
string outFastaFile = thisOutputDir + util.getRootName(util.getSimpleName(fastaFile));
map<string, string> variables;
variables["[filename]"] = outFastaFile;
outFastaFile = getOutputFileName("fasta", variables);
util.openOutputFile(outFastaFile, out);
map<string, string> nameMap;
CountTable ct;
ofstream outGroup;
string outGroupFile;
vector<string> groups;
if (nameFile != "") { util.readNames(nameFile, nameMap); }
else {
ct.readTable(countfile, true, false);
if (ct.hasGroupInfo()) {
thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(countfile); }
outGroupFile = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
variables["[filename]"] = outGroupFile;
outGroupFile = getOutputFileName("group", variables);
util.openOutputFile(outGroupFile, outGroup);
groups = ct.getNamesOfGroups();
}
}
if (m->getControl_pressed()) { out.close(); outputTypes.clear(); util.mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { outGroup.close(); util.mothurRemove(outGroupFile); } } return 0; }
ifstream in; util.openInputFile(fastaFile, in);
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); out.close(); outputTypes.clear(); util.mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { outGroup.close(); util.mothurRemove(outGroupFile); } } return 0; }
Sequence seq(in); gobble(in);
if (seq.getName() != "") {
if (nameFile != "") {
//look for sequence name in nameMap
map<string, string>::iterator it = nameMap.find(seq.getName());
if (it == nameMap.end()) { m->mothurOut("[ERROR]: Your namefile does not contain " + seq.getName() + ", aborting.\n"); m->setControl_pressed(true); }
else {
vector<string> names;
util.splitAtComma(it->second, names);
//output sequences
for (int i = 0; i < names.size(); i++) {
out << ">" << names[i] << endl;
out << seq.getAligned() << endl;
}
//remove seq from name map so we can check for seqs in namefile not in fastafile later
nameMap.erase(it);
}
}else {
if (ct.hasGroupInfo()) {
vector<int> groupCounts = ct.getGroupCounts(seq.getName());
int count = 1;
for (int i = 0; i < groups.size(); i++) {
for (int j = 0; j < groupCounts[i]; j++) {
outGroup << seq.getName()+"_"+toString(count) << '\t' << groups[i] << endl; count++;
}
}
}
int numReps = ct.getNumSeqs(seq.getName()); //will report error and set m->control_pressed if not found
for (int i = 0; i < numReps; i++) {
out << ">" << seq.getName()+"_"+toString(i+1) << endl;
out << seq.getAligned() << endl;
}
}
}
}
in.close();
out.close();
if (countfile != "") { if (ct.hasGroupInfo()) { outGroup.close(); } }
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { util.mothurRemove(outGroupFile); } }return 0; }
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
if (countfile != "") { if (ct.hasGroupInfo()) { outputNames.push_back(outGroupFile); outputTypes["group"].push_back(outGroupFile); } }
m->mothurOut("\nOutput File Names: \n");
for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************/
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