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/*
* deconvolute.cpp
* Mothur
*
* Created by Sarah Westcott on 1/21/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "uniqueseqscommand.h"
#include "sequence.hpp"
//**********************************************************************************************************************
vector<string> UniqueSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pformat("format", "Multiple", "count-name", "count", "", "", "","",false,false, true); parameters.push_back(pformat);
CommandParameter poutput("output", "Multiple", "count-name", "count", "", "", "","",false,false, true); parameters.push_back(poutput);
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["name"] = tempOutNames;
outputTypes["count"] = 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, "UniqueSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string UniqueSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The unique.seqs command reads a fastafile and creates a name or count file.\n";
helpString += "The unique.seqs command parameters are fasta, name, count and format. fasta is required, unless there is a valid current fasta file.\n";
helpString += "The name parameter is used to provide an existing name file associated with the fasta file. \n";
helpString += "The count parameter is used to provide an existing count file associated with the fasta file. \n";
helpString += "The format parameter is used to indicate what type of file you want outputted. Choices are name and count, default=count unless name file used then default=name.\n";
helpString += "The unique.seqs command should be in the following format: \n";
helpString += "unique.seqs(fasta=yourFastaFile) \n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string UniqueSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],unique,[extension]"; }
else if (type == "name") { pattern = "[filename],names-[filename],[tag],names"; }
else if (type == "count") { pattern = "[filename],count_table-[filename],[tag],count_table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "getOutputPattern");
exit(1);
}
}
/**************************************************************************************/
UniqueSeqsCommand::UniqueSeqsCommand(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); }
if (outputdir == ""){ outputdir += util.hasPath(fastafile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found"){ namefile = ""; }
else { current->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a unique.seqs command you must enter ONLY ONE of the following: count or name.\n"); abort = true; }
//allow format parameter to have two names - format or output
format = validParameter.valid(parameters, "format");
if(format == "not found"){
format = validParameter.valid(parameters, "output");
if(format == "not found"){
if (namefile != "") { format = "name"; }
else { format = "count"; }
}
}
if ((format != "name") && (format != "count")) {
m->mothurOut(format + " is not a valid format option. Options are count or name.");
if (countfile == "") { m->mothurOut("I will use count.\n"); format = "count"; }
else { m->mothurOut("I will use count.\n"); format = "count"; }
}
}
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "UniqueSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
int UniqueSeqsCommand::execute() {
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (countfile != "") { processCount(countfile); }
else if (namefile != "") { processName(namefile); }
else { //no existing duplicate data
if (format == "count") { processCount(""); }
else { processName(""); }
}
if (m->getControl_pressed()) { return 0; }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } 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("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setNameFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************/
string UniqueSeqsCommand::processCount(string countfile) { //countfile can be blank, indicating no countfile provided
try {
if (format == "name") {
if (countfile == "") { return (processName("")); }
else {
CountTable ct; ct.readTable(countfile, true, false);
map<string, int> nameMap = ct.getNameMap();
string newNamesFile = createNewNameFile(countfile, nameMap);
return (processName(newNamesFile));
}
}
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string outCountFile = getOutputFileName("count", variables);
variables["[extension]"] = util.getExtension(fastafile);
string outFastaFile = getOutputFileName("fasta", variables);
CountTable ct; CountTable newCt;
if (countfile != "") {
ct.readTable(countfile, true, false);
if (countfile == outCountFile){
//prepare filenames and open files
map<string, string> mvariables;
mvariables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
mvariables["[tag]"] = "unique";
outCountFile = getOutputFileName("count", mvariables);
}
newCt.copy(&ct);
}
if (m->getControl_pressed()) { return 0; }
ifstream in; util.openInputFile(fastafile, in);
ofstream outFasta; util.openOutputFile(outFastaFile, outFasta);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
map<string, string> sequenceStrings; //sequenceString -> list of names. "atgc...." -> seq1,seq2,seq3.
map<string, string>::iterator itStrings;
set<string> nameInFastaFile; //for sanity checking
set<string>::iterator itname;
vector<string> nameFileOrder;
int count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
Sequence seq(in); gobble(in);
if (seq.getName() != "") { //not end of file
//sanity checks
itname = nameInFastaFile.find(seq.getName());
if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName()); }
else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct.\n"); }
itStrings = sequenceStrings.find(seq.getAligned());
string seqName = seq.getName();
int numCurrentReps = 0;
if (itStrings == sequenceStrings.end()) { //this is a new unique sequence
seq.printSequence(outFasta); //output to unique fasta file
sequenceStrings[seq.getAligned()] = seqName; nameFileOrder.push_back(seq.getAligned());
if (countfile != "") { numCurrentReps = ct.getNumSeqs(seqName); } //checks to make sure seq is in table
else { newCt.push_back(seqName); }
}else { //this is a dup
if (countfile != "") {
numCurrentReps = newCt.getNumSeqs(seq.getName()); //checks to make sure seq is in table
if (numCurrentReps != 0) { //its in the table
newCt.mergeCounts(itStrings->second, seq.getName()); //merges counts and saves in uniques name
}
}else {
numCurrentReps = newCt.getNumSeqs(itStrings->second);
newCt.setNumSeqs(itStrings->second, numCurrentReps+1);
}
}
count++;
}
if(count % 1000 == 0) { m->mothurOutJustToScreen(toString(count) + "\t" + toString(sequenceStrings.size()) + "\n"); }
}
if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
in.close(); outFasta.close();
if (m->getControl_pressed()) { util.mothurRemove(outFastaFile); }
//print new names file
ofstream outCount; util.openOutputFile(outCountFile, outCount); outputTypes["count"].push_back(outCountFile); outputNames.push_back(outCountFile);
newCt.printCompressedHeaders(outCount);
for (int i = 0; i < nameFileOrder.size(); i++) {
if (m->getControl_pressed()) { break; }
itStrings = sequenceStrings.find(nameFileOrder[i]);
if (itStrings != sequenceStrings.end()) {
newCt.printCompressedSeq(outCount, itStrings->second);
}else{ m->mothurOut("[ERROR]: mismatch in namefile print.\n"); m->setControl_pressed(true); }
}
outCount.close();
if (m->getControl_pressed()) { util.mothurRemove(outFastaFile); util.mothurRemove(outCountFile); outputTypes.clear(); outputNames.clear(); }
return outFastaFile;
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "processCount");
exit(1);
}
}
/**************************************************************************************/
string UniqueSeqsCommand::processName(string namefile) { //namefile can be blank, indicating no namefile provided
try {
if (format == "count") { //if user want to convert the count file to a names file, do that first
if (namefile == "") { return (processCount("")); }
else {
//convert name to count
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(namefile));
string newCountFile = getOutputFileName("count", variables);
CountTable ct; ct.createTable(namefile, "", nullVector);
ct.printCompressedTable(newCountFile);
return (processCount(newCountFile));
}
}
//assumes output is name and namefile is given
//prepare filenames
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string outNameFile = getOutputFileName("name", variables);
variables["[extension]"] = util.getExtension(fastafile);
string outFastaFile = getOutputFileName("fasta", variables);
//check for name overwrite
if (namefile == outNameFile){
map<string, string> mvariables;
mvariables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
mvariables["[tag]"] = "unique";
outNameFile = getOutputFileName("name", mvariables);
}
map<string, string> nameMap; map<string, string>::iterator itNames;
if (namefile != "") { util.readNames(namefile, nameMap); } //add existing duplicates
//bail if error reading namefile
if (m->getControl_pressed()) { return ""; }
//open files
ifstream in; util.openInputFile(fastafile, in);
ofstream outFasta; util.openOutputFile(outFastaFile, outFasta);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
map<string, string> sequenceStrings; //sequenceString -> list of names. "atgc...." -> seq1,seq2,seq3.
map<string, string>::iterator itStrings;
set<string> nameInFastaFile; //for sanity checking
set<string>::iterator itname;
vector<string> nameFileOrder;
int count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
Sequence seq(in); gobble(in);
if (seq.getName() != "") { //not end of file
//sanity checks
itname = nameInFastaFile.find(seq.getName());
if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName()); }
else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct.\n"); }
string key = seq.getName();
if (namefile != "") {
itNames = nameMap.find(seq.getName());
if (itNames == nameMap.end()) { //namefile and fastafile do not match
m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct.\n");
}else { key = itNames->second; }
}
itStrings = sequenceStrings.find(seq.getAligned());
if (itStrings == sequenceStrings.end()) { //this is a new unique sequence
seq.printSequence(outFasta); //output to unique fasta file
//add new unique sequence to seqStrings
sequenceStrings[seq.getAligned()] = key; nameFileOrder.push_back(seq.getAligned());
}else { //this is a dup
sequenceStrings[seq.getAligned()] += "," + key;
}
count++;
}
if(count % 1000 == 0) { m->mothurOutJustToScreen(toString(count) + "\t" + toString(sequenceStrings.size()) + "\n"); }
}
if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
in.close(); outFasta.close();
if (m->getControl_pressed()) { return outFastaFile; }
ofstream outNames; util.openOutputFile(outNameFile, outNames);
outputNames.push_back(outNameFile); outputTypes["name"].push_back(outNameFile);
for (int i = 0; i < nameFileOrder.size(); i++) {
if (m->getControl_pressed()) { break; }
itStrings = sequenceStrings.find(nameFileOrder[i]);
if (itStrings != sequenceStrings.end()) {
//get rep name
int pos = (itStrings->second).find_first_of(',');
if (pos == string::npos) { // only reps itself
outNames << itStrings->second << '\t' << itStrings->second << endl;
}else {
outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
}
}else{ m->mothurOut("[ERROR]: mismatch in namefile print.\n"); m->setControl_pressed(true); }
}
outNames.close();
if (m->getControl_pressed()) { util.mothurRemove(outFastaFile); util.mothurRemove(outNameFile); outputTypes.clear(); outputNames.clear(); }
return outFastaFile;
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "processName");
exit(1);
}
}
/**************************************************************************************/
string UniqueSeqsCommand::createNewNameFile(string countfile, map<string, int> nameMap) { //namefile can be blank, indicating no namefile provided
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(countfile));
string outNameFile = getOutputFileName("name", variables);
ofstream out; util.openOutputFile(outNameFile, out);
for (map<string, int>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
string seqName = it->first;
string expandedName = seqName;
int numSeqs = it->second;
for (int i = 1; i < numSeqs; i++) { expandedName += "," + seqName + "_" + toString(i); }
out << seqName << '\t' << expandedName << endl;
}
out.close();
return outNameFile;
}
catch(exception& e) {
m->errorOut(e, "UniqueSeqsCommand", "createNewNameFile");
exit(1);
}
}
/**************************************************************************************/
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