*/
#include "deconvolutecommand.h"
+#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::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 pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ 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, "DeconvoluteCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DeconvoluteCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The unique.seqs command reads a fastafile and creates a name or count file.\n";
+ helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n";
+ helpString += "If the sequence is unique the second column will just contain its name. \n";
+ helpString += "The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.\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, "DeconvoluteCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DeconvoluteCommand::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->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+DeconvoluteCommand::DeconvoluteCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+DeconvoluteCommand::DeconvoluteCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ inFastaName = validParameter.validFile(parameters, "fasta", true);
+ if (inFastaName == "not open") { abort = true; }
+ else if (inFastaName == "not found") {
+ inFastaName = m->getFastaFile();
+ if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(inFastaName); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
+ }
+
+ oldNameMapFName = validParameter.validFile(parameters, "name", true);
+ if (oldNameMapFName == "not open") { oldNameMapFName = ""; abort = true; }
+ else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; }
+ else { m->setNameFile(oldNameMapFName); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (oldNameMapFName != "")) { m->mothurOut("When executing a unique.seqs command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
+
+ if (countfile == "") {
+ if (oldNameMapFName == "") {
+ vector<string> files; files.push_back(inFastaName);
+ parser.getNameFile(files);
+ }
+ }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}
/**************************************************************************************/
int DeconvoluteCommand::execute() {
try {
- globaldata = GlobalData::getInstance();
-
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
//prepare filenames and open files
- filename = globaldata->getFastaFile();
- outputFileName = (getRootName(filename) + "names");
- outFastafile = (getRootName(filename) + "unique.fasta");
-
- openInputFile(filename, in);
- openOutputFile(outputFileName, out);
- openOutputFile(outFastafile, outFasta);
-
- //constructor reads in file and store internally
- fastamap = new FastaMap();
-
- //two columns separated by tabs sequence name and then sequence
- fastamap->readFastaFile(in);
-
- //print out new names file
- //file contains 2 columns separated by tabs. the first column is the groupname(name of first sequence found.
- //the second column is the list of names of identical sequences separated by ','.
- fastamap->print(out);
- fastamap->printCondensedFasta(outFasta);
-
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ string outNameFile = getOutputFileName("name", variables);
+ string outCountFile = getOutputFileName("count", variables);
+ variables["[extension]"] = m->getExtension(inFastaName);
+ string outFastaFile = getOutputFileName("fasta", variables);
+
+ map<string, string> nameMap;
+ map<string, string>::iterator itNames;
+ if (oldNameMapFName != "") {
+ m->readNames(oldNameMapFName, nameMap);
+ if (oldNameMapFName == outNameFile){
+ //prepare filenames and open files
+ map<string, string> mvariables;
+ mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ mvariables["[tag]"] = "unique";
+ outNameFile = getOutputFileName("name", mvariables);
+ }
+ }
+ CountTable ct;
+ if (countfile != "") {
+ ct.readTable(countfile, true, false);
+ if (countfile == outCountFile){
+ //prepare filenames and open files
+ map<string, string> mvariables;
+ mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ mvariables["[tag]"] = "unique";
+ outCountFile = getOutputFileName("count", mvariables); }
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ ifstream in;
+ m->openInputFile(inFastaName, in);
+
+ ofstream outFasta;
+ m->openOutputFile(outFastaFile, outFasta);
+
+ 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->control_pressed) { in.close(); outFasta.close(); m->mothurRemove(outFastaFile); return 0; }
+
+ Sequence seq(in);
+
+ if (seq.getName() != "") {
+
+ //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."); m->mothurOutEndLine(); }
+
+ itStrings = sequenceStrings.find(seq.getAligned());
+
+ if (itStrings == sequenceStrings.end()) { //this is a new unique sequence
+ //output to unique fasta file
+ seq.printSequence(outFasta);
+
+ if (oldNameMapFName != "") {
+ 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."); m->mothurOutEndLine();
+ }else {
+ sequenceStrings[seq.getAligned()] = itNames->second;
+ nameFileOrder.push_back(seq.getAligned());
+ }
+ }else if (countfile != "") {
+ ct.getNumSeqs(seq.getName()); //checks to make sure seq is in table
+ sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(seq.getAligned());
+ }else { sequenceStrings[seq.getAligned()] = seq.getName(); nameFileOrder.push_back(seq.getAligned()); }
+ }else { //this is a dup
+ if (oldNameMapFName != "") {
+ 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."); m->mothurOutEndLine();
+ }else {
+ sequenceStrings[seq.getAligned()] += "," + itNames->second;
+ }
+ }else if (countfile != "") {
+ int num = ct.getNumSeqs(seq.getName()); //checks to make sure seq is in table
+ if (num != 0) { //its in the table
+ ct.mergeCounts(itStrings->second, seq.getName()); //merges counts and saves in uniques name
+ }
+ }else { sequenceStrings[seq.getAligned()] += "," + seq.getName(); }
+ }
+
+ count++;
+ }
+
+ m->gobble(in);
+
+ if(count % 1000 == 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+ }
+
+ if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+
+ in.close();
+ outFasta.close();
+
+ if (m->control_pressed) { m->mothurRemove(outFastaFile); return 0; }
+
+ //print new names file
+ ofstream outNames;
+ if (countfile == "") { m->openOutputFile(outNameFile, outNames); outputNames.push_back(outNameFile); outputTypes["name"].push_back(outNameFile); }
+ else { m->openOutputFile(outCountFile, outNames); ct.printHeaders(outNames); outputTypes["count"].push_back(outCountFile); outputNames.push_back(outCountFile); }
+
+ for (int i = 0; i < nameFileOrder.size(); i++) {
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ itStrings = sequenceStrings.find(nameFileOrder[i]);
+
+ if (itStrings != sequenceStrings.end()) {
+ if (countfile == "") {
+ //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 { ct.printSeq(outNames, itStrings->second); }
+ }else{ m->mothurOut("[ERROR]: mismatch in namefile print."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+ outNames.close();
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "DeconvoluteCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff