+++ /dev/null
-/*
- * deconvolute.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 1/21/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "deconvolutecommand.h"
-#include "sequence.hpp"
-
-//**********************************************************************************************************************
-vector<string> DeconvoluteCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- 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 namesfile.\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);
- }
-}
-//**********************************************************************************************************************
-DeconvoluteCommand::DeconvoluteCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = 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;
-
- //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; }
- }
- }
-
-
- //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); }
-
- 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 {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //prepare filenames and open files
- string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
- string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
-
- map<string, string> nameMap;
- map<string, string>::iterator itNames;
- if (oldNameMapFName != "") {
- m->readNames(oldNameMapFName, nameMap);
- if (oldNameMapFName == outNameFile){ outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique.names"; }
- }
-
- 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 { 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 { 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;
- m->openOutputFile(outNameFile, outNames);
-
- for (int i = 0; i < nameFileOrder.size(); i++) {
- //for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); m->mothurRemove(outNameFile); return 0; }
-
- 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."); m->mothurOutEndLine(); m->control_pressed = true; }
- }
- outNames.close();
-
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); m->mothurRemove(outNameFile); return 0; }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outFastaFile); m->mothurOutEndLine();
- m->mothurOut(outNameFile); m->mothurOutEndLine();
- outputNames.push_back(outFastaFile); outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile); outputTypes["name"].push_back(outNameFile);
- 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); }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "DeconvoluteCommand", "execute");
- exit(1);
- }
-}
-/**************************************************************************************/
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