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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 "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 (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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