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classifyseqscommand.cpp
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classifyseqscommand.cpp
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/*
* classifyseqscommand.cpp
* Mothur
*
* Created by westcott on 11/2/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "classifyseqscommand.h"
//**********************************************************************************************************************
vector<string> ClassifySeqsCommand::setParameters(){
try {
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptaxonomy);
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "","",false,true); parameters.push_back(pcutoff);
CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
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, "ClassifySeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ClassifySeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
helpString += "The classify.seqs command parameters are reference, fasta, name, group, count, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted, relabund and probs.\n";
helpString += "The reference, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
helpString += "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast, align and distance. The default is kmer.\n";
helpString += "The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n";
helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
helpString += "The method parameter allows you to specify classification method to use. Your options are: wang, knn and zap. The default is wang.\n";
helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n";
helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
#ifdef USE_MPI
helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
#endif
helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n";
helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n";
helpString += "The probs parameter shuts off the bootstrapping results for the wang and zap method. The default is true, meaning you want the bootstrapping to be shown.\n";
helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";
helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the wang method. The default is 100.\n";
//helpString += "The flip parameter allows you shut off mothur's The default is T.\n";
helpString += "The classify.seqs command should be in the following format: \n";
helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n";
helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n";
helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n";
helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string ClassifySeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "taxonomy") { pattern = "[filename],[tag],[tag2],taxonomy"; }
else if (type == "taxsummary") { pattern = "[filename],[tag],[tag2],tax.summary"; }
else if (type == "accnos") { pattern = "[filename],[tag],[tag2],flip.accnos"; }
else if (type == "matchdist") { pattern = "[filename],[tag],[tag2],match.dist"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
outputTypes["matchdist"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(string option) {
try {
abort = false; calledHelp = false;
rdb = ReferenceDB::getInstance(); hasName = false; hasCount=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("classify.seqs");
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["taxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
outputTypes["matchdist"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//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 = ""; }
//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("reference");
//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["reference"] = inputDir + it->second; }
}
it = parameters.find("taxonomy");
//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["taxonomy"] = inputDir + it->second; }
}
}
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " 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->splitAtDash(fastaFileName, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }
else {
m->splitAtDash(namefile, namefileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < namefileNames.size(); i++) {
bool ignore = false;
if (namefileNames[i] == "current") {
namefileNames[i] = m->getNameFile();
if (namefileNames[i] != "") { m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
namefileNames.erase(namefileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(namefileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { namefileNames[i] = inputDir + namefileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
namefileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
namefileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
//erase from file list
namefileNames.erase(namefileNames.begin()+i);
i--;
}else {
m->setNameFile(namefileNames[i]);
}
}
}
}
if (namefileNames.size() != 0) { hasName = true; }
if (namefile != "") {
if (namefileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a name file, you must have one for each fasta file."); m->mothurOutEndLine(); }
}
//check for required parameters
countfile = validParameter.validFile(parameters, "count", false);
if (countfile == "not found") {
countfile = "";
}else {
m->splitAtDash(countfile, countfileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < countfileNames.size(); i++) {
bool ignore = false;
if (countfileNames[i] == "current") {
countfileNames[i] = m->getCountTableFile();
if (countfileNames[i] != "") { m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
countfileNames.erase(countfileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(countfileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { countfileNames[i] = inputDir + countfileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
countfileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
countfileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
countfileNames.erase(countfileNames.begin()+i);
i--;
}else {
m->setCountTableFile(countfileNames[i]);
}
}
}
}
if (countfileNames.size() != 0) { hasCount = true; if (countfileNames.size() != fastaFileNames.size()) {m->mothurOut("If you provide a count file, you must have one for each fasta file."); m->mothurOutEndLine(); } }
//make sure there is at least one valid file left
if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
groupfile = validParameter.validFile(parameters, "group", false);
if (groupfile == "not found") { groupfile = ""; }
else {
m->splitAtDash(groupfile, groupfileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < groupfileNames.size(); i++) {
bool ignore = false;
if (groupfileNames[i] == "current") {
groupfileNames[i] = m->getGroupFile();
if (groupfileNames[i] != "") { m->mothurOut("Using " + groupfileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current group file, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
groupfileNames.erase(groupfileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(groupfileNames[i]);
cout << path << '\t' << inputDir << endl;
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
groupfileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
groupfileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
groupfileNames.erase(groupfileNames.begin()+i);
i--;
}else {
m->setGroupFile(groupfileNames[i]);
}
}
}
}
if (groupfile != "") {
if (groupfileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each fasta file."); m->mothurOutEndLine(); }
if (hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
}else {
for (int i = 0; i < fastaFileNames.size(); i++) { groupfileNames.push_back(""); }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
rdb->save = save;
if (save) { //clear out old references
rdb->clearMemory();
}
//this has to go after save so that if the user sets save=t and provides no reference we abort
templateFileName = validParameter.validFile(parameters, "reference", true);
if (templateFileName == "not found") {
//check for saved reference sequences
if (rdb->referenceSeqs.size() != 0) {
templateFileName = "saved";
}else {
m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the classify.seqs command.");
m->mothurOutEndLine();
abort = true;
}
}else if (templateFileName == "not open") { abort = true; }
else { if (save) { rdb->setSavedReference(templateFileName); } }
//this has to go after save so that if the user sets save=t and provides no reference we abort
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
if (taxonomyFileName == "not found") {
//check for saved reference sequences
if (rdb->wordGenusProb.size() != 0) {
taxonomyFileName = "saved";
}else {
m->mothurOut("[ERROR]: You don't have any saved taxonomy information and the taxonomy parameter is a required for the classify.seqs command.");
m->mothurOutEndLine();
abort = true;
}
}else if (taxonomyFileName == "not open") { abort = true; }
else { if (save) { rdb->setSavedTaxonomy(taxonomyFileName); } }
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "wang"; }
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){
temp = "8";
if (method == "zap") { temp = "7"; }
}
m->mothurConvert(temp, kmerSize);
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, misMatch);
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
m->mothurConvert(temp, gapOpen);
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, gapExtend);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found"){ temp = "10"; }
m->mothurConvert(temp, numWanted);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0"; }
m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
probs = m->isTrue(temp);
temp = validParameter.validFile(parameters, "relabund", false); if (temp == "not found"){ temp = "false"; }
relabund = m->isTrue(temp);
temp = validParameter.validFile(parameters, "shortcuts", false); if (temp == "not found"){ temp = "true"; }
writeShortcuts = m->isTrue(temp);
//temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "T"; }
//flip = m->isTrue(temp);
flip = true;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
m->mothurConvert(temp, iters);
if ((method == "wang") && (search != "kmer")) {
m->mothurOut("The wang method requires the kmer search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
if ((method == "zap") && ((search != "kmer") && (search != "align"))) {
m->mothurOut("The zap method requires the kmer or align search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
if (!abort) {
if (!hasCount) {
if (namefileNames.size() == 0){
if (fastaFileNames.size() != 0) {
vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
parser.getNameFile(files);
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
ClassifySeqsCommand::~ClassifySeqsCommand(){
if (abort == false) {
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
}
}
//**********************************************************************************************************************
int ClassifySeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputMethodTag = method;
if(method == "wang"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts); }
else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand()); }
else if(method == "zap"){
outputMethodTag = search + "_" + outputMethodTag;
if (search == "kmer") { classify = new KmerTree(templateFileName, taxonomyFileName, kmerSize, cutoff); }
else { classify = new AlignTree(templateFileName, taxonomyFileName, cutoff); }
}
else {
m->mothurOut(search + " is not a valid method option. I will run the command using wang.");
m->mothurOutEndLine();
classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);
}
if (m->control_pressed) { delete classify; return 0; }
for (int s = 0; s < fastaFileNames.size(); s++) {
m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
string baseTName = m->getSimpleName(taxonomyFileName);
if (taxonomyFileName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
//set rippedTaxName to
string RippedTaxName = "";
bool foundDot = false;
for (int i = baseTName.length()-1; i >= 0; i--) {
if (foundDot && (baseTName[i] != '.')) { RippedTaxName = baseTName[i] + RippedTaxName; }
else if (foundDot && (baseTName[i] == '.')) { break; }
else if (!foundDot && (baseTName[i] == '.')) { foundDot = true; }
}
//if (RippedTaxName != "") { RippedTaxName += "."; }
if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
variables["[tag]"] = RippedTaxName;
variables["[tag2]"] = outputMethodTag;
string newTaxonomyFile = getOutputFileName("taxonomy", variables);
string newaccnosFile = getOutputFileName("accnos", variables);
string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
string taxSummary = getOutputFileName("taxsummary", variables);
if ((method == "knn") && (search == "distance")) {
string DistName = getOutputFileName("matchdist", variables);
classify->setDistName(DistName); outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
}
outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile);
outputNames.push_back(taxSummary); outputTypes["taxsummary"].push_back(taxSummary);
int start = time(NULL);
int numFastaSeqs = 0;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long long> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_Comm_size(MPI_COMM_WORLD, &processors);
MPI_File inMPI;
MPI_File outMPINewTax;
MPI_File outMPITempTax;
MPI_File outMPIAcc;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
char outNewTax[1024];
strcpy(outNewTax, newTaxonomyFile.c_str());
char outTempTax[1024];
strcpy(outTempTax, tempTaxonomyFile.c_str());
char outAcc[1024];
strcpy(outAcc, newaccnosFile.c_str());
char inFileName[1024];
strcpy(inFileName, fastaFileNames[s].c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax);
MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax);
MPI_File_open(MPI_COMM_WORLD, outAcc, outMode, MPI_INFO_NULL, &outMPIAcc);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; }
if (pid == 0) { //you are the root process
MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
}
//figure out how many sequences you have to align
numSeqsPerProcessor = numFastaSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
for (int i = 1; i < processors; i++) {
int done;
MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
}
}else{ //you are a child process
MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numFastaSeqs+1);
MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = numFastaSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, outMPIAcc, MPIPos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; }
int done = 0;
MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
}
//close files
MPI_File_close(&inMPI);
MPI_File_close(&outMPINewTax);
MPI_File_close(&outMPITempTax);
MPI_File_close(&outMPIAcc);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastaFileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
#else
if (processors == 1) {
lines.push_back(new linePair(0, 1000));
}else {
positions = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs);
if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
}
}
#endif
if(processors == 1){
numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
}else{
numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, newaccnosFile, fastaFileNames[s]);
}
#endif
if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification. If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine();
outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
}else { m->mothurRemove(newaccnosFile); }
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
start = time(NULL);
#ifdef USE_MPI
if (pid == 0) { //this part does not need to be paralellized
if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush(); MPIReadNamesFile(namefileNames[s]); m->mothurOut(" Done."); m->mothurOutEndLine(); }
#else
//read namefile
if(namefile != "") {
m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
nameMap.clear(); //remove old names
m->readNames(namefileNames[s], nameMap);
m->mothurOut(" Done."); m->mothurOutEndLine();
}
#endif
string group = "";
GroupMap* groupMap = NULL;
CountTable* ct = NULL;
PhyloSummary* taxaSum;
if (hasCount) {
ct = new CountTable();
ct->readTable(countfileNames[s], true, false);
taxaSum = new PhyloSummary(taxonomyFileName, ct, relabund);
taxaSum->summarize(tempTaxonomyFile);
}else {
if (groupfile != "") { group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
taxaSum = new PhyloSummary(taxonomyFileName, groupMap, relabund);
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
if (namefile == "") { taxaSum->summarize(tempTaxonomyFile); }
else {
ifstream in;
m->openInputFile(tempTaxonomyFile, in);
//read in users taxonomy file and add sequences to tree
string name, taxon;
while(!in.eof()){
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
in >> name >> taxon; m->gobble(in);
itNames = nameMap.find(name);
if (itNames == nameMap.end()) {
m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
}else{
for (int i = 0; i < itNames->second.size(); i++) {
taxaSum->addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
}
itNames->second.clear();
nameMap.erase(itNames->first);
}
}
in.close();
}
}
m->mothurRemove(tempTaxonomyFile);
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
//print summary file
ofstream outTaxTree;
m->openOutputFile(taxSummary, outTaxTree);
taxaSum->print(outTaxTree);
outTaxTree.close();
//output taxonomy with the unclassified bins added
ifstream inTax;
m->openInputFile(newTaxonomyFile, inTax);
ofstream outTax;
string unclass = newTaxonomyFile + ".unclass.temp";
m->openOutputFile(unclass, outTax);
//get maxLevel from phylotree so you know how many 'unclassified's to add
int maxLevel = taxaSum->getMaxLevel();
//read taxfile - this reading and rewriting is done to preserve the confidence scores.
string name, taxon;
while (!inTax.eof()) {
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->mothurRemove(unclass); delete classify; return 0; }
inTax >> name >> taxon; m->gobble(inTax);
string newTax = addUnclassifieds(taxon, maxLevel);
outTax << name << '\t' << newTax << endl;
}
inTax.close();
outTax.close();
if (ct != NULL) { delete ct; }
if (groupMap != NULL) { delete groupMap; } delete taxaSum;
m->mothurRemove(newTaxonomyFile);
rename(unclass.c_str(), newTaxonomyFile.c_str());
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
#ifdef USE_MPI
}
#endif
}
delete classify;
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set taxonomy file as new current taxonomyfile
string current = "";
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
current = "";
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
try{
string newTax, taxon;
int level = 0;
//keep what you have counting the levels
while (tax.find_first_of(';') != -1) {
//get taxon
taxon = tax.substr(0,tax.find_first_of(';'))+';';
tax = tax.substr(tax.find_first_of(';')+1, tax.length());
newTax += taxon;
level++;
}
//add "unclassified" until you reach maxLevel
while (level < maxlevel) {
newTax += "unclassified;";
level++;
}
return newTax;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
exit(1);
}
}
/**************************************************************************************************/
int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string accnos, string filename) {
try {
int num = 0;
processIDS.clear();
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
num = driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", filename);
//pass numSeqs to parent
ofstream out;
string tempFile = filename + toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
out << num << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
}
}
//parent does its part