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/*
* splitgroupscommand.cpp
* Mothur
*
* Created by westcott on 9/20/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "splitgroupscommand.h"
#include "sharedutilities.h"
#include "sequenceparser.h"
#include "counttable.h"
//**********************************************************************************************************************
vector<string> SplitGroupCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",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-CountGroup", "CountGroup", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "CountGroup", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
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, "SplitGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string SplitGroupCommand::getHelpString(){
try {
string helpString = "";
helpString += "The split.groups command reads a group or count file, and parses your fasta and names or count files by groups. \n";
helpString += "The split.groups command parameters are fasta, name, group, count and groups.\n";
helpString += "The fasta and group or count parameters are required.\n";
helpString += "The groups parameter allows you to select groups to create files for. \n";
helpString += "For example if you set groups=A-B-C, you will get a .A.fasta, .A.names, .B.fasta, .B.names, .C.fasta, .C.names files. \n";
helpString += "If you want .fasta and .names files for all groups, set groups=all. \n";
helpString += "The split.groups command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n";
helpString += "Example: split.groups(fasta=abrecovery.fasta, group=abrecovery.groups).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string SplitGroupCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],[group],fasta"; }
else if (type == "name") { pattern = "[filename],[group],names"; }
else if (type == "count") { pattern = "[filename],[group],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, "SplitGroupCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand");
exit(1);
}
}
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(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("group");
//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["group"] = inputDir + it->second; }
}
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; }
}
}
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") {
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " 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(fastafile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = "";
}else { m->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
if ((countfile != "") && (groupfile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
if ((countfile == "") && (groupfile == "")) {
if (namefile == "") { //check for count then group
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else {
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You need to provide a count or group file."); m->mothurOutEndLine();
abort = true;
}
}
}else { //check for group
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You need to provide a count or group file."); m->mothurOutEndLine();
abort = true;
}
}
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else { m->splitAtDash(groups, Groups); }
//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"){
if (groupfile != "") { outputDir = m->hasPath(groupfile); }
else { outputDir = m->hasPath(countfile); }
}
if (countfile == "") {
if (namefile == "") {
vector<string> files; files.push_back(fastafile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "SplitAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
int SplitGroupCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (countfile == "" ) { runNameGroup(); }
else { runCount(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
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); }
}
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();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int SplitGroupCommand::runNameGroup(){
try {
SequenceParser* parser;
if (namefile == "") { parser = new SequenceParser(groupfile, fastafile); }
else { parser = new SequenceParser(groupfile, fastafile, namefile); }
if (m->control_pressed) { delete parser; return 0; }
vector<string> namesGroups = parser->getNamesOfGroups();
SharedUtil util; util.setGroups(Groups, namesGroups);
string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile));
string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile));
m->mothurOutEndLine();
for (int i = 0; i < Groups.size(); i++) {
m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
map<string, string> variables;
variables["[filename]"] = fastafileRoot;
variables["[group]"] = Groups[i];
string newFasta = getOutputFileName("fasta",variables);
variables["[filename]"] = namefileRoot;
string newName = getOutputFileName("name",variables);
parser->getSeqs(Groups[i], newFasta, false);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (namefile != "") {
parser->getNameMap(Groups[i], newName);
outputNames.push_back(newName); outputTypes["name"].push_back(newName);
}
if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
delete parser;
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "runNameGroup");
exit(1);
}
}
//**********************************************************************************************************************
int SplitGroupCommand::runCount(){
try {
CountTable ct;
ct.readTable(countfile, true, false);
if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, cannot split by group.\n"); m->control_pressed = true; }
if (m->control_pressed) { return 0; }
vector<string> namesGroups = ct.getNamesOfGroups();
SharedUtil util; util.setGroups(Groups, namesGroups);
//fill filehandles with neccessary ofstreams
map<string, ofstream*> ffiles;
map<string, ofstream*> cfiles;
ofstream* temp;
for (int i=0; i<Groups.size(); i++) {
temp = new ofstream;
ffiles[Groups[i]] = temp;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
variables["[group]"] = Groups[i];
string newFasta = getOutputFileName("fasta",variables);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
m->openOutputFile(newFasta, (*temp));
temp = new ofstream;
cfiles[Groups[i]] = temp;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
string newCount = getOutputFileName("count",variables);
m->openOutputFile(newCount, (*temp));
outputNames.push_back(newCount); outputTypes["count"].push_back(newCount);
(*temp) << "Representative_Sequence\ttotal\t" << Groups[i] << endl;
}
ifstream in;
m->openInputFile(fastafile, in);
while (!in.eof()) {
Sequence seq(in); m->gobble(in);
if (m->control_pressed) { break; }
if (seq.getName() != "") {
vector<string> thisSeqsGroups = ct.getGroups(seq.getName());
for (int i = 0; i < thisSeqsGroups.size(); i++) {
if (m->inUsersGroups(thisSeqsGroups[i], Groups)) { //if this sequence belongs to a group we want them print
seq.printSequence(*(ffiles[thisSeqsGroups[i]]));
int numSeqs = ct.getGroupCount(seq.getName(), thisSeqsGroups[i]);
(*(cfiles[thisSeqsGroups[i]])) << seq.getName() << '\t' << numSeqs << '\t' << numSeqs << endl;
}
}
}
}
in.close();
//close and delete ofstreams
for (int i=0; i<Groups.size(); i++) {
(*ffiles[Groups[i]]).close(); delete ffiles[Groups[i]];
(*cfiles[Groups[i]]).close(); delete cfiles[Groups[i]];
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "runCount");
exit(1);
}
}
//**********************************************************************************************************************
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