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/*
* makegroupcommand.cpp
* Mothur
*
* Created by westcott on 5/7/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "makegroupcommand.h"
#include "sequence.hpp"
//**********************************************************************************************************************
vector<string> MakeGroupCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
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, "MakeGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MakeGroupCommand::getHelpString(){
try {
string helpString = "";
helpString += "The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n";
helpString += "The make.group command parameters are fasta, groups and output. Fasta and group are required.\n";
helpString += "The output parameter allows you to specify the name of groupfile created. \n";
helpString += "The make.group command should be in the following format: \n";
helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string MakeGroupCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "group") { pattern = "[filename],groups"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
exit(1);
}
}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(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["group"] = 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 = ""; }
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();
filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));
}
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]; }
}
ifstream in;
int 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 you can't open it, try default location
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{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); m->setFastaFile(fastaFileNames[i]); }
}
}
//prevent giantic file name
map<string, string> variables;
variables["[filename]"] = filename;
if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
filename = getOutputFileName("group",variables);
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
//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 = ""; }
output = validParameter.validFile(parameters, "output", false);
if (output == "not found") { output = ""; }
else{ filename = output; }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
else { m->splitAtDash(groups, groupsNames); }
if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MakeGroupCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
filename = outputDir + filename;
ofstream out;
m->openOutputFile(filename, out);
for (int i = 0; i < fastaFileNames.size(); i++) {
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
ifstream in;
m->openInputFile(fastaFileNames[i], in);
while (!in.eof()) {
Sequence seq(in, "no align"); m->gobble(in);
if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(filename); return 0; }
if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
}
in.close();
}
out.close();
m->mothurOutEndLine();
m->mothurOut("Output File Names: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
m->mothurOutEndLine();
//set group file as new current groupfile
string current = "";
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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