--- /dev/null
+/*
+ * 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"
+
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::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 pgroup("group", "InputTypes", "", "", "none", "none", "none",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.group command reads a group file, and parses your fasta and names files by groups. \n";
+ helpString += "The split.group command parameters are fasta, name, group and groups.\n";
+ helpString += "The fasta and group 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.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n";
+ helpString += "Example: split.group(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);
+ }
+}
+//**********************************************************************************************************************
+SplitGroupCommand::SplitGroupCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = 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;
+
+ //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; }
+ }
+
+ }
+
+
+ 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 = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setGroupFile(groupfile); }
+
+ 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"){ outputDir = m->hasPath(groupfile); }
+
+ 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; }
+
+ 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();
+
+ string newFasta = fastafileRoot + Groups[i] + ".fasta";
+ string newName = namefileRoot + Groups[i] + ".names";
+
+ 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;
+
+ 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); }
+ }
+
+ 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);
+ }
+}
+//**********************************************************************************************************************
+
+
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