--- /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"
+
+//**********************************************************************************************************************
+SplitGroupCommand::SplitGroupCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"name","group","groups","fasta","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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; }
+ }
+
+ //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") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the split.group command. "); m->mothurOutEndLine(); abort = true; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the split.group command. "); 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"){ outputDir = m->hasPath(groupfile); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitGroupCommand", "SplitAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void SplitGroupCommand::help(){
+ try {
+ m->mothurOut("The split.group command reads a group file, and parses your fasta and names files by groups. \n");
+ m->mothurOut("The split.group command parameters are fasta, name, group and groups.\n");
+ m->mothurOut("The fasta and group parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to select groups to create files for. \n");
+ m->mothurOut("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");
+ m->mothurOut("If you want .fasta and .names files for all groups, set groups=all. \n");
+ m->mothurOut("The split.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n");
+ m->mothurOut("Example: split.group(fasta=abrecovery.fasta, group=abrecovery.groups).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitGroupCommand", "help");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SplitGroupCommand::~SplitGroupCommand(){ }
+//**********************************************************************************************************************
+int SplitGroupCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ SharedUtil util; util.setGroups(Groups, groupMap->namesOfGroups);
+
+ if (namefile != "") { readNames(); }
+ splitFasta();
+
+ delete groupMap;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ 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::readNames() {
+ try {
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; m->gobble(in);
+
+ vector<string> names;
+ m->splitAtComma(secondCol, names);
+
+ nameMap[firstCol] = names;
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitGroupCommand", "readNames");
+ exit(1);
+ }
+}
+
+/**********************************************************************************************************************/
+int SplitGroupCommand::splitFasta() {
+ try {
+
+ string filerootFasta = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string filerootName = outputDir + m->getRootName(m->getSimpleName(namefile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+"fasta"] = temp;
+ m->openOutputFile(filerootFasta + Groups[i] + ".fasta", *(filehandles[Groups[i]+"fasta"]));
+ outputNames.push_back(filerootFasta + Groups[i] + ".fasta");
+
+ if (namefile != "") {
+ temp2 = new ofstream;
+ filehandles[Groups[i]+"name"] = temp2;
+ m->openOutputFile(filerootName + Groups[i] + ".names", *(filehandles[Groups[i]+"name"]));
+ outputNames.push_back(filerootName + Groups[i] + ".names");
+ }
+ }
+
+ //open input file
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) {
+ if (namefile != "") { m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine(); }
+ else { //no names file given
+ string group = groupMap->getGroup(seq.getName());
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ seq.printSequence(*(filehandles[group+"fasta"]));
+ }else if(group == "not found") {
+ m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+ }else{
+ vector<string> names = itNames->second;
+ map<string, string> group2Names;
+ map<string, string>::iterator it;
+
+ for (int i = 0; i < names.size(); i++) { //build strings for new group names file, will select rep below
+ string group = groupMap->getGroup(names[i]);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ it = group2Names.find(group);
+ if (it == group2Names.end()) {
+ group2Names[group] = names[i] + ",";
+ }else{
+ group2Names[group] += names[i] + ",";
+ }
+ }else if(group == "not found") {
+ m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+
+ for (map<string, string>::iterator itGroups = group2Names.begin(); itGroups != group2Names.end(); itGroups++) {
+ //edit names string, by grabbing the first guy as the rep and removing the last comma
+ string newNames = itGroups->second;
+ newNames = newNames.substr(0, newNames.length()-1);
+ string repName = "";
+
+ int pos = newNames.find_first_of(',');
+ if (pos == newNames.npos) { //only one sequence so it represents itself
+ repName = newNames;
+ }else{
+ repName = newNames.substr(0, pos);
+ }
+
+ *(filehandles[itGroups->first+"name"]) << repName << '\t' << newNames << endl;
+ *(filehandles[itGroups->first+"fasta"]) << ">" << repName << endl << seq.getAligned() << endl;
+ }
+ }
+ }
+ }
+
+ in.close();
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ delete it3->second;
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitGroupCommand", "splitFasta");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+
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