#include "splitgroupscommand.h"
#include "sharedutilities.h"
+#include "sequenceparser.h"
//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getValidParameters(){
- try {
- string Array[] = {"name","group","groups","fasta","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+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", "getValidParameters");
+ m->errorOut(e, "SplitGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredParameters(){
+string SplitGroupCommand::getHelpString(){
try {
- string Array[] = {"fasta","group"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ 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", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "getRequiredFiles");
+ m->errorOut(e, "SplitGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"name","group","groups","fasta","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = 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->mothurOut("fasta is a required parameter for the split.group command. "); m->mothurOutEndLine(); 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->mothurOut("group is a required parameter for the split.group command. "); m->mothurOutEndLine(); 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 = ""; }
//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);
+ }
}
}
}
}
//**********************************************************************************************************************
-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; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ SequenceParser* parser;
- SharedUtil util; util.setGroups(Groups, groupMap->namesOfGroups);
+ if (namefile == "") { parser = new SequenceParser(groupfile, fastafile); }
+ else { parser = new SequenceParser(groupfile, fastafile, namefile); }
- if (namefile != "") { readNames(); }
- splitFasta();
-
- delete groupMap;
+ if (m->control_pressed) { delete parser; return 0; }
+
+ vector<string> namesGroups = parser->getNamesOfGroups();
+ SharedUtil util; util.setGroups(Groups, namesGroups);
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile));
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; }
+ for (int i = 0; i < Groups.size(); i++) {
- string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
+ m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
- vector<string> names;
- m->splitAtComma(secondCol, names);
+ string newFasta = fastafileRoot + Groups[i] + ".fasta";
+ string newName = namefileRoot + Groups[i] + ".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;
+ 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; }
- 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"); outputTypes["fasta"].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"); outputTypes["name"].push_back(filerootFasta + Groups[i] + ".names");
+ if (namefile != "") {
+ parser->getNameMap(Groups[i], newName);
+ outputNames.push_back(newName); outputTypes["name"].push_back(newName);
}
- }
- //open input file
- ifstream in;
- m->openInputFile(fastafile, in);
-
- while (!in.eof()) {
- if (m->control_pressed) { break; }
+ if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ }
- 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;
- }
- }
- }
+ 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); }
}
-
- in.close();
-
- for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
- (*(filehandles[it3->first])).close();
- delete it3->second;
+
+ 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", "splitFasta");
+ m->errorOut(e, "SplitGroupCommand", "execute");
exit(1);
}
}
-/**********************************************************************************************************************/
+//**********************************************************************************************************************
+
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