#include "splitgroupscommand.h"
#include "sharedutilities.h"
+#include "sequenceparser.h"
+#include "counttable.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","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", "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.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", "getRequiredParameters");
+ m->errorOut(e, "SplitGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "getRequiredFiles");
- 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");
//allow user to run help
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();
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 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") { 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 = "";
+ }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"){ outputDir = m->hasPath(groupfile); }
+ 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);
+ }
+ }
}
}
}
}
//**********************************************************************************************************************
-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) { if (calledHelp) { return 0; } return 2; }
- 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; }
+ 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->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();
exit(1);
}
}
-/**********************************************************************************************************************/
-int SplitGroupCommand::readNames() {
+//**********************************************************************************************************************
+int SplitGroupCommand::runNameGroup(){
try {
- //open input file
- ifstream in;
- m->openInputFile(namefile, in);
+ 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);
- while (!in.eof()) {
- if (m->control_pressed) { break; }
+ 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++) {
- string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
+ m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
- vector<string> names;
- m->splitAtComma(secondCol, names);
+ 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);
+ }
- nameMap[firstCol] = names;
+ if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
- in.close();
-
- return 0;
+
+ delete parser;
+
+ return 0;
- }
+ }
catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "readNames");
+ m->errorOut(e, "SplitGroupCommand", "runNameGroup");
exit(1);
}
}
-
-/**********************************************************************************************************************/
-int SplitGroupCommand::splitFasta() {
+//**********************************************************************************************************************
+int SplitGroupCommand::runCount(){
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"); 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");
- }
- }
-
- //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;
- }
-
- vector<string> newOutputNames;
- //remove blank files
- for (int i = 0; i < outputNames.size(); i++) {
- if (m->isBlank(outputNames[i])) {
- remove(outputNames[i].c_str());
- }else { newOutputNames.push_back(outputNames[i]); }
- }
- outputNames = newOutputNames;
-
- return 0;
+
+ CountTable ct;
+ ct.readTable(countfile, true);
+ 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", "splitFasta");
+ m->errorOut(e, "SplitGroupCommand", "runCount");
exit(1);
}
}
-/**********************************************************************************************************************/
+//**********************************************************************************************************************
+
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