#include "splitgroupscommand.h"
#include "sharedutilities.h"
#include "sequenceparser.h"
+#include "counttable.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);
+ 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); }
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 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.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 += "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;
}
}
}
//**********************************************************************************************************************
-string SplitGroupCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SplitGroupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "name") { outputFileName = "names"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "getOutputFileNameTag");
- exit(1);
- }
+ 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 {
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand");
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; }
+ }
}
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 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 (namefile == "") {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- SequenceParser* parser;
+ 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->setFastaFile(current); }
+ }
+ itTypes = outputTypes.find("name");
+ 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();
+ 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::runNameGroup(){
+ try {
+ 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);
m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
- string newFasta = fastafileRoot + Groups[i] + "." + getOutputFileNameTag("fasta");
- string newName = namefileRoot + Groups[i] + "." + getOutputFileNameTag("name");
+ 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);
}
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;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitGroupCommand", "runNameGroup");
+ exit(1);
}
+}
+//**********************************************************************************************************************
+int SplitGroupCommand::runCount(){
+ try {
+
+ 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", "execute");
+ m->errorOut(e, "SplitGroupCommand", "runCount");
exit(1);
}
}
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