#include "sharedutilities.h"
//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getValidParameters(){
- try {
- string Array[] = {"name","group","groups","fasta","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","group"};
- 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", "getRequiredParameters");
+ m->errorOut(e, "SplitGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SplitGroupCommand::getRequiredFiles(){
+string SplitGroupCommand::getHelpString(){
try {
- vector<string> myArray;
- 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", "getRequiredFiles");
+ m->errorOut(e, "SplitGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
- //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; }
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 = ""; }
}
}
//**********************************************************************************************************************
-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();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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(); }
(*(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;
projects / mothur.git / blobdiff