//**********************************************************************************************************************
vector<string> SplitGroupCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "CountGroup", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "CountGroup", "none",false,false); 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 or count file, and parses your fasta and names or count files by groups. \n";
- helpString += "The split.group command parameters are fasta, name, group, count and groups.\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 if (type == "count") { outputFileName = "count_table"; }
- 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 {
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);
try {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true, false);
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; }
for (int i=0; i<Groups.size(); i++) {
temp = new ofstream;
ffiles[Groups[i]] = temp;
- string newFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + Groups[i] + "." + getOutputFileNameTag("fasta");
+ 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;
- string newCount = outputDir + m->getRootName(m->getSimpleName(countfile)) + Groups[i] + "." + getOutputFileNameTag("count");
+ 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;
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(), Groups[i]);
+ int numSeqs = ct.getGroupCount(seq.getName(), thisSeqsGroups[i]);
(*(cfiles[thisSeqsGroups[i]])) << seq.getName() << '\t' << numSeqs << '\t' << numSeqs << endl;
}
}
projects / mothur.git / blobdiff