try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
helpString += "The make.group command should be in the following format: \n";
helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n";
return helpString;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
+string MakeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //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 == "group") { outputFileName = "groups"; }
+ 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, "MakeGroupCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
try {
abort = true; calledHelp = true;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (inputDir != "") {
- string path = m->hasPath(fastaFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
- }
-
- ifstream in;
- int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+
+ bool ignore = false;
+ if (fastaFileNames[i] == "current") {
+ fastaFileNames[i] = m->getFastaFile();
+ if (fastaFileNames[i] != "") {
+ m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine();
+ filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));
+ }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
}
}
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ if (!ignore) {
+ if (inputDir != "") {
+ string path = m->hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
- }
- in.close();
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
- }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); }
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); m->setFastaFile(fastaFileNames[i]); }
+ }
}
//prevent giantic file name
- if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
- else { filename += "groups"; }
+ if (fastaFileNames.size() > 3) { filename = outputDir + "merge." + getOutputFileNameTag("group"); }
+ else { filename += getOutputFileNameTag("group"); }
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
ifstream in;
m->openInputFile(fastaFileNames[i], in);
Sequence seq(in, "no align"); m->gobble(in);
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(filename.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(filename); return 0; }
if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
}
projects / mothur.git / blobdiff