//***************************************************************************************************************
-ScreenSeqsCommand::ScreenSeqsCommand(){
+ScreenSeqsCommand::ScreenSeqsCommand(string option){
try {
globaldata = GlobalData::getInstance();
- if(globaldata->getFastaFile() == "") { cout << "you must provide a fasta formatted file" << endl; }
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //check for required parameters
+ fastafile = validParameter->validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
+ else if (fastafile == "not open") { abort = true; }
+ else { globaldata->setFastaFile(fastafile); }
+
+ groupfile = validParameter->validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else {
+ globaldata->setGroupFile(groupfile);
+ }
+
+ namefile = validParameter->validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else {
+ globaldata->setNameFile(namefile);
+ }
+
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string temp;
+ temp = validParameter->validFile(parameters, "start", false); if (temp == "not found") { temp = "-1"; }
+ convert(temp, startPos);
+
+ temp = validParameter->validFile(parameters, "end", false); if (temp == "not found") { temp = "-1"; }
+ convert(temp, endPos);
+
+ temp = validParameter->validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
+ convert(temp, maxAmbig);
+
+ temp = validParameter->validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "-1"; }
+ convert(temp, maxHomoP);
+
+ temp = validParameter->validFile(parameters, "minlength", false); if (temp == "not found") { temp = "-1"; }
+ convert(temp, minLength);
+
+ temp = validParameter->validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; }
+ convert(temp, maxLength);
+
+ delete validParameter;
+ }
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function ScreenSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+//**********************************************************************************************************************
+
+void ScreenSeqsCommand::help(){
+ try {
+ cout << "The screen.seqs command reads a fastafile and creates ....." << "\n";
+ cout << "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group." << "\n";
+ cout << "The fasta parameter is required." << "\n";
+ cout << "The start parameter .... The default is -1." << "\n";
+ cout << "The end parameter .... The default is -1." << "\n";
+ cout << "The maxambig parameter .... The default is -1." << "\n";
+ cout << "The maxhomop parameter .... The default is -1." << "\n";
+ cout << "The minlength parameter .... The default is -1." << "\n";
+ cout << "The maxlength parameter .... The default is -1." << "\n";
+ cout << "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile." << "\n";
+ cout << "The screen.seqs command should be in the following format: " << "\n";
+ cout << "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, " << "\n";
+ cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) " << "\n";
+ cout << "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...)." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ScreenSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
//***************************************************************************************************************
int ScreenSeqsCommand::execute(){
try{
- int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
- convert(globaldata->getStartPos(), startPos);
- convert(globaldata->getEndPos(), endPos);
- convert(globaldata->getMaxAmbig(), maxAmbig);
- convert(globaldata->getMaxHomoPolymer(), maxHomoP);
- convert(globaldata->getMinLength(), minLength);
- convert(globaldata->getMaxLength(), maxLength);
+ if (abort == true) { return 0; }
+
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fastafile, inFASTA);
set<string> badSeqNames;
- string goodSeqFile = getRootName(globaldata->getFastaFile()) + "good" + getExtension(globaldata->getFastaFile());
- string badSeqFile = getRootName(globaldata->getFastaFile()) + "bad" + getExtension(globaldata->getFastaFile());
+ string goodSeqFile = getRootName(fastafile) + "good" + getExtension(fastafile);
+ string badSeqFile = getRootName(fastafile) + "bad" + getExtension(fastafile);
ofstream goodSeqOut; openOutputFile(goodSeqFile, goodSeqOut);
ofstream badSeqOut; openOutputFile(badSeqFile, badSeqOut);
}
gobble(inFASTA);
}
- if(globaldata->getNameFile() != ""){
+ if(namefile != ""){
screenNameGroupFile(badSeqNames);
}
- else if(globaldata->getGroupFile() != ""){
+ else if(groupfile != ""){
screenGroupFile(badSeqNames);
}
projects / mothur.git / blobdiff