//***************************************************************************************************************
-TrimSeqsCommand::TrimSeqsCommand(){
+TrimSeqsCommand::TrimSeqsCommand(string option){
try {
globaldata = GlobalData::getInstance();
+ abort = false;
- oligos = 0;
-
- if(globaldata->getFastaFile() == ""){
- cout << "you need to at least enter a fasta file name" << endl;
- }
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- if(isTrue(globaldata->getFlip())) { flip = 1; }
- if(globaldata->getOligosFile() != "") { oligos = 1; }
-
- if(globaldata->getMaxAmbig() != "-1") { maxAmbig = atoi(globaldata->getMaxAmbig().c_str()); }
- else { maxAmbig = -1; }
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
- if(globaldata->getMaxHomoPolymer() != "-1") { maxHomoP = atoi(globaldata->getMaxHomoPolymer().c_str()); }
- else { maxHomoP = 0; }
+ //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); }
- if(globaldata->getMinLength() != "-1") { minLength = atoi(globaldata->getMinLength().c_str()); }
- else { minLength = 0; }
- if(globaldata->getMaxLength() != "-1") { maxLength = atoi(globaldata->getMaxLength().c_str()); }
- else { maxLength = 0; }
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ string temp;
+ temp = validParameter->validFile(parameters, "flip", false); if (temp == "not found") { temp = "0"; }
+ if(isTrue(temp)) { flip = 1; }
- if(!flip && !oligos && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP ){ cout << "huh?" << endl; }
+ temp = validParameter->validFile(parameters, "oligos", false); if (temp == "not found") { temp = ""; }
+ if(temp != "") { oligos = 1; }
+ else { oligos = 0; }
+
+ 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 = "0"; }
+ convert(temp, maxHomoP);
+
+ temp = validParameter->validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, minLength);
+
+ temp = validParameter->validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, maxLength);
+
+ if(!flip && !oligos && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP ){ cout << "huh?" << endl; }
+
+ delete validParameter;
+ }
}
catch(exception& e) {
exit(1);
}
}
+//**********************************************************************************************************************
+
+void TrimSeqsCommand::help(){
+ try {
+ cout << "The trim.seqs command reads a fastafile and creates ....." << "\n";
+ cout << "The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength." << "\n";
+ cout << "The fasta parameter is required." << "\n";
+ cout << "The flip parameter .... The default is 0." << "\n";
+ cout << "The oligos parameter .... The default is ""." << "\n";
+ cout << "The maxambig parameter .... The default is -1." << "\n";
+ cout << "The maxhomop parameter .... The default is 0." << "\n";
+ cout << "The minlength parameter .... The default is 0." << "\n";
+ cout << "The maxlength parameter .... The default is 0." << "\n";
+ cout << "The trim.seqs command should be in the following format: " << "\n";
+ cout << "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, " << "\n";
+ cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) " << "\n";
+ cout << "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., 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 TrimSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TrimSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
//***************************************************************************************************************
int TrimSeqsCommand::execute(){
try{
+
+ if (abort == true) { return 0; }
+
getOligos();
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fastafile, inFASTA);
ofstream outFASTA;
- string trimSeqFile = getRootName(globaldata->getFastaFile()) + "trim.fasta";
+ string trimSeqFile = getRootName(fastafile) + "trim.fasta";
openOutputFile(trimSeqFile, outFASTA);
ofstream outGroups;
- string groupFile = getRootName(globaldata->getFastaFile()) + "groups";
+ string groupFile = getRootName(fastafile) + "groups";
openOutputFile(groupFile, outGroups);
ofstream scrapFASTA;
- string scrapSeqFile = getRootName(globaldata->getFastaFile()) + "scrap.fasta";
+ string scrapSeqFile = getRootName(fastafile) + "scrap.fasta";
openOutputFile(scrapSeqFile, scrapFASTA);
bool success;
void TrimSeqsCommand::getOligos(){
ifstream inOligos;
- openInputFile(globaldata->getOligosFile(), inOligos);
+ //openInputFile(globaldata->getOligosFile(), inOligos);
string type, oligo, group;
projects / mothur.git / blobdiff