ScreenSeqsCommand::ScreenSeqsCommand(string option){
try {
- globaldata = GlobalData::getInstance();
abort = false;
//allow user to run help
else {
//valid paramters for this command
- string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
+ string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
+ "name", "group", "alignreport"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
- 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; }
+ for (map<string,string>::iterator 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; }
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
- else { globaldata->setFastaFile(fastafile); }
-
- groupfile = validParameter->validFile(parameters, "group", true);
+
+ 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);
+ namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else {
- globaldata->setNameFile(namefile);
- }
-
+ alignreport = validParameter.validFile(parameters, "alignreport", true);
+ if (alignreport == "not open") { abort = true; }
+ else if (alignreport == "not found") { alignreport = ""; }
+
//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"; }
+ 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"; }
+ 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"; }
+ 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"; }
+ 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"; }
+ 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"; }
+ 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";
+ errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error 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";
+ mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
+ mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group.\n");
+ mothurOut("The fasta parameter is required.\n");
+ mothurOut("The start parameter .... The default is -1.\n");
+ mothurOut("The end parameter .... The default is -1.\n");
+ mothurOut("The maxambig parameter .... The default is -1.\n");
+ mothurOut("The maxhomop parameter .... The default is -1.\n");
+ mothurOut("The minlength parameter .... The default is -1.\n");
+ mothurOut("The maxlength parameter .... The default is -1.\n");
+ mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
+ mothurOut("The screen.seqs command should be in the following format: \n");
+ mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
+ mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
+ mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+ mothurOut("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";
+ errorOut(e, "ScreenSeqsCommand", "help");
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);
- }
}
//***************************************************************************************************************
}
gobble(inFASTA);
}
- if(namefile != ""){
- screenNameGroupFile(badSeqNames);
- }
- else if(groupfile != ""){
- screenGroupFile(badSeqNames);
- }
+ if(namefile != "" && groupfile != "") { screenNameGroupFile(badSeqNames); } // this screens both names and groups
+ else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the groups
+ if(alignreport != "") { screenAlignReport(badSeqNames); }
+ goodSeqOut.close();
+ badSeqOut.close();
+ inFASTA.close();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ScreenSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ScreenSeqsCommand", "execute");
exit(1);
}
-
}
//***************************************************************************************************************
void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
ifstream inputNames;
- openInputFile(globaldata->getNameFile(), inputNames);
+ openInputFile(namefile, inputNames);
set<string> badSeqGroups;
string seqName, seqList, group;
set<string>::iterator it;
- string goodNameFile = getRootName(globaldata->getNameFile()) + "good" + getExtension(globaldata->getNameFile());
- string badNameFile = getRootName(globaldata->getNameFile()) + "bad" + getExtension(globaldata->getNameFile());
+ string goodNameFile = getRootName(namefile) + "good" + getExtension(namefile);
+ string badNameFile = getRootName(namefile) + "bad" + getExtension(namefile);
ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
if(it != badSeqNames.end()){
badSeqNames.erase(it);
badNameOut << seqName << '\t' << seqList << endl;
- if(globaldata->getNameFile() != ""){
+ if(namefile != ""){
int start = 0;
for(int i=0;i<seqList.length();i++){
if(seqList[i] == ','){
goodNameOut.close();
badNameOut.close();
- if(globaldata->getGroupFile() != ""){
+ if(groupfile != ""){
ifstream inputGroups;
- openInputFile(globaldata->getGroupFile(), inputGroups);
+ openInputFile(groupfile, inputGroups);
- string goodGroupFile = getRootName(globaldata->getGroupFile()) + "good" + getExtension(globaldata->getGroupFile());
- string badGroupFile = getRootName(globaldata->getGroupFile()) + "bad" + getExtension(globaldata->getGroupFile());
+ string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
+ string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
ifstream inputGroups;
- openInputFile(globaldata->getGroupFile(), inputGroups);
+ openInputFile(groupfile, inputGroups);
string seqName, group;
set<string>::iterator it;
- string goodGroupFile = getRootName(globaldata->getGroupFile()) + "good" + getExtension(globaldata->getGroupFile());
- string badGroupFile = getRootName(globaldata->getGroupFile()) + "bad" + getExtension(globaldata->getGroupFile());
+ string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
+ string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
//***************************************************************************************************************
+void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
+
+ ifstream inputAlignReport;
+ openInputFile(alignreport, inputAlignReport);
+ string seqName, group;
+ set<string>::iterator it;
+
+ string goodAlignReportFile = getRootName(alignreport) + "good" + getExtension(alignreport);
+ string badAlignReportFile = getRootName(alignreport) + "bad" + getExtension(alignreport);
+
+ ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
+ ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
+
+ while (!inputAlignReport.eof()) { // need to copy header
+ char c = inputAlignReport.get();
+ goodAlignReportOut << c;
+ badAlignReportOut << c;
+ if (c == 10 || c == 13){ break; }
+ }
+
+ while(!inputAlignReport.eof()){
+ inputAlignReport >> seqName;
+ it = badSeqNames.find(seqName);
+ string line;
+ while (!inputAlignReport.eof()) { // need to copy header
+ char c = inputAlignReport.get();
+ line += c;
+ if (c == 10 || c == 13){ break; }
+ }
+
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
+ badAlignReportOut << seqName << '\t' << line;;
+ }
+ else{
+ goodAlignReportOut << seqName << '\t' << line;
+ }
+ gobble(inputAlignReport);
+ }
+ inputAlignReport.close();
+ goodAlignReportOut.close();
+ badAlignReportOut.close();
+
+}
+
+//***************************************************************************************************************
+