#include "listvector.hpp"
//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::getValidParameters(){
+vector<string> RemoveSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta","name", "group", "alignreport", "accnos", "qfile","list","taxonomy","outputdir","inputdir", "dups" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
+ 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); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getValidParameters");
+ m->errorOut(e, "RemoveSeqsCommand", "setParameters");
exit(1);
}
}
+//**********************************************************************************************************************
+string RemoveSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n";
+ helpString += "It outputs a file containing the sequences NOT in the .accnos file.\n";
+ helpString += "The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n";
+ helpString += "The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n";
+ helpString += "The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
+ helpString += "Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
}
}
//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"accnos"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> RemoveSeqsCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getRequiredFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(string option) {
try {
abort = false; calledHelp = false;
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport", "accnos", "qfile", "list","taxonomy","outputdir","inputdir", "dups" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { abort = true; }
- else if (accnosfile == "not found") { accnosfile = ""; m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }
+ else if (accnosfile == "not found") {
+ accnosfile = m->getAccnosFile();
+ if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; }
- if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
}
}
}
//**********************************************************************************************************************
-void RemoveSeqsCommand::help(){
- try {
- m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n");
- m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
- m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n");
- m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n");
- m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
- m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int RemoveSeqsCommand::execute(){
try {
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