#include "endiannessmacros.h"
//**********************************************************************************************************************
-vector<string> SffInfoCommand::getValidParameters(){
- try {
- string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+vector<string> SffInfoCommand::setParameters(){
+ try {
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
+ CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
+ CommandParameter pflow("flow", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflow);
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
+ CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
+ 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, "SffInfoCommand", "getValidParameters");
+ m->errorOut(e, "SffInfoCommand", "setParameters");
exit(1);
}
}
+//**********************************************************************************************************************
+string SffInfoCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file.\n";
+ helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n";
+ helpString += "The sff parameter allows you to enter the sff file you would like to extract data from. You may enter multiple files by separating them by -'s.\n";
+ helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated. Default=True. \n";
+ helpString += "The qfile parameter allows you to indicate if you would like a quality file generated. Default=True. \n";
+ helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated. Default=False. \n";
+ helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n";
+ helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
+ helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. Default=True. \n";
+ helpString += "The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n";
+ helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+
//**********************************************************************************************************************
SffInfoCommand::SffInfoCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["flow"] = tempOutNames;
}
}
//**********************************************************************************************************************
-vector<string> SffInfoCommand::getRequiredParameters(){
- try {
- string Array[] = {"sff", "sfftxt", "or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SffInfoCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "getRequiredFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
SffInfoCommand::SffInfoCommand(string option) {
try {
else {
//valid paramters for this command
- string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
else if (sfftxtFilename == "not open") { sfftxtFilename = ""; }
}
- if ((sfftxtFilename == "") && (filenames.size() == 0)) { m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true; }
+ if ((sfftxtFilename == "") && (filenames.size() == 0)) {
+ //if there is a current fasta file, use it
+ string filename = m->getSFFFile();
+ if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true; }
+ }
}
}
catch(exception& e) {
exit(1);
}
}
-//**********************************************************************************************************************
-
-void SffInfoCommand::help(){
- try {
- m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file..\n");
- m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
- m->mothurOut("The sff parameter allows you to enter the sff file you would like to extract data from. You may enter multiple files by separating them by -'s.\n");
- m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated. Default=True. \n");
- m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated. Default=True. \n");
- m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated. Default=False. \n");
- m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n");
- m->mothurOut("If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n");
- m->mothurOut("The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. Default=True. \n");
- m->mothurOut("The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n");
- m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-SffInfoCommand::~SffInfoCommand(){}
-
//**********************************************************************************************************************
int SffInfoCommand::execute(){
try {
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