#include "qualityscores.h"
//**********************************************************************************************************************
-vector<string> ReverseSeqsCommand::getValidParameters(){
+vector<string> ReverseSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "qfile", "outputdir", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); 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, "ReverseSeqsCommand", "getValidParameters");
+ m->errorOut(e, "ReverseSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(){
+string ReverseSeqsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
+ string helpString = "";
+ helpString += "The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n";
+ helpString += "The reverse.seqs command parameters fasta or qfile are required.\n";
+ helpString += "The reverse.seqs command should be in the following format: \n";
+ helpString += "reverse.seqs(fasta=yourFastaFile) \n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+ m->errorOut(e, "ReverseSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-
-vector<string> ReverseSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta", "qfile"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
- exit(1);
- }
+string ReverseSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],rc,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],rc,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
-
-vector<string> ReverseSeqsCommand::getRequiredFiles(){
+ReverseSeqsCommand::ReverseSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
exit(1);
}
-}//***************************************************************************************************************
+}
+//***************************************************************************************************************
ReverseSeqsCommand::ReverseSeqsCommand(string option) {
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta", "qfile", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
+
+ it = parameters.find("qfile");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["qfile"] = inputDir + it->second; }
+ }
}
//check for required parameters
fastaFileName = validParameter.validFile(parameters, "fasta", true);
if (fastaFileName == "not open") { abort = true; }
else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else { m->setFastaFile(fastaFileName); }
qualFileName = validParameter.validFile(parameters, "qfile", true);
if (qualFileName == "not open") { abort = true; }
else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
-
- if(fastaFileName == "not open" && qualFileName == "not open"){
- m->mothurOut("fasta or qfile is a required parameter for the reverse.seqs command.");
- m->mothurOutEndLine();
- abort = true;
+ else { m->setQualFile(qualFileName); }
+
+ if((fastaFileName == "") && (qualFileName == "")){
+ fastaFileName = m->getFastaFile();
+ if (fastaFileName != "") { m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else {
+ qualFileName = m->getQualFile();
+ if (qualFileName != "") { m->mothurOut("Using " + qualFileName + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current files for fasta or qfile, and fasta or qfile is a required parameter for the reverse.seqs command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += m->hasPath(fastaFileName); //if user entered a file with a path then preserve it
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ReverseSeqsCommand::help(){
- try {
- m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
- m->mothurOut("The reverse.seqs command parameters fasta or qfile are required.\n");
- m->mothurOut("The reverse.seqs command should be in the following format: \n");
- m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ReverseSeqsCommand::~ReverseSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
m->openInputFile(fastaFileName, inFASTA);
ofstream outFASTA;
- fastaReverseFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
+ string tempOutputDir = outputDir;
+ if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
+ variables["[extension]"] = m->getExtension(fastaFileName);
+ fastaReverseFileName = getOutputFileName("fasta", variables);
m->openOutputFile(fastaReverseFileName, outFASTA);
while(!inFASTA.eof()){
- if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(fastaReverseFileName.c_str()); return 0; }
+ if (m->control_pressed) { inFASTA.close(); outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
m->openInputFile(qualFileName, inQual);
ofstream outQual;
- string qualReverseFileName = outputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
- m->openOutputFile(qualReverseFileName, outQual);
+ string tempOutputDir = outputDir;
+ if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
+ variables["[extension]"] = m->getExtension(qualFileName);
+ string qualReverseFileName = getOutputFileName("qfile", variables);
+ m->openOutputFile(qualReverseFileName, outQual);
while(!inQual.eof()){
- if (m->control_pressed) { inQual.close(); outQual.close(); remove(qualReverseFileName.c_str()); return 0; }
+ if (m->control_pressed) { inQual.close(); outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
currQual = QualityScores(inQual); m->gobble(inQual);
currQual.flipQScores();
currQual.printQScores(outQual);
outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
}
- if (m->control_pressed) { remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
//set fasta file as new current fastafile
string current = "";
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for(int i=0;i<outputNames.size();i++){
m->mothurOut(outputNames[i]);
m->mothurOutEndLine();
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