#include "reversecommand.h"
#include "sequence.hpp"
+#include "qualityscores.h"
-
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::setParameters(){
+ try {
+ 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", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ReverseSeqsCommand::getHelpString(){
+ try {
+ 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", "getHelpString");
+ 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);
+ }
+}
+//**********************************************************************************************************************
+ReverseSeqsCommand::ReverseSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(string option){
+ReverseSeqsCommand::ReverseSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ 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"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
-
+ map<string,string>::iterator it;
+
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //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["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
- fasta = validParameter.validFile(parameters, "fasta", true);
- if (fasta == "not open") { abort = true; }
- else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true; }
+ 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); }
- }
- }
- catch(exception& e) {
- errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
+ 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; }
+ 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 = "";
+ }
-void ReverseSeqsCommand::help(){
- try {
- mothurOut("The reverse.seqs command reads a fastafile and ....\n");
- mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
- mothurOut("The reverse.seqs command should be in the following format: \n");
- mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
+ }
}
catch(exception& e) {
- errorOut(e, "ReverseSeqsCommand", "help");
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
exit(1);
}
}
-
-//***************************************************************************************************************
-
-ReverseSeqsCommand::~ReverseSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ReverseSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ifstream inFASTA;
- openInputFile(fasta, inFASTA);
+ string fastaReverseFileName;
- ofstream outFASTA;
- string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
- openOutputFile(reverseFile, outFASTA);
+ if(fastaFileName != ""){
+ ifstream inFASTA;
+ m->openInputFile(fastaFileName, inFASTA);
+
+ ofstream outFASTA;
+ 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(); m->mothurRemove(fastaReverseFileName); return 0; }
+
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
+ if (currSeq.getName() != "") {
+ currSeq.reverseComplement();
+ currSeq.printSequence(outFASTA);
+ }
+ }
+ inFASTA.close();
+ outFASTA.close();
+ outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName);
+ }
- while(!inFASTA.eof()){
- Sequence currSeq(inFASTA); gobble(inFASTA);
- if (currSeq.getName() != "") {
- currSeq.reverseComplement();
- currSeq.printSequence(outFASTA);
+ string qualReverseFileName;
+
+ if(qualFileName != ""){
+ QualityScores currQual;
+
+ ifstream inQual;
+ m->openInputFile(qualFileName, inQual);
+
+ ofstream 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(); m->mothurRemove(qualReverseFileName); return 0; }
+ currQual = QualityScores(inQual); m->gobble(inQual);
+ currQual.flipQScores();
+ currQual.printQScores(outQual);
}
+ inQual.close();
+ outQual.close();
+ outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
}
- inFASTA.close();
- outFASTA.close();
- return 0;
+ if (m->control_pressed) { m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for(int i=0;i<outputNames.size();i++){
+ m->mothurOut(outputNames[i]);
+ m->mothurOutEndLine();
+ }
+
+
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ReverseSeqsCommand", "execute");
+ m->errorOut(e, "ReverseSeqsCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff