#include "reversecommand.h"
#include "sequence.hpp"
+#include "qualityscores.h"
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "qfile", "outputdir", "inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ReverseSeqsCommand::ReverseSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+ 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);
+ }
+}
+
+//**********************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(string option){
+vector<string> ReverseSeqsCommand::getRequiredFiles(){
try {
- abort = false;
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}//***************************************************************************************************************
+
+ReverseSeqsCommand::ReverseSeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string Array[] = {"fasta"};
+ string Array[] = {"fasta", "qfile", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
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; }
+ }
+ }
+
//check for required parameters
- fasta = validParameter.validFile(parameters, "fasta", true);
- if (fasta == "not open") { abort = true; }
- else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; 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; }
+
+ 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;
+ }
+ //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
+ }
+
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void ReverseSeqsCommand::help(){
try {
- cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
- cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
- cout << "The reverse.seqs command should be in the following format: " << "\n";
- cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//***************************************************************************************************************
int ReverseSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ string fastaReverseFileName;
+
+ if(fastaFileName != ""){
+ ifstream inFASTA;
+ m->openInputFile(fastaFileName, inFASTA);
+
+ ofstream outFASTA;
+ fastaReverseFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
+ m->openOutputFile(fastaReverseFileName, outFASTA);
+
+ while(!inFASTA.eof()){
+ if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(fastaReverseFileName.c_str()); 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);
+ }
+
+ string qualReverseFileName;
+
+ if(qualFileName != ""){
+ QualityScores currQual;
+
+ ifstream inQual;
+ m->openInputFile(qualFileName, inQual);
+
+ ofstream outQual;
+ string qualReverseFileName = outputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
+ m->openOutputFile(qualReverseFileName, outQual);
+
+ while(!inQual.eof()){
+ if (m->control_pressed) { inQual.close(); outQual.close(); remove(qualReverseFileName.c_str()); 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);
+ }
+
+ if (m->control_pressed) { remove(qualReverseFileName.c_str()); remove(fastaReverseFileName.c_str()); return 0; }
- ifstream inFASTA;
- openInputFile(fasta, inFASTA);
+ //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); }
+ }
- ofstream outFASTA;
- string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
- openOutputFile(reverseFile, outFASTA);
- while(!inFASTA.eof()){
- Sequence currSeq(inFASTA);
- currSeq.reverseComplement();
- currSeq.printSequence(outFASTA);
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ for(int i=0;i<outputNames.size();i++){
+ m->mothurOut(outputNames[i]);
+ m->mothurOutEndLine();
}
- inFASTA.close();
- outFASTA.close();
- return 0;
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReverseSeqsCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff