#include "parsefastaqcommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::getValidParameters(){
+ try {
+ string Array[] = {"fastq", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ParseFastaQCommand::ParseFastaQCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fastq"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option){
try {
else {
//valid paramters for this command
- string Array[] = {"fastaq", "outputdir", "inputdir"};
+ string Array[] = {"fastq", "outputdir", "inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qual"] = 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("fastaq");
+ it = parameters.find("fastq");
//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["fastaq"] = inputDir + it->second; }
+ if (path == "") { parameters["fastq"] = inputDir + it->second; }
}
}
//check for required parameters
- fastaQFile = validParameter.validFile(parameters, "fastaq", true);
- if (fastaQFile == "not found") { m->mothurOut("fastaq is a required parameter for the parse.fastaq command."); m->mothurOutEndLine(); abort = true; }
+ fastaQFile = validParameter.validFile(parameters, "fastq", true);
+ if (fastaQFile == "not found") { m->mothurOut("fastq is a required parameter for the fastq.info command."); m->mothurOutEndLine(); abort = true; }
else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
void ParseFastaQCommand::help(){
try {
- m->mothurOut("The parse.fastaq command reads a fastaQ file and creates a fasta and quality file.\n");
- m->mothurOut("The parse.fastaq command parameter is fastaq, and it is required.\n");
- m->mothurOut("The parse.fastaq command should be in the following format: parse.fastaq(fastaq=yourFastaQFile).\n");
- m->mothurOut("Example parse.fastaq(fastaq=test.fastaq).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fastaq), '=' and yourFastaQFile.\n");
+ m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n");
+ m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
+ m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
+ m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n");
m->mothurOutEndLine();
}
catch(exception& e) {
string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
ofstream outFasta, outQual;
- m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile);
- m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile);
+ m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
+ m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qual"].push_back(qualFile);
ifstream in;
m->openInputFile(fastaQFile, in);
if (qual == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
//sanity check sequence length and number of quality scores match
- if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
//convert quality scores
outFasta.close();
outQual.close();
- if (m->control_pressed) { remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();