--- /dev/null
+/*
+ * parsefastaqcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/30/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "parsefastaqcommand.h"
+#include "sequence.hpp"
+
+//**********************************************************************************************************************
+vector<string> ParseFastaQCommand::setParameters(){
+ try {
+ CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
+ CommandParameter pfasta("fasta", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
+ CommandParameter pqual("qfile", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pqual);
+ 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, "ParseFastaQCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ParseFastaQCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
+ helpString += "The fastq.info command parameters are fastq, fasta and qfile; fastq is required.\n";
+ helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+ helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
+ helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
+ helpString += "Example fastq.info(fastaq=test.fastaq).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ParseFastaQCommand::ParseFastaQCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ParseFastaQCommand::ParseFastaQCommand(string option){
+ try {
+ abort = false; calledHelp = false;
+
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ 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++) {
+ 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("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["fastq"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ 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
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastaQFile); }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "fasta", false); if(temp == "not found"){ temp = "T"; }
+ fasta = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "qfile", false); if(temp == "not found"){ temp = "T"; }
+ qual = m->isTrue(temp);
+
+ if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ParseFastaQCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //open Output Files
+ string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
+ string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
+ ofstream outFasta, outQual;
+
+ if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); }
+ if (qual) { m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); }
+
+ ifstream in;
+ m->openInputFile(fastaQFile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ //read sequence name
+ string name = m->getline(in); m->gobble(in);
+ if (name == "") { m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ else { name = name.substr(1); }
+
+ //read sequence
+ string sequence = m->getline(in); m->gobble(in);
+ if (sequence == "") { m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; break; }
+
+ //read sequence name
+ string name2 = m->getline(in); m->gobble(in);
+ if (name2 == "") { m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+ else { name2 = name2.substr(1); }
+
+ //read quality scores
+ string quality = m->getline(in); m->gobble(in);
+ if (quality == "") { 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 (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 (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+
+ //print sequence info to files
+ if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
+
+ if (qual) {
+ vector<int> qualScores = convertQual(quality);
+ outQual << ">" << name << endl;
+ for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
+ outQual << endl;
+ }
+ }
+
+ in.close();
+ if (fasta) { outFasta.close(); }
+ if (qual) { outQual.close(); }
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); 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(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<int> ParseFastaQCommand::convertQual(string qual) {
+ try {
+ vector<int> qualScores;
+
+ int controlChar = int('!');
+
+ for (int i = 0; i < qual.length(); i++) {
+ int temp = int(qual[i]);
+ temp -= controlChar;
+
+ qualScores.push_back(temp);
+ }
+
+ return qualScores;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "convertQual");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff