+++ /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