--- /dev/null
+//
+// sracommand.cpp
+// Mothur
+//
+// Created by SarahsWork on 10/28/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#include "sracommand.h"
+
+//**********************************************************************************************************************
+vector<string> SRACommand::setParameters(){
+ try {
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","sra",false,false); parameters.push_back(psff);
+ CommandParameter pfastqfile("fastqfile", "InputTypes", "", "", "none", "none", "none","sra",false,false); parameters.push_back(pfastqfile);
+ //choose only one multiple options
+ CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform);
+ //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
+ 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, "SRACommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SRACommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The sra command creates a sequence read archive from sff or fastq files.\n";
+ helpString += "The sra command parameters are: sff, fastqfiles, oligos, platform....\n";
+ helpString += "The sffiles parameter is used to provide a file containing a \n";
+ helpString += "The new command should be in the following format: \n";
+ helpString += "new(...)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SRACommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "sra") { pattern = "[filename],sra"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SRACommand::SRACommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["sra"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "SRACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SRACommand::SRACommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ //valid paramters for this command
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+
+ //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("sfffiles");
+ //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["sfffiles"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fastqfiles");
+ //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["fastqfiles"] = inputDir + it->second; }
+ }
+ }
+
+ //check for parameters
+ fastqfiles = validParameter.validFile(parameters, "fastqfiles", true);
+ if (fastqfiles == "not open") { fastqfiles = ""; abort = true; }
+ else if (fastqfiles == "not found") { fastqfiles = ""; }
+
+ sfffiles = validParameter.validFile(parameters, "sfffiles", true);
+ if (sfffiles == "not open") { sfffiles = ""; abort = true; }
+ else if (sfffiles == "not found") { sfffiles = ""; }
+
+ if ((fastqfiles == "") && (sfffiles == "")) {
+ m->mothurOut("No valid current files. You must provide a sfffiles or fastqfiles file before you can use the sra command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ //use only one Mutliple type
+ platform = validParameter.validFile(parameters, "platform", false);
+ if (platform == "not found") { platform = "454"; }
+
+ if ((platform == "454") || (platform == "????") || (platform == "????") || (platform == "????")) { }
+ else { m->mothurOut("Not a valid platform option. Valid platform options are 454, ...."); m->mothurOutEndLine(); abort = true; }
+
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SRACommand", "SRACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int SRACommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+
+
+ //output files created by command
+ 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, "SRACommand", "SRACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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