X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sracommand.cpp;fp=sracommand.cpp;h=c291ddda5369fcb1a87a3420867934e55acc61aa;hb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;hp=0000000000000000000000000000000000000000;hpb=fe08eacea5a2d34cd4bd27e8451fd2872102a80a;p=mothur.git

diff --git a/sracommand.cpp b/sracommand.cpp
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+++ b/sracommand.cpp
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+//
+//  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);
+	}
+}
+//**********************************************************************************************************************
+
+