--- /dev/null
+//
+// makelookupcommand.cpp
+// Mothur
+//
+// Created by SarahsWork on 5/14/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#include "makelookupcommand.h"
+
+//**********************************************************************************************************************
+vector<string> MakeLookupCommand::setParameters(){
+ try {
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","lookup",false,true,true); parameters.push_back(pflow);
+ CommandParameter perrors("error", "InputTypes", "", "", "none", "none", "none","none",false,true,true); parameters.push_back(perrors);
+ CommandParameter pbarcode("barcode", "String", "", "AACCGTGTC", "", "", "","",false,false); parameters.push_back(pbarcode);
+ CommandParameter pkey("key", "String", "", "TCAG", "", "", "","",false,false); parameters.push_back(pkey);
+ CommandParameter pthreshold("threshold", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter porder("order", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder);
+ 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, "MakeLookupCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MakeLookupCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The make.lookup command allows you to create custom lookup files for use with shhh.flows.\n";
+ helpString += "The make.lookup command parameters are: reference, flow, error, barcode, key, threshold and order.\n";
+ helpString += "The reference file needs to be in the same direction as the flow data and it must start with the forward primer sequence. It is required.\n";
+ helpString += "The flow parameter is used to provide the flow data. It is required.\n";
+ helpString += "The error parameter is used to provide the error summary. It is required.\n";
+ helpString += "The barcode parameter is used to provide the barcode sequence. Default=AACCGTGTC.\n";
+ helpString += "The key parameter is used to provide the key sequence. Default=TACG.\n";
+ helpString += "The threshold parameter is ....\n";
+ helpString += "The order parameter options are A, B or I. Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n";
+ helpString += "The make.lookup should be in the following format: make.lookup(reference=HMP_MOCK.v53.fasta, flow=H3YD4Z101.mock3.flow_450.flow, error=H3YD4Z101.mock3.flow_450.error.summary, barcode=AACCTGGC)\n";
+ helpString += "new(...)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MakeLookupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "lookup") { pattern = "[filename],lookup"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MakeLookupCommand::MakeLookupCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["lookup"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "MakeLookupCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MakeLookupCommand::MakeLookupCommand(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; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["lookup"] = 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("flow");
+ //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["flow"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("error");
+ //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["error"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("reference");
+ //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["reference"] = inputDir + it->second; }
+ }
+
+ }
+
+ //check for parameters
+ errorFileName = validParameter.validFile(parameters, "error", true);
+ if (errorFileName == "not open") { errorFileName = ""; abort = true; }
+ else if (errorFileName == "not found") { errorFileName = ""; m->mothurOut("[ERROR]: error parameter is required."); m->mothurOutEndLine(); abort = true; }
+
+ flowFileName = validParameter.validFile(parameters, "flow", true);
+ if (flowFileName == "not open") { flowFileName = ""; abort = true; }
+ else if (flowFileName == "not found") { flowFileName = ""; m->mothurOut("[ERROR]: flow parameter is required."); m->mothurOutEndLine(); abort = true; }
+ else { m->setFlowFile(flowFileName); }
+
+ refFastaFileName = validParameter.validFile(parameters, "reference", true);
+ if (refFastaFileName == "not open") { abort = true; }
+ else if (refFastaFileName == "not found") { refFastaFileName = ""; m->mothurOut("[ERROR]: reference parameter is required."); m->mothurOutEndLine(); 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(flowFileName); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "10000"; }
+ m->mothurConvert(temp, thresholdCount);
+
+ barcodeSequence = validParameter.validFile(parameters, "barcode", false); if (barcodeSequence == "not found"){ barcodeSequence = "AACCGTGTC"; }
+
+ keySequence = validParameter.validFile(parameters, "key", false); if (keySequence == "not found"){ keySequence = "TCAG"; }
+
+ temp = validParameter.validFile(parameters, "order", false); if (temp == "not found"){ temp = "A"; }
+ if (temp.length() > 1) { m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true;
+ }
+ else {
+ if (toupper(temp[0]) == 'A') { flowOrder = "TACG"; }
+ else if(toupper(temp[0]) == 'B'){
+ flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC"; }
+ else if(toupper(temp[0]) == 'I'){
+ flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC"; }
+ else {
+ m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true;
+ }
+ }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "MakeLookupCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int MakeLookupCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ cout.setf(ios::fixed, ios::floatfield);
+ cout.setf(ios::showpoint);
+
+ double gapOpening = 10;
+ int maxHomoP = 101;
+ vector<vector<double> > penaltyMatrix(maxHomoP);
+ for(int i=0;i<maxHomoP;i++){
+ penaltyMatrix[i].resize(maxHomoP, 5);
+ penaltyMatrix[i][i] = 0;
+ }
+
+ //Create flows for reference sequences...
+ ifstream refFASTA;
+ m->openInputFile(refFastaFileName, refFASTA); // * open reference sequence file
+ map<string, vector<double> > refFlowgrams;
+
+ while(!refFASTA.eof()){
+ if (m->control_pressed) { refFASTA.close(); return 0; }
+ Sequence seq(refFASTA); m->gobble(refFASTA);
+
+ string fullSequence = keySequence + barcodeSequence + seq.getAligned(); // * concatenate the keySequence, barcodeSequence, and
+ // referenceSequences
+ refFlowgrams[seq.getName()] = convertSeqToFlow(fullSequence, flowOrder); // * translate concatenated sequences into flowgram
+ }
+ refFASTA.close();
+
+ vector<vector<double> > lookupTable(1000);
+ for(int i=0;i<1000;i++){
+ lookupTable[i].resize(11, 0);
+ }
+
+
+ //Loop through each sequence in the flow file and the error summary file.
+ ifstream flowFile;
+ m->openInputFile(flowFileName, flowFile);
+ int numFlows;
+ flowFile >> numFlows;
+
+ ifstream errorFile;
+ m->openInputFile(errorFileName, errorFile);
+ m->getline(errorFile); //grab headers
+
+ string errorQuery, flowQuery, referenceName, dummy;
+ string chimera;
+ float intensity;
+
+ vector<double> std(11, 0);
+
+ while(errorFile && flowFile){
+
+ if (m->control_pressed) { errorFile.close(); flowFile.close(); return 0; }
+
+ // * if it's chimeric, chuck it
+ errorFile >> errorQuery >> referenceName;
+ for(int i=2;i<40;i++){
+ errorFile >> dummy;
+ }
+ errorFile >> chimera;
+
+
+ if(chimera == "2"){
+ m->getline(flowFile);
+ }
+ else{
+
+ flowFile >> flowQuery >> dummy;
+ if(flowQuery != errorQuery){ cout << flowQuery << " != " << errorQuery << endl; }
+
+ vector<double> refFlow = refFlowgrams[referenceName]; // * compare sequence to its closest reference
+
+ vector<double> flowgram(numFlows);
+
+ for(int i=0;i<numFlows;i++){
+ flowFile >> intensity;
+ flowgram[i] = intensity;// (int)round(100 * intensity);
+ }
+ m->gobble(flowFile);
+
+ alignFlowGrams(flowgram, refFlow, gapOpening, penaltyMatrix, flowOrder);
+
+ if (m->control_pressed) { errorFile.close(); flowFile.close(); return 0; }
+
+ for(int i=0;i<flowgram.size();i++){
+ int count = (int)round(100*flowgram[i]);
+ if(count > 1000){count = 999;}
+ if(abs(flowgram[i]-refFlow[i])<=0.50){
+ lookupTable[count][int(refFlow[i])]++; // * build table
+ std[int(refFlow[i])] += (100*refFlow[i]-count)*(100*refFlow[i]-count);
+ }
+ }
+
+ }
+ m->gobble(errorFile);
+ m->gobble(flowFile);
+ }
+ errorFile.close(); flowFile.close();
+
+ //get probabilities
+ vector<int> counts(11, 0);
+ int totalCount = 0;
+ for(int i=0;i<1000;i++){
+ for(int j=0;j<11;j++){
+ counts[j] += lookupTable[i][j];
+ totalCount += lookupTable[i][j];
+ }
+ }
+
+ int N = 11;
+ for(int i=0;i<11;i++){
+ if(counts[i] < thresholdCount){ N = i; break; } //bring back
+ std[i] = sqrt(std[i]/(double)(counts[i])); //bring back
+ }
+
+ regress(std, N); //bring back
+
+ if (m->control_pressed) { return 0; }
+
+ double minProbability = 0.1 / (double)totalCount;
+
+ //calculate the negative log probabilities of each intensity given the actual homopolymer length; impute with a guassian when counts are too low
+ double sqrtTwoPi = 2.50662827463;//pow(2.0 * 3.14159, 0.5);
+
+ for(int i=0;i<1000;i++){
+ if (m->control_pressed) { return 0; }
+
+ for(int j=0;j<N;j++){
+ if(lookupTable[i][j] == 0){
+ lookupTable[i][j] = 1; //bring back
+ }
+ lookupTable[i][j] = -log(lookupTable[i][j]/double(counts[j])); //bring back
+ }
+
+ for(int j=N;j<11;j++){ //bring back
+ double normalProbability = 1.0/((double)std[j] * sqrtTwoPi) * exp(-double(i - j*100)* double(i - j*100)/ double(2*std[j]*std[j]));
+ if(normalProbability > minProbability){
+ lookupTable[i][j] = -log(normalProbability);
+ }
+ else{
+ lookupTable[i][j] = -log(minProbability);
+ }
+ }
+ }
+
+
+ //calculate the probability of each homopolymer length
+ vector<double> negLogHomoProb(11, 0.00); //bring back
+ for(int i=0;i<N;i++){
+ negLogHomoProb[i] = -log(counts[i] / (double)totalCount);
+ }
+ regress(negLogHomoProb, N);
+
+ if (m->control_pressed) { return 0; }
+
+ //output data table. column one is the probability of each homopolymer length
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string outputFile = getOutputFileName("lookup",variables);
+ outputNames.push_back(outputFile); outputTypes["lookup"].push_back(outputFile);
+
+ ofstream lookupFile;
+ m->openOutputFile(outputFile, lookupFile);
+ lookupFile.precision(8);
+
+ for(int j=0;j<11;j++){
+ // lookupFile << counts[j];
+ lookupFile << showpoint << negLogHomoProb[j]; //bring back
+ for(int i=0;i<1000;i++){
+ lookupFile << '\t' << lookupTable[i][j];
+ }
+ lookupFile << endl;
+ }
+ lookupFile.close();
+
+ m->mothurOut("\nData for homopolymer lengths of " + toString(N) + " and longer were imputed for this analysis\n\n");
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ 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, "MakeLookupCommand", "execute");
+ exit(1);
+ }
+}
+//******************************************************************************************************************************
+
+vector<double> MakeLookupCommand::convertSeqToFlow(string sequence, string order){
+ try {
+ int seqLength = (int)sequence.length();
+ int numFlows = (int)order.length();
+ vector<double> flowgram;
+
+ int orderIndex = 0;
+ int sequenceIndex = 0;
+
+ while(orderIndex < numFlows && sequenceIndex < seqLength){
+
+ if (m->control_pressed) { return flowgram; }
+
+ int homopolymerLength = 1;
+
+ char base = sequence[sequenceIndex];
+
+ while(base == sequence[sequenceIndex+1] && sequenceIndex < seqLength){
+ homopolymerLength++;
+ sequenceIndex++;
+ }
+
+ sequenceIndex++;
+
+ for(int i=orderIndex; i<orderIndex+numFlows;i++){
+ if(order[i%numFlows] == base){
+ //flowgram[i] = homopolymerLength;
+ orderIndex = i%numFlows;
+ break;
+ }else { flowgram.push_back(0); }
+ }
+
+ //flowgram[orderIndex] = homopolymerLength;
+ flowgram.push_back(homopolymerLength);
+
+ orderIndex++;
+ orderIndex = orderIndex % numFlows;
+ }
+
+ return flowgram;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "convertSeqToFlow");
+ exit(1);
+ }
+}
+//******************************************************************************************************************************
+
+int MakeLookupCommand::alignFlowGrams(vector<double>& flowgram, vector<double>& refFlow, double gapOpening, vector<vector<double> > penaltyMatrix, string flowOrder){
+ try {
+ int numQueryFlows = (int)flowgram.size();
+ int numRefFlows = (int)refFlow.size();
+
+ //cout << numQueryFlows << '\t' << numRefFlows << endl;
+
+ vector<vector<double> > scoreMatrix(numQueryFlows+1);
+ vector<vector<char> > directMatrix(numQueryFlows+1);
+
+ for(int i=0;i<=numQueryFlows;i++){
+ if (m->control_pressed) { return 0; }
+ scoreMatrix[i].resize(numRefFlows+1, 0.00);
+ directMatrix[i].resize(numRefFlows+1, 'x');
+
+ scoreMatrix[i][0] = i * gapOpening;
+ directMatrix[i][0] = 'u';
+ }
+
+ //cout << numQueryFlows << '\t' << numRefFlows << endl;
+
+
+ for(int i=0;i<=numRefFlows;i++){
+ scoreMatrix[0][i] = i * gapOpening;
+ directMatrix[0][i] = 'l';
+ }
+
+ for(int i=1;i<=numQueryFlows;i++){
+ for(int j=1;j<=numRefFlows;j++){
+ if (m->control_pressed) { return 0; }
+ double diagonal = 1000000000;
+ if(flowOrder[i%flowOrder.length()] == flowOrder[j%flowOrder.length()]){
+ diagonal = scoreMatrix[i-1][j-1] + penaltyMatrix[round(flowgram[i-1])][refFlow[j-1]];
+ }
+ double up = scoreMatrix[i-1][j] + gapOpening;
+ double left = scoreMatrix[i][j-1] + gapOpening;
+
+ double minScore = diagonal;
+ char direction = 'd';
+
+ if(left < diagonal && left < up){
+ minScore = left;
+ direction = 'l';
+ }
+ else if(up < diagonal && up < left){
+ minScore = up;
+ direction = 'u';
+ }
+
+ scoreMatrix[i][j] = minScore;
+ directMatrix[i][j] = direction;
+
+ }
+ }
+
+ int minRowIndex = numQueryFlows;
+ double minRowScore = scoreMatrix[numQueryFlows][numRefFlows];
+ for(int i=0;i<numQueryFlows;i++){
+ if (m->control_pressed) { return 0; }
+ if(scoreMatrix[i][numRefFlows] < minRowScore){
+ minRowScore = scoreMatrix[i][numRefFlows];
+ minRowIndex = i;
+ }
+ }
+
+ int minColumnIndex = numRefFlows;
+ double minColumnScore = scoreMatrix[numQueryFlows][numRefFlows];
+ for(int i=0;i<numQueryFlows;i++){
+ if (m->control_pressed) { return 0; }
+ if(scoreMatrix[numQueryFlows][i] < minColumnScore){
+ minColumnScore = scoreMatrix[numQueryFlows][i];
+ minColumnIndex = i;
+ }
+ }
+
+
+ int i=minRowIndex;
+ int j= minColumnIndex;
+
+ vector<double> newFlowgram;
+ vector<double> newRefFlowgram;
+
+ while(i > 0 && j > 0){
+ if (m->control_pressed) { return 0; }
+ if(directMatrix[i][j] == 'd'){
+ newFlowgram.push_back(flowgram[i-1]);
+ newRefFlowgram.push_back(refFlow[j-1]);
+
+ i--;
+ j--;
+ }
+ else if(directMatrix[i][j] == 'l'){
+ newFlowgram.push_back(0);
+ newRefFlowgram.push_back(refFlow[j-1]);
+
+ j--;
+ }
+ else if(directMatrix[i][j] == 'u'){
+ newFlowgram.push_back(flowgram[i-1]);
+ newRefFlowgram.push_back(0);
+
+ i--;
+ }
+ }
+
+ flowgram = newFlowgram;
+ refFlow = newRefFlowgram;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "alignFlowGrams");
+ exit(1);
+ }
+}
+
+//******************************************************************************************************************************
+
+int MakeLookupCommand::regress(vector<double>& data, int N){
+ try {
+ //fit data for larger values of N
+ double xMean = 0;
+ double yMean = 0;
+
+ for(int i=1;i<N;i++){
+ if (m->control_pressed) { return 0; }
+ xMean += i;
+ yMean += data[i];
+ }
+ xMean /= (N-1);
+ yMean /= (N-1);
+
+ double numerator = 0;
+ double denomenator = 0;
+ for(int i=1;i<N;i++){
+ if (m->control_pressed) { return 0; }
+ numerator += (i-xMean)*(data[i] - yMean);
+ denomenator += (i-xMean) * (i-xMean);
+ }
+ double slope = numerator / denomenator;
+ double intercept = yMean - slope * xMean;
+
+ for(int i=N;i<11;i++){
+ data[i] = intercept + i * slope;
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeLookupCommand", "regress");
+ exit(1);
+ }
+}
+
+//******************************************************************************************************************************
+
+//**********************************************************************************************************************
+
+
projects / mothur.git / commitdiff