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|
//
// 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=TCAG.\n";
helpString += "The threshold parameter is ....Default=10000.\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; penaltyMatrix.resize(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);
if (m->debug) { m->mothurOut("[DEBUG]: seq = " + seq.getName() + ".\n"); }
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; lookupTable.resize(1000);
for(int i=0;i<1000;i++){
lookupTable[i].resize(11, 0);
}
if (m->debug) { m->mothurOut("[DEBUG]: here .\n"); }
//Loop through each sequence in the flow file and the error summary file.
ifstream flowFile;
m->openInputFile(flowFileName, flowFile);
int numFlows;
flowFile >> numFlows;
if (m->debug) { m->mothurOut("[DEBUG]: numflows = " + toString(numFlows) + ".\n"); }
ifstream errorFile;
m->openInputFile(errorFileName, errorFile);
m->getline(errorFile); //grab headers
string errorQuery, flowQuery, referenceName, dummy;
string chimera;
float intensity;
vector<double> std; std.resize(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; }
map<string, vector<double> >::iterator it = refFlowgrams.find(referenceName); // * compare sequence to its closest reference
if (it == refFlowgrams.end()) {
m->mothurOut("[WARNING]: missing reference flow " + referenceName + ", ignoring flow " + flowQuery + ".\n");
m->getline(flowFile); m->gobble(flowFile);
}else {
vector<double> refFlow = it->second;
vector<double> flowgram; flowgram.resize(numFlows);
if (m->debug) { m->mothurOut("[DEBUG]: flowQuery = " + flowQuery + ".\t" + "refName " + referenceName+ ".\n"); }
for(int i=0;i<numFlows;i++){
flowFile >> intensity;
flowgram[i] = intensity;// (int)round(100 * intensity);
}
m->gobble(flowFile);
if (m->debug) { m->mothurOut("[DEBUG]: before align.\n"); }
alignFlowGrams(flowgram, refFlow, gapOpening, penaltyMatrix, flowOrder);
if (m->debug) { m->mothurOut("[DEBUG]: after align.\n"); }
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; counts.resize(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; negLogHomoProb.resize(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; scoreMatrix.resize(numQueryFlows+1);
vector<vector<char> > directMatrix; directMatrix.resize(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<numRefFlows;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);
}
}
//******************************************************************************************************************************
//**********************************************************************************************************************
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