<?php
include '../REDTools/REDLog.php';
include '../database/DatabaseManager.php';
include '../database/DatabaseConnect.php';
include '../filters/denovo/SpliceJunctionFilter.php';
include '../database/TableCreator.php';
include '../REDTools/REDTools.php';
include '../REDTools/SiteBean.php';
$con = DatabaseConnect::mysqlConnect();
$args = array("2");
$previousTable = "bj22n_qcfilter_rrfilter";
$currentFilterName = SpliceJunctionFilter::getName();
$currentTable = REDTools::getFirstHalfTableName($previousTable) . $currentFilterName;
SpliceJunctionFilter::performSpliceJunctionFilter($con, $previousTable, $currentTable, $args);
static function executeFilters()
{
$startInfo = "RNA Editing Detector start\r\n" . "--------------------------\r\n" . "--------------------------\r\n";
REDLog::writeInfoLog($startInfo);
$infoPath = "../infoFile";
if (($lineArray = REDTools::readInfoFile($infoPath)) != false) {
$con = DatabaseConnect::mysqlConnect();
$userid = $lineArray[0];
$rnaVcfName = $lineArray[1];
$dnaVcfName = $lineArray[2];
$etArgs = $lineArray[3];
$qcArray = explode('/', $lineArray[4]);
$qcArgs = array($qcArray[0], $qcArray[1]);
$rrArgs = array(0);
$sjArgs = array($lineArray[5]);
$ksArgs = array(0);
$drArgs = array();
//assignment in DRMode
$lrArgs = array();
$storgePath = "G:/Taruca/data/";
$rnaVcfFilePath = $storgePath . $rnaVcfName;
$dnaVcfFilePath = $storgePath . $dnaVcfName;
if ($rnaVcfName !== "null") {
//denove mode
//load RNAVcfFile
$rnaVcfTableNameArray = RNAVCFParser::parseMultiRNAVCFFile($con, $rnaVcfFilePath, $userid);
if ($dnaVcfName !== "null") {
$dnaVcfTableNameArray = DNAVCFParser::parseMultiDNAVCFFile($con, $dnaVcfFilePath, $userid);
}
if (count($rnaVcfTableNameArray) != 0) {
$i = 0;
foreach ($rnaVcfTableNameArray as $rnaVcfTableName) {
$etTableName = REDTools::getFirstHalfTableName($rnaVcfTableName) . EditingTypeFilter::getName() . "_" . date("Ymdhisa");
EditingTypeFilter::performEditingTypeFilter($con, $rnaVcfTableName, $etTableName, $etArgs);
$qcTableName = REDTools::getFirstHalfTableName($etTableName) . QualityControlFilter::getName() . "_" . date("Ymdhisa");
QualityControlFilter::performQualityControlFilter($con, $etTableName, $qcTableName, $qcArgs);
$rrTableName = REDTools::getFirstHalfTableName($qcTableName) . RepeatRegionsFilter::getName() . "_" . date("Ymdhisa");
RepeatRegionsFilter::performRepeatRegionsFilter($con, $qcTableName, $rrTableName, $rrArgs);
$sjTableName = REDTools::getFirstHalfTableName($rrTableName) . SpliceJunctionFilter::getName() . "_" . date("Ymdhisa");
SpliceJunctionFilter::performSpliceJunctionFilter($con, $rrTableName, $sjTableName, $sjArgs);
$ksTableName = REDTools::getFirstHalfTableName($sjTableName) . KnownSNPFilter::getName() . "_" . date("Ymdhisa");
KnownSNPFilter::performKnownSNPFilter($con, $sjTableName, $ksTableName, $ksArgs);
if ($dnaVcfName == "null") {
REDTools::writeTableIntoDb($con, $userid, $ksTableName);
} else {
if (count($dnaVcfTableNameArray) == count($rnaVcfTableNameArray)) {
$drTableName = REDTools::getFirstHalfTableName($ksTableName) . DNARNAFilter::getName() . "_" . date("Ymdhisa");
$drArgs[0] = $dnaVcfTableNameArray[$i];
$drArgs[1] = $lineArray[6];
DNARNAFilter::performDNARNAFilter($con, $ksTableName, $drTableName, $drArgs);
$lrTableName = REDTools::getFirstHalfTableName($drTableName) . LikelihoodRateFilter::getName() . "_" . date("Ymdhisa");
$lrArgs[0] = $dnaVcfTableNameArray[$i];
$lrArgs[1] = $lineArray[7];
LikelihoodRateFilter::performLikelihoodRateFilter($con, $drTableName, $lrTableName, $lrArgs);
REDTools::writeTableIntoDb($con, $userid, $lrTableName);
} else {
REDLog::writeErrLog("The num of DNA sample is different from RNA sample, please check your vcf file");
}
}
$i++;
}
} else {
REDLog::writeErrLog("There is no rnaVcfTables");
}
}
$endInfo = "------------------------\r\n" . "------------------------\r\n" . "RNA Editing Detector end\r\n";
REDLog::writeInfoLog("{$endInfo}");
} else {
//sleep 10 minute，20s to test
sleep(20);
self::executeFilters();
}
}