static function performDNARNAFilter($con, $previousTable, $currentTable, $args)
{
if ($args == null || count($args) == 0) {
return;
} else {
if (count($args) != 2) {
REDLog::writeErrLog("Args for DNA-RNA Filter are incomplete, please have a check");
}
}
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing DNA-RNA Filter");
$dnaVcfTable = $args[0];
$editingType = $args[1];
$negativeType = REDTools::getNegativeStrandEditingType($editingType);
try {
$num1 = substr($editingType, 0, 1);
$num2 = substr($negativeType, 0, 1);
$sqlClause = "insert into {$currentTable} select * from {$previousTable} where exists (select chrom\nfrom {$dnaVcfTable} where ({$dnaVcfTable}.chrom={$previousTable}.chrom and {$dnaVcfTable}.pos={$previousTable}.pos and (\n{$dnaVcfTable}.ref='{$num1}' or {$dnaVcfTable}.ref='{$num2}')))";
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in performDNARNAFilter");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing DNA-RNA Filter");
}
static function performRepeatRegionsFilter($con, $previousTable, $currentTable, $args)
{
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing Repeat Regions Filter");
$repeatTable = "repeat_masker";
try {
$sqlClause1 = "insert into " . $currentTable . " select * from " . $previousTable . " where not exists (select * from " . $repeatTable . " where (" . $repeatTable . ".chrom= " . $previousTable . ".chrom and " . $repeatTable . ".begin<=" . $previousTable . ".pos and " . $repeatTable . ".end>=" . $previousTable . ".pos)) ";
$a = mysqli_query($con, $sqlClause1);
if (!$a) {
throw new Exception("Error execute sqlA clause in performRepeatRegionsFilter");
}
REDLog::writeInfoLog("Start finding sites in Alu Regions");
$tempTable = REDTools::getRandomString(10);
$sqlClause2 = "create temporary table {$tempTable} like {$currentTable}";
$b = mysqli_query($con, $sqlClause2);
if (!$b) {
throw new Exception("Error execute sqlB clause in performRepeatRegionsFilter");
}
$sqlClause3 = "insert into {$tempTable} select * from {$previousTable} where exists (select chrom from {$repeatTable}\nwhere {$repeatTable}.chrom = {$previousTable}.chrom and {$repeatTable}.begin<={$previousTable}.pos and\n{$repeatTable}.end>={$previousTable}.pos and {$repeatTable}.type='SINE/Alu')";
$c = mysqli_query($con, $sqlClause3);
if (!$c) {
throw new Exception("Error execute sqlC clause in performRepeatRegionsFilter");
}
$sqlClause4 = "update {$tempTable} set alu='T'";
$d = mysqli_query($con, $sqlClause4);
if (!$d) {
throw new Exception("Error execute sqlD clause in performRepeatRegionsFilter");
}
$sqlClause5 = "insert into {$currentTable} select * from {$tempTable}";
$e = mysqli_query($con, $sqlClause5);
if (!$e) {
throw new Exception("Error execute sqlE clause in performRepeatRegionsFilter");
}
DatabaseManager::deleteTable($con, $tempTable);
REDLog::writeInfoLog("End finding sites in Alu Regions");
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing Repeat Regions Filter");
}
static function performEditingTypeFilter($con, $previousTable, $currentTable, $args)
{
REDLog::writeInfoLog('Star executing Editing Type Filter');
TableCreator::createFilterTable($con, $previousTable, $currentTable);
$refAlt = $args;
$refAlt2 = REDTools::getNegativeStrandEditingType($refAlt);
$sql11 = substr($refAlt, 0, 1);
$sql12 = substr($refAlt, 1);
$sql21 = substr($refAlt2, 0, 1);
$sql22 = substr($refAlt2, 1);
$sql1 = "insert into " . $currentTable . " select * from " . $previousTable . " WHERE REF='{$sql11}' AND ALT='{$sql12}' AND GT!='0/0'";
$v = DatabaseManager::insertClause($con, $sql1);
if (!$v) {
REDLog::writeErrLog('There is a syntax error for SQL clause:' . $sql1);
}
$sql2 = "insert into " . $currentTable . " select * from " . $previousTable . " WHERE REF='{$sql21}' AND ALT='{$sql22}' AND GT!='0/0'";
$v = DatabaseManager::insertClause($con, $sql2);
if (!$v) {
REDLog::writeErrLog('There is a syntax error for SQL clause:' . $sql2);
}
REDLog::writeInfoLog('End executing Editing Type Filter');
}
<?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);
<?php
include "../REDTools/REDTools.php";
$tableName1 = "1_bj22n_rnavcf_20151117113605am";
$tableName2 = "1_bj22n_rnavcf_etfilter_20151117113905am";
$firstHalf1 = REDTools::getFirstHalfTableName($tableName1);
$firstHalf2 = REDTools::getFirstHalfTableName($tableName2);
echo "{$firstHalf1}";
echo "<hr>";
echo "{$firstHalf2}";
<?php
include '../REDTools/REDTools.php';
echo REDTools::getNegativeStrandEditingType('TC');
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();
}
}
<?php include "../REDTools/REDTools.php"; include "../REDTools/REDLog.php"; $dirPath = "../infoFile"; $fileArray = REDTools::readInfoFile($dirPath); //var_dump($fileArray); //echo count($fileArray); echo $fileArray;
<?php
include "../database/DatabaseConnect.php";
include "../database/DatabaseManager.php";
include "../database/TableCreator.php";
include "../dataparser/DNAVCFParser.php";
include "../dataparser/RNAVCFParser.php";
include "../filters/denovo/EditingTypeFilter.php";
include "../filters/denovo/KnownSNPFilter.php";
include "../filters/denovo/QualityControlFilter.php";
include "../filters/denovo/RepeatRegionsFilter.php";
include "../filters/denovo/SpliceJunctionFilter.php";
include "../filters/dnaran/DNARNAFilter.php";
include "../filters/dnaran/LikelihoodRateFilter.php";
include "../REDTools/REDLog.php";
include "../REDTools/REDTools.php";
include "../REDTools/SiteBean.php";
$infoPath = "../infoFile";
if (REDTools::readInfoFile($infoPath) != false) {
} else {
}
<?php include "../REDTools/REDTools.php"; echo REDTools::getRandomString(10); echo "<hr>"; echo REDTools::getRandomString(5);
<?php include '../database/DatabaseConnect.php'; include '../database/DatabaseManager.php'; include "../REDTools/REDTools.php"; $con = DatabaseConnect::mysqlConnect(); $userid = "1"; $tableName = "testwrite"; REDTools::writeTableIntoDb($con, $userid, $tableName); echo "end";