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");
}
<?php include "../REDTools/REDTools.php"; echo REDTools::getRandomString(10); echo "<hr>"; echo REDTools::getRandomString(5);
