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 performLikelihoodRateFilter($con, $previousTable, $currentTable, $args)
{
if ($args == null || count($args) == 0) {
return;
} else {
if (count($args) != 2) {
REDLog::writeErrLog("Args for Likelihood Rate Test Filter are incomplete, please have a check");
}
}
$dnaVcfTable = $args[0];
$threshold = (double) $args[1];
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing Likelihood Rate Test Filter");
$sqlClause1 = "select {$previousTable}.chrom,{$previousTable}.pos,{$previousTable}.AD,\n{$dnaVcfTable}.qual from {$previousTable},{$dnaVcfTable} where {$previousTable}.chrom=\n{$dnaVcfTable}.chrom and {$previousTable}.pos={$dnaVcfTable}.pos";
$rs = DatabaseManager::query1($con, $sqlClause1);
$i = 0;
while ($row = mysqli_fetch_array($rs)) {
$chr = (string) $row[0];
$pos = (int) $row[1];
$ad = (string) $row[2];
$qual = (double) $row[3];
$pb = new SiteBean();
$pb->SiteBean1($chr, $pos);
$pb->setAd($ad);
$pb->setQual($qual);
$siteBeans[$i] = $pb;
$i++;
}
DatabaseManager::setAutoCommit($con, false);
$count = 0;
for ($j = 0; $j < $i; $j++) {
$str = $siteBeans[$j]->getAd();
$section = explode("/", $str);
$ref = (int) $section[0];
$alt = (int) $section[1];
if ($ref + $alt > 0) {
$f_ml = 1.0 * $ref / ($ref + $alt);
$y = pow($f_ml, $ref) * pow(1 - $f_ml, $alt);
$y = log($y) / log(10.0);
$judge = $y + $siteBeans[$j]->getQual() / 10.0;
if ($judge >= $threshold) {
$siteChr = $siteBeans[$j]->getChr();
$sitePos = $siteBeans[$j]->getPos();
$sqlClause2 = "insert into {$currentTable} select * from {$previousTable} where chrom='" . $siteChr . "' and pos=" . $sitePos;
DatabaseManager::insertClause($con, $sqlClause2);
if (++$count % 10000 == 0) {
DatabaseManager::commit($con);
}
}
}
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
REDLog::writeInfoLog("End performing Likelihood Rate Test Filter");
}
static function performQualityControlFilter($con, $previousTable, $currentTable, $args)
{
$COMMIT_COUNTS_PER_ONCE = 10000;
if ($args == null || count($args) == 0) {
return;
} elseif (count($args) != 2) {
REDLog::writeErrLog("Args for Quality Control Filter are incomplete, please have a check");
}
$quality = (double) $args[0];
$depth = (int) $args[1];
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing Quality Control Filter");
try {
$count = 0;
$str = array("CHROM", "POS", "AD");
$rs = DatabaseManager::query2($con, $previousTable, $str, null, null);
$i = 0;
while ($row = mysqli_fetch_array($rs)) {
if ($row[2] != null) {
$siteBean = new SiteBean();
$siteBean->SiteBean1($row[0], $row[1]);
$siteBean->setAd($row[2]);
$siteBeans[$i] = $siteBean;
$i = $i + 1;
}
}
DatabaseManager::setAutoCommit($con, false);
for ($j = 0; $j < $i; $j++) {
$str = $siteBeans[$j]->getAd();
$section = explode("/", $str);
$ref_n = (int) $section[0];
$alt_n = (int) $section[1];
$pos = $siteBeans[$j]->getPos();
$chr = $siteBeans[$j]->getChr();
if ($ref_n + $alt_n >= $depth) {
$sqlClause = "insert into " . $currentTable . " (select * from " . $previousTable . " where filter='PASS' and pos={$pos} and qual>=" . $quality . " and chrom='" . $chr . "')";
$v = mysqli_query($con, $sqlClause);
if (++$count % $COMMIT_COUNTS_PER_ONCE == 0) {
DatabaseManager::commit($con);
}
}
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
if (!$v) {
throw new Exception("Error execute sql clause in QualityControlFilter:performFilter()");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing Quality Control Filter");
}
static function performKnownSNPFilter($con, $previousTable, $currentTable, $args)
{
REDLog::writeInfoLog("Start performing Known SNP Filter");
TableCreator::createFilterTable($con, $previousTable, $currentTable);
$dbSnpTable = "dbsnp_database";
try {
$sqlClause = "insert into {$currentTable} select * from {$previousTable} where not exists (select chrom from\n{$dbSnpTable} where ({$dbSnpTable}.chrom={$previousTable}.chrom and {$dbSnpTable}.pos={$previousTable}.pos))";
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in performKnownSNPFilter");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing Known SNP 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:' . $sql2);
}
REDLog::writeInfoLog('End executing Editing Type Filter');
}
static function performSpliceJunctionFilter($con, $previousTable, $currentTable, $args)
{
if ($args == null || $args == 0) {
return;
} else {
if (count($args) != 1) {
REDLog::writeErrLog("Args for Splice Junction Filter are incomplete, please have a check");
}
}
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing Splice Junction Filter...");
$spliceJunctionTable = "splice_junction";
$edge = (int) $args[0];
try {
$sqlClause = "insert into {$currentTable} select * from {$previousTable} where not exists (select chrom from\n{$spliceJunctionTable} where ({$spliceJunctionTable}.type='CDS' and {$spliceJunctionTable}.chrom={$previousTable}.chrom\nand (({$spliceJunctionTable}.begin<{$previousTable}.pos+{$edge} and {$spliceJunctionTable}.begin>{$previousTable}.pos-{$edge})\nor ({$spliceJunctionTable}.end<{$previousTable}.pos+{$edge} and {$spliceJunctionTable}.end>{$previousTable}.pos-{$edge}))))";
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in performSpliceJunctionFilter");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing Splice Junction Filter...");
}
<?php include '../database/DatabaseConnect.php'; include '../database/TableCreator.php'; include '../database/DatabaseManager.php'; include '../REDTools/REDLog.php'; $con = DatabaseConnect::mysqlConnect(); TableCreator::createFilterTable($con, 'users', 'test'); echo 'success';
