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';