static function loadDbSNPTable($con, $dbSNPPath)
{
REDLog::writeInfoLog("Start loading dbSNP file into database");
$dbSNPTable = "dbsnp_database";
try {
if (!DatabaseManager::hasEstablishTable($con, $dbSNPTable)) {
self::createDBSNPTable($con, $dbSNPTable);
$count = 0;
$fp = fopen($dbSNPPath, 'r');
while ($line = fgets($fp) != null) {
if (strpos($line, "#") === 0) {
$count++;
} else {
break;
}
}
fclose($fp);
$sqlClause = "load data local infile '{$dbSNPPath}' into table {$dbSNPTable} IGNORE {$count} LINES";
//fields terminated by '\t' lines terminated by '\n'
echo $sqlClause;
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in loadDbSNPTable()");
}
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End loading dbSNP file into database");
}
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 loadRepeatTable($con, $repeatPath)
{
REDLog::writeInfoLog("Start loading RepeatMasker file into database");
$repeatTable = "repeat_masker";
try {
if (!DatabaseManager::hasEstablishTable($con, $repeatTable)) {
self::createRepeatRegionsTable($con, $repeatTable);
DatabaseManager::setAutoCommit($con, false);
$count = 0;
$fp = fopen($repeatPath, 'r');
fgets($fp);
fgets($fp);
fgets($fp);
while (($line = fgets($fp)) != null) {
$line1 = trim($line);
$section = explode(" ", preg_replace("/\\s(?=\\s)/", "\\1", $line1));
# /[\s]+/
$sqlClause = "insert into {$repeatTable}(chrom,begin,end,type) values('{$section['4']}','{$section['5']}','{$section['6']}','{$section['10']}')";
$v = mysqli_query($con, $sqlClause);
if (++$count % 10000 == 0) {
DatabaseManager::commit($con);
}
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
if (!$v) {
throw new Exception("Error execute sql clause in loadRepeatTable()\n");
}
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
fclose($fp);
REDLog::writeInfoLog("End loading RepeatMasker file into database");
}
static function performLikelihoodRateFilter($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 loadDarnedTable($con, $darnedPath)
{
REDLog::writeInfoLog("Start loading DARNED file into database");
$darnedTable = "darned_database";
if (!DatabaseManager::hasEstablishTable($con, $darnedTable)) {
self::createDARNEDTable($con, $darnedTable);
try {
$count = 0;
DatabaseManager::setAutoCommit($con, false);
$fp = fopen($darnedPath, 'r');
fgets($fp);
while (($line = fgets($fp)) != null) {
$line1 = trim($line);
$section = explode("\t", $line1);
$stringBulider = "insert into " . $darnedTable . "(chrom,coordinate,strand,inchr,inrna) values(";
for ($i = 0; $i < 5; $i++) {
if ($i == 0) {
$stringBulider = $stringBulider . "'chr" . $section[$i] . "',";
} else {
if ($i == 4) {
$sec = str_replace("I", "G", $section[$i]);
$stringBulider = $stringBulider . "'" . $sec . "'";
} else {
if ($i == 1) {
$stringBulider = $stringBulider . $section[$i] . ",";
} else {
$stringBulider = $stringBulider . "'" . $section[$i] . "',";
}
}
}
}
$stringBulider = $stringBulider . ")";
$v = mysqli_query($con, $stringBulider);
if (!$v) {
throw new Exception("Error execute sql clause in loadDarnedTable()");
}
if (++$count % 10000 == 0) {
DatabaseManager::commit($con);
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
}
REDLog::writeInfoLog("End loading DARNED file into database");
}
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 loadSpliceJunctionTable($con, $spliceJunctionPath)
{
REDLog::writeInfoLog("Start loading Gene Annotation File into database");
$spliceJunctionTable = "splice_junction";
if (!DatabaseManager::hasEstablishTable($con, $spliceJunctionTable)) {
self::createSpliceJunctionTable($con, $spliceJunctionTable);
try {
$sqlClause = "load data local infile '{$spliceJunctionPath}' into table {$spliceJunctionTable}";
/*fields terminated by '\t' lines terminated by '\n'*/
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in loadSpliceJunctionTable()");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
}
REDLog::writeInfoLog("End loading Gene Annotation File into database");
}
static function createReferenceTable($con, $tableName, $columnNames, $columnParams, $index)
{
if ($columnNames == null || $columnParams == null || count($columnNames) == 0 || count($columnNames) != count($columnParams)) {
REDLog::writeErrLog("Column names and column parameters can not be null or zero-length");
}
$stringBuilder = "create table if not exists {$tableName}({$columnNames['0']} {$columnParams['0']}";
for ($i = 1, $len = count($columnNames); $i < $len; $i++) {
$stringBuilder = $stringBuilder . ", {$columnNames[$i]} {$columnParams[$i]}";
}
$stringBuilder = $stringBuilder . ",{$index})";
try {
$v = mysqli_query($con, $stringBuilder);
if (!$v) {
throw new Exception("There is a syntax error for SQL clause: {$stringBuilder}");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
return $v;
}
static function loadRefSeqGeneTable($con, $refSeqGenePath)
{
REDLog::writeInfoLog("Start loading Ref Seq Gene File into database");
$refseqGeneTableName = "reference_gene";
if (!DatabaseManager::hasEstablishTable($con, $refseqGeneTableName)) {
self::createRefSeqGeneTable($con, $refseqGeneTableName);
try {
$sqlClause = "load data local infile '" . $refSeqGenePath . "' into table " . $refseqGeneTableName;
/*." fields terminated"
."by '\t' lines terminated by '\n'";*/
/*echo $sqlClause;*/
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in loadRefSeqGeneTable()");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
}
REDLog::writeInfoLog("End loading Ref Seq Gene File into database");
}
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 '../REDTools/REDLog.php'; include '../database/DatabaseManager.php'; $errInfo = '123'; REDLog::writeErrLog($errInfo);
static function getCurrentTables($con, $database)
{
$v = mysqli_query($con, "use {$database}");
if (!$v) {
REDLog::writeErrLog("can not use database: {$database} when getCurrentTables");
}
$rs = mysqli_query($con, "show tables");
$i = 0;
while ($row = mysqli_fetch_array($rs)) {
$tableLists[$i] = $row;
$i++;
}
return $tableLists;
}
static function parseMultiRNAVCFFile($con, $vcfPath, $userid)
{
$altColumn = 4;
$infoColumn = 7;
$formatColumnIndex = 8;
$columnLength = 0;
REDLog::writeInfoLog("Start parsing RNA VCF file");
try {
$fp = fopen($vcfPath, 'r');
DatabaseManager::setAutoCommit($con, false);
$lineCount = 0;
$hasEstablishTable = false;
while (($line1 = fgets($fp)) != null) {
$line = trim($line1);
if (strpos($line, "##") === 0) {
continue;
}
if (strpos($line, "#") === 0) {
$columnStrings = explode("\t", substr($line, 1));
$columnLength = count($columnStrings);
$sampleNamesLength = $columnLength - $formatColumnIndex - 1;
for ($j = 0; $j < $sampleNamesLength; $j++) {
$sampleNames[$j] = $columnStrings[$formatColumnIndex + 1 + $j];
}
$tableBuilders = "{$columnStrings['0']} varchar(30),{$columnStrings['1']} int,{$columnStrings['2']} varchar(30),\n\t\t\t\t {$columnStrings['3']} varchar(5),{$columnStrings['4']} varchar(5),{$columnStrings['5']} float(10,2),\n\t\t\t\t {$columnStrings['6']} text,{$columnStrings['7']} text,";
continue;
}
if ($sampleNames == null) {
throw new Exception("There are no samples in this vcf file");
}
$sections = explode("\t", $line);
for ($i = $formatColumnIndex + 1; $i < $columnLength; $i++) {
if (!strpos($sections[$i], ".")) {
$contain = false;
$rr = 1;
} else {
$contain = true;
$rr = 2;
}
if (strcmp($sections[$altColumn], ".") == 0 || $contain) {
continue;
}
$formatColumns = explode(":", $sections[$formatColumnIndex]);
$formatLength = count($formatColumns);
$dataColumns = explode(":", str_replace(",", "/", $sections[$i]));
$dataColumnLength = count($dataColumns);
if ($formatLength != $dataColumnLength) {
continue;
}
if (!$hasEstablishTable) {
for ($j = 0; $j < $formatLength; $j++) {
$formatColumn = $formatColumns[$j];
$tableBuilders = $tableBuilders . $formatColumn . " text,";
}
$tableBuilders = $tableBuilders . "alu varchar(1) default 'F',index(chrom,pos)";
for ($j = 0, $len = count($sampleNames); $j < $len; $j++) {
$tableName[$j] = $userid . "_" . $sampleNames[$j] . "_rnavcf" . "_" . date("Ymdhisa");
DatabaseManager::deleteTable($con, $tableName[$j]);
$createClause = "create table " . $tableName[$j] . "({$tableBuilders})";
$v = mysqli_query($con, $createClause);
if (!$v) {
throw new Exception("Error create RNATable.");
}
}
DatabaseManager::commit($con);
$hasEstablishTable = true;
}
$sqlClause = "insert into " . $tableName[$i - $formatColumnIndex - 1] . "(";
for ($j = 0; $j < $formatColumnIndex; $j++) {
$sqlClause = $sqlClause . $columnStrings[$j] . ",";
}
for ($j = 0; $j < $formatLength; $j++) {
$formatColumn = $formatColumns[$j];
$sqlClause = $sqlClause . $formatColumn . ",";
}
$sqlClause = substr($sqlClause, 0, strlen($sqlClause) - 1);
$sqlClause = $sqlClause . ") values('";
if (strpos($sections[0], "ch") === 0 && !(strpos($sections[0], "chr") === 0)) {
$str = str_replace("ch", "chr", $sections[0]) . "'";
$sqlClause = $sqlClause . $str;
} else {
if (strlen($sections[0]) < 3) {
$sqlClause = $sqlClause . "chr" . $sections[0] . "'";
} else {
$sqlClause = $sqlClause . $sections[0] . "'";
}
}
for ($j = 1; $j < $formatColumnIndex; $j++) {
$sqlClause = $sqlClause . ",'" . $sections[$j] . "'";
}
for ($j = 0; $j < count($dataColumns); $j++) {
$dataColumn = $dataColumns[$j];
$sqlClause = $sqlClause . ",'" . $dataColumn . "'";
}
$sqlClause = $sqlClause . ")";
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause: {$sqlClause}");
}
if (++$lineCount % 10000 == 0) {
DatabaseManager::commit($con);
}
}
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
} catch (Exception $e) {
REDLog::writeInfoLog($e->getMessage());
}
REDLog::writeInfoLog("End parsing RNA VCF file...");
return $tableName;
}
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();
}
}
