/**
* Method to execute the command
* @param $command
* @return mixed
*/
public function execute($command)
{
try {
$this->db->beginTransaction();
$response = $this->decoratedBus->execute($command);
$this->db->commit();
return $response;
} catch (PDOException $e) {
$this->db->rollback();
throw new Exceptions\InternalException($e->getMessage());
}
}
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 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;
}
