static function createFisherExactTestTable($con, $refTable, $darnedResultTable)
{
DatabaseManager::deleteTable($con, $darnedResultTable);
self::createFilterTable($con, $refTable, $darnedResultTable);
try {
$v = mysqli_query($con, "alter table " . $darnedResultTable . " add level float,add pvalue float,add fdr float");
if (!$v) {
throw new Exception("Can not create Fisher Exact Test Table.");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
}
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 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;
}