PHP DatabaseManager::deleteTable方法代码示例

 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) {
//.........这里部分代码省略.........