Ejemplo n.º 1
0
<?php

include '../REDTools/REDLog.php';
include '../database/DatabaseManager.php';
include '../database/DatabaseConnect.php';
include '../filters/denovo/KnownSNPFilter.php';
include '../database/TableCreator.php';
include '../REDTools/REDTools.php';
include '../REDTools/SiteBean.php';
$con = DatabaseConnect::mysqlConnect();
$args = array(0);
$previousTable = "bj22n_rrfilter_sjfilter";
$currentFilterName = KnownSNPFilter::getName();
$currentTable = REDTools::getFirstHalfTableName($previousTable) . $currentFilterName;
KnownSNPFilter::performKnownSNPFilter($con, $previousTable, $currentTable, $args);
Ejemplo n.º 2
0
 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();
     }
 }