From a82422f5ea78e1dd9fd2ba9dbbd15ffce076dd66 Mon Sep 17 00:00:00 2001 From: Yuchen Jiang Date: Fri, 17 Jul 2015 00:09:14 -0400 Subject: [PATCH] added cpg track --- VQI_GenomeBrowser.js | 35 +- cpg_site_hg19.txt | 1 + dynamic_loading.php | 87 +- shelve_chr1.txt | 9797 ++++++++++++++++++++++++++++++++++++++++++ shoer_chr1.txt | 9797 ++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 19701 insertions(+), 16 deletions(-) create mode 100644 shelve_chr1.txt create mode 100644 shoer_chr1.txt diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js index f245e48..4476c17 100755 --- a/VQI_GenomeBrowser.js +++ b/VQI_GenomeBrowser.js @@ -26,9 +26,11 @@ function VQI_GenomeBrowser(id) { var isready = false; var zoomOnly = false; + var trackInfo = []; - trackInfo[0] = {name: "HG19", type: "bed", fileHandle: "upload1436481988"}; - trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", fileHandle: "upload1436411775"}; + trackInfo[0] = {name: "HG19", type: "bed", fileHandle: "upload1436481988"}; + trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", fileHandle: "upload1436411775"}; + trackInfo[2] = {name: "cpg", type: "cpg", fileHandle: "upload1437097194,upload1437098473,upload1437098556"}; // $("#" + id).append("
CPG:Shore:Shelve:
"); @@ -488,7 +490,7 @@ function VQI_GenomeBrowser(id) { // var xScale = d3.scale.linear() // .domain([-3953, 249241810]) // .range([0,1000]); - var fileHandle = "upload1435711655"; + var chrom = "chr1"; $.ajax({ @@ -497,8 +499,8 @@ function VQI_GenomeBrowser(id) { dataType: "json", data: { "getTrackData": "", - "fileHandles": [trackInfo[0].fileHandle,trackInfo[1].fileHandle], - "name": [trackInfo[0].name,trackInfo[1].name], + "fileHandles": [trackInfo[0].fileHandle,trackInfo[1].fileHandle,trackInfo[2].fileHandle], + "name": [trackInfo[0].name,trackInfo[1].name,trackInfo[2].name], "chrom": chrom, "start": start, "end": end @@ -507,19 +509,27 @@ function VQI_GenomeBrowser(id) { }).success(function (returnData) { //console.log(returnData); var i = getTrackIndexByName("HG19"); - trackList[i] = returnData[0][0]; + trackList[i] = returnData["HG19"][0]; trackList[i]['name'] = "HG19"; trackList[i]['type'] = "bed"; //console.log(trackList); - addBEDTrack(returnData[0][0], "HG19",returnData[0][1]); + addBEDTrack(returnData["HG19"][0], "HG19",returnData["HG19"][1]); var i = getTrackIndexByName("Tile2 Content Snp"); - trackList[i] = returnData[1]; + trackList[i] = returnData["Tile2 Content Snp"]; trackList[i]['name'] = "Tile2 Content Snp"; trackList[i]['type'] = "bed"; //console.log(trackList); - addBEDTrack(returnData[1], "Tile2 Content Snp"); + addBEDTrack(returnData["Tile2 Content Snp"], "Tile2 Content Snp"); + //console.log(trackList); + + var i = getTrackIndexByName("cpg"); + trackList[i] = returnData["cpg"]; + trackList[i]['name'] = "cpg"; + trackList[i]['type'] = "cpg"; //console.log(trackList); + addCpgTrack(returnData["cpg"], "cpg"); + zoomOnly = true; zoomed(); @@ -1185,7 +1195,7 @@ function VQI_GenomeBrowser(id) { // var xScale = d3.scale.linear() // .domain([-3953, 249241810]) // .range([0,1000]); - var fileHandle = "upload1436411775"; + var chrom = "chr1"; @@ -1195,8 +1205,8 @@ function VQI_GenomeBrowser(id) { dataType: "json", data: { "getStartEndTrackData": "", - "fileHandles": [trackInfo[0].fileHandle,trackInfo[1].fileHandle], - "name": [trackInfo[0].name, trackInfo[1].name], + "fileHandles": [trackInfo[0].fileHandle,trackInfo[1].fileHandle,trackInfo[2].fileHandle], + "name": [trackInfo[0].name, trackInfo[1].name,trackInfo[2].name], "chrom": chrom } @@ -1204,6 +1214,7 @@ function VQI_GenomeBrowser(id) { //console.log(returnData); thisObj.addTrack(returnData[0], "HG19", "bed"); thisObj.addTrack(returnData[1], "Tile2 Content Snp", "bed"); + thisObj.addTrack(returnData[2], "cpg", "cpg"); isready = true; updateTrack(); }).error(function (req, status, error) { diff --git a/cpg_site_hg19.txt b/cpg_site_hg19.txt index 00094a9..da6f305 100644 --- a/cpg_site_hg19.txt +++ b/cpg_site_hg19.txt @@ -1,3 +1,4 @@ +CHROM START END chr10 93098 93818 chr10 94002 94165 chr10 94527 95302 diff --git a/dynamic_loading.php b/dynamic_loading.php index a9acc6e..39e1b03 100644 --- a/dynamic_loading.php +++ b/dynamic_loading.php @@ -292,13 +292,78 @@ return [$resArray,$resExon]; } + function getCpgTrackData($fileHandle,$chrom,$start,$end){ + $db_name = $GLOBALS['db_name']; + $link = $GLOBALS['DBlink']; + $resArray = []; + $scale = 1000/($end - $start); + + $fileHangleArray = explode(",", $fileHandle); + $cpgFile = $fileHangleArray[0]; + $shelveFile = $fileHangleArray[1]; + $shoreFile = $fileHangleArray[2]; + + foreach ($fileHangleArray as $key => $handle) { + $type = ""; + if ($key == 0){ + $type = "cpg"; + } + else if ($key == 1){ + $type = "shelve"; + } + else { + $type = "shore"; + } + + $sql = "SELECT `CHROM`, `START`, `END` FROM {$db_name}.{$handle}"; + $sql .= " WHERE `CHROM` = '".$chrom."'"; + $sql .= " AND (((`START` BETWEEN $start AND $end) OR (`END` BETWEEN $start AND $end))"; + $sql .= " OR (`START` <= $start AND `END` >= $end))"; + $sql .= " ORDER BY `START` * 1 ASC"; + + $res = mysqli_query ($link,$sql); + + $mergedRect = []; + $firstRow = mysqli_fetch_row($res); + + $mergedRect = [$chrom,$firstRow[1],$firstRow[2],$type]; + + while($row = mysqli_fetch_row($res)){ + + if ($row[1] - $mergedRect[2] > 1/$scale){ + array_push($resArray, $mergedRect); + $mergedRect[1] = $row[1]; + $mergedRect[2] = $row[2]; + $mergedRect[3] = $type; + } + else{ + if ($mergedRect[2] < $row[2]){ + $mergedRect[2] = $row[2]; + $mergedRect[3] = $type; + } + } + } + $LastElement = end($resArray); + reset($resArray); + if ($mergedRect[1] != $LastElement[1]){ + array_push($resArray, $mergedRect); + } + } + return $resArray; + } + function getTrackData($fileHandles,$name,$chrom,$start,$end){ $returnArray = []; foreach ($fileHandles as $key => $value) { # code... if ($name[$key] == "HG19"){ $resArray = getHG19TrackData($fileHandles[$key],$chrom,$start,$end); - array_push($returnArray, $resArray); + $returnArray["HG19"] = $resArray; + continue; + } + if ($name[$key] == "cpg"){ + $resArray = getCpgTrackData($fileHandles[$key],$chrom,$start,$end); + $returnArray["cpg"] = $resArray; continue; } @@ -363,7 +428,7 @@ } - array_push($returnArray, $resArray); + $returnArray[$name[$key]] = $resArray; } return $returnArray; } @@ -387,12 +452,19 @@ if ($name[$key] == "HG19"){ $minsql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score` FROM {$db_name}.{$fileHandle} ORDER BY `txStart` * 1 ASC LIMIT 1"; } + if ($name[$key] == "cpg"){ + $temp = explode(",", $fileHandle); + $shelveFile = $temp[1]; + $minsql = "SELECT `CHROM`, `START`, `END` FROM {$db_name}.{$shelveFile} ORDER BY `START` * 1 ASC LIMIT 1"; + } $minres = mysqli_query ($link,$minsql); while($row = mysqli_fetch_row($minres)) { $minRect = [$chrom,$row[1],$row[2],"",""]; - + if ($name[$key] == "cpg"){ + $minRect = [$chrom,$row[1],$row[2],"shelve"]; + } array_push($resArray, $minRect); } @@ -400,12 +472,19 @@ if ($name[$key] == "HG19"){ $maxsql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score` FROM {$db_name}.{$fileHandle} ORDER BY `txEnd` * 1 DESC LIMIT 1"; } + if ($name[$key] == "cpg"){ + $temp = explode(",", $fileHandle); + $shelveFile = $temp[1]; + $maxsql = "SELECT `CHROM`, `START`, `END` FROM {$db_name}.{$shelveFile} ORDER BY `END` * 1 DESC LIMIT 1"; + } $maxres = mysqli_query ($link,$maxsql); while($row = mysqli_fetch_row($maxres)) { $maxRect = [$chrom,$row[1],$row[2],"",""]; - + if ($name[$key] == "cpg"){ + $maxRect = [$chrom,$row[1],$row[2],"shelve"]; + } array_push($resArray, $maxRect); } diff --git a/shelve_chr1.txt b/shelve_chr1.txt new file mode 100644 index 0000000..de314c5 --- /dev/null +++ b/shelve_chr1.txt @@ -0,0 +1,9797 @@ +CHROM START END +chr1 6497 8497 +chr1 13241 15241 +chr1 24705 26705 +chr1 31791 33791 +chr1 131086 133086 +chr1 132164 134164 +chr1 133665 135665 +chr1 137805 139805 +chr1 139362 141362 +chr1 140121 142121 +chr1 224635 226635 +chr1 230770 232770 +chr1 322015 324015 +chr1 322944 324944 +chr1 323550 325550 +chr1 328481 330481 +chr1 329293 331293 +chr1 330356 332356 +chr1 432854 434854 +chr1 438019 440019 +chr1 440161 442161 +chr1 444345 446345 +chr1 445296 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