From: miles Date: Mon, 13 Aug 2012 20:06:37 +0000 (+0000) Subject: Added Web page files X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=e52b1179059e2f29423f9362fdf70e7b43419fdb;p=old-jaiswallab-svn%2F.git Added Web page files svn path=/; revision=372 --- diff --git a/Personnel/miles/Web Page/.directory b/Personnel/miles/Web Page/.directory new file mode 100644 index 0000000..eaa2d4b --- /dev/null +++ b/Personnel/miles/Web Page/.directory @@ -0,0 +1,4 @@ +[Dolphin] +AdditionalInfoV2=Details_Size,Details_Date,CustomizedDetails +Timestamp=2012,7,26,16,13,9 +Version=2 diff --git a/Personnel/miles/Web Page/.heatMap.php.kate-swp b/Personnel/miles/Web Page/.heatMap.php.kate-swp new file mode 100644 index 0000000..e40f5aa Binary files /dev/null and b/Personnel/miles/Web Page/.heatMap.php.kate-swp differ diff --git a/Personnel/miles/Web Page/ClusterInfo.php b/Personnel/miles/Web Page/ClusterInfo.php new file mode 100644 index 0000000..dda7d0f --- /dev/null +++ b/Personnel/miles/Web Page/ClusterInfo.php @@ -0,0 +1,39 @@ + + + + +Cluster Details + + + + + + +
"; + +$row = mysql_fetch_row($results); +while($row != null) { + $str=$row[1] . " (" . $row[0] . ")"; + echo "" . $str . "
"; + $row = mysql_fetch_row($results); + } + +mysql_close($connection); + +?> + \ No newline at end of file diff --git a/Personnel/miles/Web Page/ClusterSpeciesInfo.php b/Personnel/miles/Web Page/ClusterSpeciesInfo.php new file mode 100644 index 0000000..98a8c97 --- /dev/null +++ b/Personnel/miles/Web Page/ClusterSpeciesInfo.php @@ -0,0 +1,40 @@ + + + + +Cluster-Species Details + + + +
"; + +$row = mysql_fetch_row($results); +while($row != null) { + echo "" . $row[0] . "
"; + $row = mysql_fetch_row($results); + } + +mysql_close($connection); + +?> + diff --git a/Personnel/miles/Web Page/Heatmap.jar b/Personnel/miles/Web Page/Heatmap.jar new file mode 100644 index 0000000..fa7e9ec Binary files /dev/null and b/Personnel/miles/Web Page/Heatmap.jar differ diff --git a/Personnel/miles/Web Page/Main Page.html b/Personnel/miles/Web Page/Main Page.html new file mode 100644 index 0000000..6fabc80 --- /dev/null +++ b/Personnel/miles/Web Page/Main Page.html @@ -0,0 +1,26 @@ + + + +Heat Chart Creation + + + +Please enter all the gene IDs you would like the Heat Map to reference, +each on its own line. Click "Submit" when done: + + +
+

+ + +

+ +
+ + +
+ + + + \ No newline at end of file diff --git a/Personnel/miles/Web Page/SpeciesInfo.php b/Personnel/miles/Web Page/SpeciesInfo.php new file mode 100644 index 0000000..15a317c --- /dev/null +++ b/Personnel/miles/Web Page/SpeciesInfo.php @@ -0,0 +1,72 @@ + + + + +Species Details + + + + + + +
"; + +echo "GENE ID -------------------- CLUSTER ID
"; + +$data; +$i=0; +for($row = mysql_fetch_row($results); $row != null; $row = mysql_fetch_row($results)) { + $data[$i] = $ids[(string)$row[1]] . "," . $row[0]; + $i = $i+1; + } + +sort($data); +$i = 0; +$species = str_replace(" ", "_", $species); +while($i < sizeof($data)) { +$temp = explode(",", $data[$i]); +$str = $temp[1] . " ----------- " . $temp[0]; +echo "" . $str . "
"; +$i++; +} + +//id + gene -> sort -> split -> print; +// $row = mysql_fetch_row($results); + +mysql_close($connection); +?> + diff --git a/Personnel/miles/Web Page/heatMap.php b/Personnel/miles/Web Page/heatMap.php new file mode 100644 index 0000000..294e0f7 --- /dev/null +++ b/Personnel/miles/Web Page/heatMap.php @@ -0,0 +1,511 @@ + + + +Heat Chart + + +"; +$input = trim($_POST["genelist"]); +} +else { +echo "Click on a Species, Cluster, or Cell for more details.
Click on a gene name to see which cell it belongs to."; +$input = preg_replace("/(^[\r\n]*|[\r\n]+)[\s\t]*[\r\n]+/", " ", $_POST["geneIDs"]); +if(!preg_match("/[a-zA-Z0-9\.]/", substr($input,-1))) { + $input = substr_replace($input ,"",-1); + } +} +exec("java -jar Heatmap.jar " . $input, $output); + +//main heatmap data parsing +$tmp; +for ($i = 0; $i < sizeof($output); $i ++) { + $tmp[$i] = explode(",", $output[$i]); + } + + +$allSpecies; +for ($s = 0; $s < sizeof($tmp) - 2; $s ++) // the last array in tmp is the list of cluster IDs + { + $allSpecies[$s] = $tmp[$s][0]; + } + + +$allClusterIDs; +for ($c = 0; $c < sizeof($tmp[sizeof($tmp) - 2]); $c ++) + { + $allClusterIDs[$c] = $tmp[sizeof($tmp) - 2][$c]; + } + + +$heatMapData; +for ($s = 0; $s < (sizeof($tmp) - 2); $s ++) + { + for ($c = 0; $c < sizeof($allClusterIDs); $c ++) + $heatMapData[$s][$c] = $tmp[$s][$c+1]; + } + +$geneIDs = explode(" ", $input); +$maxCount = $output[sizeof($output)-1]; +$clusterCount = sizeof($allClusterIDs); +$speciesCount = sizeof($allSpecies); + +$temp; +for ($i = 0; $i < sizeof($heatMapData); $i ++) + { + $temp[$i] = implode(",", $heatMapData[$i]); + } +$finalHeatMapData = $temp; + +// extra goodies from the mysql database +$username="inparanoid-read-user"; +$password="inparanoid-read-user_pw"; +$database="inparanoid_data"; +$url="floret.cgrb.oregonstate.edu:3306"; + +$connection=mysql_connect($url,$username,$password); +$logic="gene like "; +for($i=0; $i Database error, could not list tables."; + } + +$clickableGenes; +$k=0; +for($row=mysql_fetch_row($results); $row != null; $k++) { + $clickableGenes[$k] = ($row[0] . "," . $row[1] . "," . (array_search2d($row[2], $allClusterIDs)+1)); + $row=mysql_fetch_row($results); + + + + +$width = 25*$speciesCount + 100; +$height = 25 * $clusterCount + 200 + 20 * sizeof($clickableGenes); +} + +?> + + +





+ + + +Click on a species name, cluster number, or cell for more information. +
Scroll down to see more clusters, right to see more species (if any exist). +
+ There are " . $speciesCount . " species in the heatmap."; ?> + +
+ +
+ + +
+ + +
+ + +
+ +Your browser does not support the canvas element. + + + + + + + + \ No newline at end of file diff --git a/Personnel/miles/Web Page/planteome_example.php b/Personnel/miles/Web Page/planteome_example.php new file mode 100644 index 0000000..63b05ae --- /dev/null +++ b/Personnel/miles/Web Page/planteome_example.php @@ -0,0 +1,314 @@ + +
File uploaded successfully! Now proceed to choose other options

"; + } + //when the user enters gene ids into the textarea + else if (isset($_POST['gene'])) { + $gene = $_POST['gene']; + $geneArray=explode("\n",$gene); + $count = count($geneArray); + if($count > 0 && trim($geneArray[$count-1]) == ""){ + unset($geneArray[$count -1]); + } + } + } + //db Config values + $dbHost = "floret.cgrb.oregonstate.local"; + $dbUser = "planteome_php"; + $dbPwd = "planteome_php-pw"; + + //global variables to hold the list of species values. This is passed to download.php for downloading protein sequence in fasta format + $specieslist=""; + $geneids=""; + + //global variables to hold the list of results. This is passed to download.php for downloading the results as a text file. + $pairSearchResult = ""; + $superClusterSearchResult = ""; + + $showFastaDownloadLink = true; + $showDataDownloadLink = true; + $sep="~"; + + //function that fetches all results from the db + function mysql_fetch_all($query, $conn) { + $result = mysql_query($query, $conn); + if (!$result) { + echo "DB Error, could not find cluster id
"; + echo "MySQL Error: " . mysql_error() . "
"; + } + $rows = array(); + while($row = mysql_fetch_assoc($result)) { + $rows[] = $row; + } + return $rows; + } + + //function that builds query from the geneArray + function buildQueryFromGeneArray($query,$geneArray){ + for($i=0;$i<=count($geneArray)-1;){ + if(trim($geneArray[$i]) != ""){ + $query = $query . " gene LIKE '%".trim($geneArray[$i])."%'"; + } + $i++; + if($i!=count($geneArray) && trim($geneArray[$i]) != ""){ + $query = $query. " OR "; + } + } + return $query; + } +?> + +

Upload a .txt file containing the list of gene ids. Make sure the file contains only one gene id per line

+
+ + + +
+or +

Enter gene id(s) in the textarea below. Make sure you enter only one gene id per line.

+
+ + + + + + + + + + + + + + + + + + + + +
Species 1: + "; + while($arrayRow = mysql_fetch_row($rsrcResult)) { + if (isset($spec1)&&$spec1==$arrayRow[0]) { + echo ""; + }else{ + echo ""; + } + //echo "$rsrcResult"; + //echo "Table: {$arrayRow[0]}\n"; + } + echo ""; + ?> +
Species 2: + "; + while($arrayRow = mysql_fetch_row($rsrcResult)) { + if (isset($spec2)&&$spec2==$arrayRow[0]) { + echo ""; + }else{ + echo ""; + } + //echo "$rsrcResult"; + //echo "Table: {$arrayRow[0]}\n"; + } + echo ""; + ?> +
+ +
+ +
+
+ +
+
+ +"; + echo "MySQL Error: " . mysql_error(). "
"; + } + $num = mysql_num_rows($query2Result); + if($num > 0) { + if($showFastaDownloadLink){ + echo "Click here to download all results as a FASTA file
"; + //this link has to be shown only one. so set the variable $showFastaDownloadLink to false after first time; + $showFastaDownloadLink = false; + } + if($showDataDownloadLink){ + echo "Click here to download all results as a text file
"; + //this link has to be shown only one. so set the variable $showDataDownloadLink to false after first time; + $showDataDownloadLink = false; + } + } + if($i==0){ + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; + } + $j=0; + while ($j <$num) { + $bit_score=mysql_result($query2Result,$j,"bit_score"); + $species=mysql_result($query2Result,$j,"species"); + $score=mysql_result($query2Result,$j,"score"); + $gene_return=mysql_result($query2Result,$j,"gene"); + $gene_return_url="$gene_return"; + + $specieslist= $specieslist == "" ? $species : $specieslist.','.$species; + $geneids = $geneids == "" ? $gene_return : $geneids.','.$gene_return; + + if($score ==1) {$score = '1.00';} + echo ""; + echo ""; + echo ""; + $j++; + $res = $clust_id.$sep.$bit_score.$sep.$species.$sep.$score.$sep.$gene_return; + if($pairSearchResult != "") + $pairSearchResult=$pairSearchResult.",".$res; + else + $pairSearchResult=$res; + } + } + echo "
Results for species-species pair search
bit scorespeciesorthology scoregene
$bit_score".str_replace('_',' ',$species)."$score$gene_return_url
"; + mysql_close(); + } +} + +if(isset($super)) { + $connection = mysql_connect($dbHost,$dbUser,$dbPwd); + mysql_select_db("inparanoid_data_eucalyptus"); + if(isset($geneArray)){ + $query1 = "select super_id from super_clust where "; + $query1 = buildQueryFromGeneArray($query1,$geneArray); + } + $rowArray = mysql_fetch_all($query1,$connection); + for($i=0;$i<=count($rowArray)-1;$i++){ + $row = $rowArray[$i]; + $super_id = $row["super_id"]; + $query2 = "select * from super_clust where super_id = '$super_id'"; + $query2Result = mysql_query($query2); + if (!$query2Result) { + echo "DB Error, could not find cluster
"; + echo "MySQL Error: " . mysql_error(). "
"; + } + $num = mysql_num_rows($query2Result); + if($num > 0) { + if($showFastaDownloadLink){ + echo "Click here to download all results as a FASTA file
"; + //this link has to be shown only one. so set the variable $showFastaDownloadLink to false after first time; + $showFastaDownloadLink = false; + } + if($showDataDownloadLink){ + echo "Click here to download all results as a text file
"; + //this link has to be shown only one. so set the variable $showDataDownloadLink to false after first time; + $showDataDownloadLink = false; + } + } + if($i==0){ + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; + } + $j = 0; + while ($j < $num) { + $super_id_result=mysql_result($query2Result,$j,"super_id"); + $species=mysql_result($query2Result,$j,"species"); + $gene_result=mysql_result($query2Result,$j,"gene"); + $gene_result_url="$gene_result"; + + $specieslist= $specieslist == "" ? $species : $specieslist.','.$species; + $geneids = $geneids == "" ? $gene_result : $geneids.','.$gene_result; + + echo ""; + echo ""; + echo ""; + $j++; + $res = $super_id_result.$sep.$species.$sep.$gene_result; + if($superClusterSearchResult != "") + $superClusterSearchResult=$superClusterSearchResult.",".$res; + else + $superClusterSearchResult=$res; + } + } + echo "
Results from supercluster search
supercluster idspeciesgene
$super_id_result".str_replace('_',' ',$species)."$gene_result_url
"; + mysql_close(); +} + //to be used for downloading protein sequence is fasta format + if(isset($geneArray)){ + $genelist = implode(',', $geneArray); + } +?> + + + diff --git a/Personnel/miles/Web Page/testing b/Personnel/miles/Web Page/testing new file mode 100644 index 0000000..0e5b4e2 --- /dev/null +++ b/Personnel/miles/Web Page/testing @@ -0,0 +1,4 @@ +mgf009407m +RMZM2G457201_T02 +LOC_Os03g53530.1 +Bradi3g44220.1 diff --git a/Personnel/miles/Web Page/testing.txt b/Personnel/miles/Web Page/testing.txt new file mode 100644 index 0000000..da660c7 --- /dev/null +++ b/Personnel/miles/Web Page/testing.txt @@ -0,0 +1,1000 @@ +16041819 +OTTHUMP00000011946 +AC233651_18 +LOC_Os06g31860.1 +16971567 +ENSRNOG00000000415 +Glyma07g32610.1 +ppa019648m +Sb10g004160 +mgf015929m +Sb07g004520 +OTTMUSP00000017073 +gene07278 +Glyma08g09400.1 +ENSRNOG00000033917 +ENSDARG00000079543 +16050800 +GRMZM2G092776_T07 +1882832 +mgf019760m +Bradi4g02950.1 +gene19772 +LOC_Os08g21490.1 +OTTHUMP00000177975 +OTTHUMP00000177816 +FBpp0072415 +ppa011342m +GRMZM2G099619_T01 +CBN80114.1 +LOC_Os11g02550.1 +15421740 +POPTR_0005s12280 +POPTR_0011s06930 +gene27168 +MGG_04661T0 +1897707 +ppa016666m +Medtr2g091610 +cassava6461.valid.m1 +Medtr3g148610 +15410417 +1901110 +ppa004337m +PHUM009840-PA +GRMZM2G053111_T01 +cassava29270.valid.m1 +mgf024342m +Glyma02g07510.1 +cassava3187.m1 +Bradi2g06370.1 +OTTHUMP00000224162 +POPTR_0005s17820 +GSVIVT00016075001 +POPTR_0013s10540 +1885627 +FBpp0086358 +OTTHUMP00000077232 +NCU06496T0 +gene10784 +Glyma04g37320.1 +ENSRNOG00000014846 +Glyma13g32310.1 +YFL061W +LOC_Os04g51780.1 +GRMZM2G164020_T01 +CBJ30107.1 +16044512 +302523 +Glyma14g38110.1 +16061997 +LOC_Os02g12740.1 +16040072 +1901581 +16055301 +gene19518 +OTTHUMP00000202240 +gene20319 +ppa006614m +Bradi3g39120.1 +GRMZM2G470942_T03 +mgf000634m +POPTR_0006s07610 +MGG_04485T0 +1889536 +cassava2789.m1 +CU571152_16 +1900571 +GRMZM2G116010_T01 +cassava9605.m1 +GRMZM2G131321_T03 +PHUM538540-PA +FBpp0077793 +cassava41111.m1 +ENSDARG00000074874 +Medtr7g076460 +ABG51617.1 +gene12112 +OTTMUSP00000040338 +Medtr1g122290 +AT1G66650.1 +LOC_Os06g24760.1 +GSVIVT00021990001 +ENSDARG00000079945 +mgf013174m +16963255 +OTTHUMP00000209353 +15415563 +Sb06g032460 +1903881 +RO3G_08626.1 +1893212 +cassava16122.m1 +PHUM529430-PA +16974574 +Glyma06g39470.1 +AT1G69820.1 +mgf005090m +RO3G_01500.1 +Bradi1g44170.1 +POPTR_0009s07610 +RO3G_05990.1 +ENSDARG00000078344 +Sb05g025260 +RO3G_13634.1 +POPTR_0008s08850 +OTTHUMP00000021630 +16972652 +OTTMUSP00000012948 +gene25178 +FBpp0082382 +Glyma06g44890.1 +LOC_Os08g36170.1 +Medtr8g146170 +ENSRNOG00000001065 +ppa000711m +GRMZM2G122145_T02 +Bradi3g09740.1 +NCU01401T0 +OTTHUMP00000076886 +GRMZM2G040069_T04 +LOC_Os04g29900.1 +POPTR_0007s11250 +OTTHUMP00000206045 +ENSRNOG00000016319 +GSVIVT00015473001 +OTTMUSP00000026695 +ENSRNOG00000009718 +Bradi2g17320.1 +16978466 +AT4G32630.1 +Medtr5g103290 +YNR034W +Au9.Cre12.g561100.t1 +FBpp0088258 +WBGene00007434 +GRMZM2G388684_T01 +15407591 +Medtr2g077070 +GSVIVT00006426001 +cassava40155.m1 +Glyma07g09560.1 +16064370 +cassava15189.m1 +RO3G_17100.1 +OTTMUSP00000017027 +Glyma09g40860.1 +Glyma19g28310.1 +ENSDARG00000005092 +OTTMUSP00000005781 +OTTHUMP00000211147 +cassava29309.valid.m1 +Glyma12g06640.1 +16973369 +slr0545 +15408865 +POPTR_0007s02570 +Sb06g020120 +POPTR_0005s15840 +ENSDARG00000055357 +Glyma15g20160.1 +Glyma03g37410.1 +FBpp0076231 +GRMZM2G389895_T01 +GRMZM2G356178_T01 +POPTR_0014s10750 +SPAC27E2.08 +Glyma08g40980.1 +ppb021310m +OTTMUSP00000032409 +LOC_Os08g08040.1 +ENSRNOG00000003936 +GRMZM2G017941_T01 +16961828 +FBpp0073768 +PHUM600210-PA +GRMZM2G048106_T01 +1891261 +FBpp0073950 +LOC_Os11g03570.1 +gene22545 +ENSRNOG00000043510 +Sb10g003400 +NCU07821T0 +16958567 +29801.t000184 +ENSRNOG00000007890 +OTTMUSP00000020183 +cassava31801.valid.m1 +30131.t000259 +gene29954 +OTTHUMP00000176123 +POPTR_0014s17280 +POPTR_0005s18990 +OTTHUMP00000196170 +GRMZM2G439860_T01 +mgf001071m +POPTR_0006s03650 +cassava20410.m1 +GRMZM2G127050_T02 +cassava2204.valid.m1 +OTTHUMP00000002064 +OTTMUSP00000031772 +POPTR_0009s12160 +Bradi1g35050.1 +Glyma02g47430.1 +GRMZM2G061745_T04 +FBpp0073496 +OTTMUSP00000019683 +YGR108W +MGG_05706T0 +cassava25232.valid.m1 +GSVIVT00013254001 +cassava22552.valid.m1 +16054887 +1910193 +ppa008674m +PHUM221330-PA +16050261 +Medtr7g103920 +16977627 +mgf025524m +gene21327 +AT2G39730.1 +FBpp0083065 +evm.TU.supercontig_8.134 +Medtr8g146690 +29687.t000036 +ppa018355m +LOC_Os03g06980.1 +AT3G29635.1 +16043070 +Sb07g023575 +Glyma20g27560.1 +30677.t000001 +ENSDARG00000076385 +GRMZM2G031954_T03 +15421995 +mgf015141m +ENSDARG00000038770 +16046251 +15414203 +gene27714 +cassava31671.valid.m1 +ENSRNOG00000017994 +FBpp0075837 +AT4G13690.1 +RO3G_15864.1 +POPTR_0008s15160 +Medtr2g017370 +OTTMUSP00000023785 +15403135 +OTTHUMP00000033825 +GSVIVT00021841001 +16046165 +AT5G20730.1 +PHUM207310-PA +Medtr1g116980 +16039424 +POPTR_0005s21180 +RO3G_12936.1 +LOC_Os01g72200.1 +RO3G_11426.1 +187336 +FBpp0291340 +RO3G_14076.1 +Sb03g001710 +Sb02g007840 +mgf013511m +Glyma20g01780.1 +POPTR_0009s14230 +Glyma04g07140.1 +YPR072W +16957930 +FBpp0070683 +GSVIVT00022031001 +LOC_Os06g02200.1 +ENSDARG00000070786 +gene02640 +15414410 +MGG_13015T0 +ENSDARG00000008212 +POPTR_0004s13590 +cassava12930.valid.m1 +OTTHUMP00000071851 +ENSDARG00000079590 +ENSRNOG00000021896 +OTTMUSP00000001202 +SPAPB24D3.04c +ENSDARG00000040001 +SPBC20F10.09 +Bradi1g70600.1 +WBGene00016341 +Bradi2g30160.1 +gene17539 +cassava7167.valid.m1 +gene20217 +OTTHUMP00000201395 +OTTHUMP00000204858 +OTTHUMP00000076447 +GRMZM2G151425_T01 +Glyma15g05310.1 +AT5G45430.1 +MGG_11391T0 +16953381 +PHUM601890-PA +cassava242.valid.m1 +PHUM363550-PA +OTTMUSP00000024855 +16065756 +cassava6040.valid.m1 +AC218900.3_FGT001 +GRMZM2G134421_T01 +cassava29134.valid.m1 +Medtr4g100690 +POPTR_0015s08000 +ppa012962m +Glyma11g06000.1 +ppa025030m +256696 +mgf017810m +OTTHUMP00000204451 +GSVIVT00029206001 +16040076 +cassava2036.valid.m1 +16063126 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"
"; +} +else +{ + $fileType=$_FILES["genelistFile"]["type"]; + if(strtolower($fileType) != "text/plain"){ + echo "

$fileType - Invalid file type. Please submit only .txt files

Click here again to upload a valid file" ; + } + else{ + $fh = fopen($_FILES['genelistFile']['tmp_name'], "r"); + if ($fh) { + while (($line = fgets($fh, 4096)) !== false) { + if($data == "")$data = trim($line); + else $data = $data . " " . trim($line); + } + if (!feof($fh)) { + echo "fgets error"; + } + fclose($fh); + } + $goToNode10 = true; +// echo $data; + } +} +?> + +
+ +
+ + + +