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viewAlleleCatalog.php
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viewAlleleCatalog.php
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<?php
$TITLE = "Soybean Phenotype Distribution Tool";
// include '../header.php';
include '../config.php';
include './php/pdoResultFilter.php';
include './php/getTableNames.php';
include './php/getSummarizedDataQueryString.php';
?>
<link rel="stylesheet" href="https://code.jquery.com/ui/1.13.1/themes/base/jquery-ui.css"></link>
<script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
<script src="https://code.jquery.com/ui/1.13.1/jquery-ui.js"></script>
<link rel="stylesheet" href="css/modal.css" />
<!-- Back button -->
<a href="/SoybeanPhenoDistTool/"><button> < Back </button></a>
<br />
<br />
<!-- Modal -->
<div id="info-modal" class="info-modal">
<!-- Modal content -->
<div class="modal-content">
<span class="modal-close">×</span>
<div id="modal-content-div" style='width:100%; height:auto; border:3px solid #000; overflow:scroll;max-height:1000px;'></div>
<div id="modal-content-comment"></div>
</div>
</div>
<!-- Get and process the variables -->
<?php
$dataset = trim($_GET['Dataset']);
$gene = trim($_GET['Gene']);
$chromosome = trim($_GET['Chromosome']);
$position = trim($_GET['Position']);
$phenotype = trim($_GET['Phenotype']);
$db = "soykb";
// Table names and datasets
$table_names = getTableNames($dataset);
$gff_table = $table_names["gff_table"];
$accession_mapping_table = $table_names["accession_mapping_table"];
?>
<!-- Query data from database and render data-->
<?php
// Color for functional effects
$ref_color_code = "#D1D1D1";
$missense_variant_color_code = "#7FC8F5";
$frameshift_variant_color_code = "#F26A55";
$exon_loss_variant_color_code = "#F26A55";
$lost_color_code = "#F26A55";
$gain_color_code = "#F26A55";
$disruptive_color_code = "#F26A55";
$conservative_color_code = "#FF7F50";
$splice_color_code = "#9EE85C";
// Generate SQL string
$query_str = "";
if ($query_str == "") {
if (isset($chromosome) && isset($position)) {
if (!empty($chromosome) && !empty($position)) {
$query_str = "SELECT Chromosome, Start, End, Name AS Gene ";
$query_str = $query_str . "FROM " . $db . "." . $gff_table . " ";
$query_str = $query_str . "WHERE (Chromosome = '" . $chromosome . "') AND ((Start <= " . $position . ") AND (End >= " . $position . "));";
}
}
}
if ($query_str == "") {
if (isset($gene)) {
if (!empty($gene)) {
$query_str = "SELECT Chromosome, Start, End, Name AS Gene ";
$query_str = $query_str . "FROM " . $db . "." . $gff_table . " ";
$query_str = $query_str . "WHERE (Name = '" . $gene . "');";
}
}
}
if ($query_str == "") {
exit();
}
// Execute SQL string
$stmt = $PDO->prepare($query_str);
$stmt->execute();
$result = $stmt->fetchAll();
$gene_result_arr = pdoResultFilter($result);
if (isset($gene_result_arr)) {
if (!empty($gene_result_arr)) {
if (is_array($gene_result_arr)) {
if (count($gene_result_arr) > 0) {
echo "<p>* Significant position(s) are highlighted in red. </p>";
for ($i = 0; $i < count($gene_result_arr); $i++) {
// Generate query string
$query_str = getSummarizedDataQueryString(
$dataset,
$gene_result_arr[$i]["Gene"],
$gene_result_arr[$i]["Chromosome"],
$db,
$gff_table,
$accession_mapping_table,
""
);
// Execute SQL string
$stmt = $PDO->prepare($query_str);
$stmt->execute();
$result = $stmt->fetchAll();
$result_arr = pdoResultFilter($result);
// Generate query string
$phenotype_distribution_table = "pDist_" . $dataset . "_" . $gene_result_arr[$i]["Chromosome"] . "";
$query_str = "SELECT DISTINCT PHENO.Chromosome, ";
$query_str = $query_str . "PHENO.Position, ";
$query_str = $query_str . "PHENO.Gene ";
$query_str = $query_str . "FROM " . $db . "." . $phenotype_distribution_table . " AS PHENO ";
$query_str = $query_str . "WHERE (PHENO.Phenotype IN ('" . $phenotype . "')) ";
$query_str = $query_str . "AND (PHENO.Gene = '" . $gene . "') ";
$query_str = $query_str . "ORDER BY PHENO.Position, PHENO.Chromosome, PHENO.Gene; ";
// Execute SQL string
$stmt = $PDO->prepare($query_str);
$stmt->execute();
$result = $stmt->fetchAll();
$phenotype_distribution_result_arr = pdoResultFilter($result);
$phenotype_distribution_position_array = array();
for ($j=0; $j < count($phenotype_distribution_result_arr); $j++) {
array_push($phenotype_distribution_position_array, $phenotype_distribution_result_arr[$j]["Position"]);
}
if (isset($result_arr)) {
if (!empty($result_arr)) {
if (is_array($result_arr)) {
if (count($result_arr) > 0) {
// Make table
echo "<div style='width:100%; height:auto; border:3px solid #000; overflow:scroll; max-height:1000px;'>";
echo "<table style='text-align:center;'>";
// Table header
echo "<tr>";
echo "<th></th>";
foreach ($result_arr[0] as $key => $value) {
if ($key != "Gene" && $key != "Chromosome" && $key != "Position" && $key != "Genotype" && $key != "Genotype_Description") {
// Improvement status count section
echo "<th style=\"border:1px solid black; min-width:80px;\">" . $key . "</th>";
} elseif ($key == "Gene") {
echo "<th style=\"border:1px solid black; min-width:80px;\">" . $key . "</th>";
} elseif ($key == "Chromosome") {
echo "<th style=\"border:1px solid black; min-width:80px;\">" . $key . "</th>";
} elseif ($key == "Position") {
// Position and genotype_description section
$position_array = preg_split("/[;, \n]+/", $value);
for ($j = 0; $j < count($position_array); $j++) {
if (in_array($position_array[$j], $phenotype_distribution_position_array)) {
echo "<th style=\"border:1px solid black; min-width:80px; color:red;\"><a style=\"color:red;\" href=\"/SoybeanPhenoDistTool/viewVariantAndPhenotypeFigures.php?Dataset=" . $dataset . "&Chromosome=" . $gene_result_arr[$i]["Chromosome"] . "&Position=" . $position_array[$j] . "&Phenotype=" . $phenotype . "\" target=\"_blank\">" . $position_array[$j] . "</a></th>";
} else {
echo "<th style=\"border:1px solid black; min-width:80px;\">" . $position_array[$j] . "</th>";
}
}
}
}
echo "<th></th>";
echo "</tr>";
// Table body
for ($j = 0; $j < count($result_arr); $j++) {
$tr_bgcolor = ($j % 2 ? "#FFFFFF" : "#DDFFDD");
$row_id_prefix = $result_arr[$j]["Gene"] . "_" . $result_arr[$j]["Chromosome"] . "_" . $j;
echo "<tr bgcolor=\"" . $tr_bgcolor . "\">";
echo "<td><input type=\"checkbox\" id=\"" . $row_id_prefix . "_l" . "\" name=\"" . $row_id_prefix . "_l" . "\" value=\"" . $row_id_prefix . "_l" . "\" onclick=\"checkHighlight(this)\"></td>";
foreach ($result_arr[$j] as $key => $value) {
if ($key != "Gene" && $key != "Chromosome" && $key != "Position" && $key != "Genotype" && $key != "Genotype_Description") {
// Improvement status count section
if (intval($value) > 0) {
echo "<td style=\"border:1px solid black;min-width:80px;\">";
echo "<a href=\"javascript:void(0);\" onclick=\"queryMetadataByImprovementStatusAndGenotypeCombination('" . strval($dataset) . "', '" . strval($key) . "', '" . $result_arr[$j]["Gene"] . "', '" . $result_arr[$j]["Chromosome"] . "', '" . $result_arr[$j]["Position"] . "', '" . $result_arr[$j]["Genotype"] . "', '" . $result_arr[$j]["Genotype_Description"] . "')\">";
echo $value;
echo "</a>";
echo "</td>";
} else {
echo "<td style=\"border:1px solid black;min-width:80px;\">" . $value . "</td>";
}
} elseif ($key == "Gene") {
echo "<td style=\"border:1px solid black;min-width:80px;\">" . $value . "</td>";
} elseif ($key == "Chromosome") {
echo "<td style=\"border:1px solid black;min-width:80px;\">" . $value . "</td>";
} elseif ($key == "Genotype_Description") {
// Position and genotype_description section
$position_array = preg_split("/[;, \n]+/", $result_arr[$j]["Position"]);
$genotype_description_array = preg_split("/[;, \n]+/", $value);
for ($k = 0; $k < count($genotype_description_array); $k++) {
// Change genotype_description background color
$td_bg_color = "#FFFFFF";
if (preg_match("/missense.variant/i", $genotype_description_array[$k])) {
$td_bg_color = $missense_variant_color_code;
$temp_value_arr = preg_split("/[;, |\n]+/", $genotype_description_array[$k]);
$genotype_description_array[$k] = (count($temp_value_arr) > 2 ? $temp_value_arr[0] . "|" . $temp_value_arr[2] : $genotype_description_array[$k]);
} else if (preg_match("/frameshift/i", $genotype_description_array[$k])) {
$td_bg_color = $frameshift_variant_color_code;
} else if (preg_match("/exon.loss/i", $genotype_description_array[$k])) {
$td_bg_color = $exon_loss_variant_color_code;
} else if (preg_match("/lost/i", $genotype_description_array[$k])) {
$td_bg_color = $lost_color_code;
$temp_value_arr = preg_split("/[;, |\n]+/", $genotype_description_array[$k]);
$genotype_description_array[$k] = (count($temp_value_arr) > 2 ? $temp_value_arr[0] . "|" . $temp_value_arr[2] : $genotype_description_array[$k]);
} else if (preg_match("/gain/i", $genotype_description_array[$k])) {
$td_bg_color = $gain_color_code;
$temp_value_arr = preg_split("/[;, |\n]+/", $genotype_description_array[$k]);
$genotype_description_array[$k] = (count($temp_value_arr) > 2 ? $temp_value_arr[0] . "|" . $temp_value_arr[2] : $genotype_description_array[$k]);
} else if (preg_match("/disruptive/i", $genotype_description_array[$k])) {
$td_bg_color = $disruptive_color_code;
} else if (preg_match("/conservative/i", $genotype_description_array[$k])) {
$td_bg_color = $conservative_color_code;
} else if (preg_match("/splice/i", $genotype_description_array[$k])) {
$td_bg_color = $splice_color_code;
} else if (preg_match("/ref/i", $genotype_description_array[$k])) {
$td_bg_color = $ref_color_code;
}
echo "<td id=\"" . $row_id_prefix . "_" . $position_array[$k] . "\" style=\"border:1px solid black;min-width:80px;background-color:" . $td_bg_color . "\">" . $genotype_description_array[$k] . "</td>";
}
}
}
echo "<td><input type=\"checkbox\" id=\"" . $row_id_prefix . "_r" . "\" name=\"" . $row_id_prefix . "_r" . "\" value=\"" . $row_id_prefix . "_r" . "\" onclick=\"checkHighlight(this)\"></td>";
echo "</tr>";
}
echo "</table>";
echo "</div>";
echo "<div style='margin-top:10px;' align='right'>";
echo "<button onclick=\"queryAllCountsByGeneChromosomePositions('" . $dataset . "', '" . $gene_result_arr[$i]["Gene"] . "', '" . $gene_result_arr[$i]["Chromosome"] . "')\" style=\"margin-right:20px;\"> Download (Accession Counts)</button>";
echo "<button onclick=\"queryAllByGeneChromosomePositions('" . $dataset . "', '" . $gene_result_arr[$i]["Gene"] . "', '" . $gene_result_arr[$i]["Chromosome"] . "')\"> Download (All Accessions)</button>";
echo "</div>";
echo "<br />";
echo "<br />";
}
}
}
}
}
}
}
}
}
?>
<script type="text/javascript" language="javascript" src="./js/modal.js"></script>
<script type="text/javascript" language="javascript" src="./js/viewAlleleCatalog.js"></script>
<?php include '../footer.php'; ?>