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viewAllByGenes.php
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<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<script src="https://code.jquery.com/jquery-3.7.1.min.js" integrity="sha256-/JqT3SQfawRcv/BIHPThkBvs0OEvtFFmqPF/lYI/Cxo=" crossorigin="anonymous"></script>
<?php
$TITLE = "Soybean Allele Catalog Tool";
include '../config.php';
include './php/pdoResultFilter.php';
include './php/getTableNames.php';
include './php/getSummarizedDataQueryString.php';
include './php/getDataQueryString.php';
?>
<link rel="stylesheet" href="./css/modal.css" />
<!-- Back button -->
<a href="/SoybeanAlleleCatalogTool/"><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
$gene = $_GET['gene_1'];
$dataset = $_GET['dataset_1'];
$improvement_status_array = $_GET['improvement_status_1'];
$gene = clean_malicious_input($gene);
$dataset = clean_malicious_input($dataset);
$dataset = preg_replace('/\s+/', '', $dataset);
$improvement_status_array = clean_malicious_input($improvement_status_array);
if (is_string($gene)) {
$gene = trim($gene);
$temp_gene_array = preg_split("/[;, \n]+/", $gene);
$gene_array = array();
for ($i = 0; $i < count($temp_gene_array); $i++) {
if (!empty(preg_replace('/\s+/', '', $temp_gene_array[$i]))) {
array_push($gene_array, preg_replace('/\s+/', '', $temp_gene_array[$i]));
}
}
} elseif (is_array($gene)) {
$temp_gene_array = $gene;
$gene_array = array();
for ($i = 0; $i < count($temp_gene_array); $i++) {
if (!empty(preg_replace('/\s+/', '', $temp_gene_array[$i]))) {
array_push($gene_array, preg_replace('/\s+/', '', $temp_gene_array[$i]));
}
}
}
$db = "soykb";
// Table names and datasets
$table_names = getTableNames($dataset);
$key_column = $table_names["key_column"];
$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";
$splice_color_code = "#9EE85C";
for ($i = 0; $i < count($gene_array); $i++) {
// Generate SQL string
$query_str = "SELECT Chromosome, Start, End, Name AS Gene ";
$query_str = $query_str . "FROM " . $db . "." . $gff_table . " ";
$query_str = $query_str . "WHERE (Name = '" . $gene_array[$i] . "') OR (UPPER(Name) = UPPER('" . $gene_array[$i] . "'));";
$stmt = $PDO->prepare($query_str);
$stmt->execute();
$result = $stmt->fetchAll();
$gene_result_arr = pdoResultFilter($result);
// Generate query string
$query_str = getSummarizedDataQueryString(
$dataset,
$db,
$gff_table,
$accession_mapping_table,
$gene_result_arr[0]["Gene"],
$gene_result_arr[0]["Chromosome"],
$improvement_status_array,
""
);
$stmt = $PDO->prepare($query_str);
$stmt->execute();
$result = $stmt->fetchAll();
$result_arr = pdoResultFilter($result);
// Render result to a table
if (isset($result_arr) && is_array($result_arr) && !empty($result_arr)) {
// Make table
echo "<div style='width:100%; height:auto; border:3px solid #000; overflow:scroll; max-height:1000px;'>";
echo "<table style='text-align:center;'>";
// Table header
echo "<tr>";
echo "<th></th>";
foreach ($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++) {
// echo "<th style=\"border:1px solid black; min-width:80px;\">" . $position_array[$j] . "</th>";
echo "<th style=\"border:1px solid black; min-width:80px;\"><a href=\"/SoybeanAlleleCatalogTool/viewVariantAndPhenotype.php?dataset=" . $dataset . "&chromosome=" . $result_arr[0]["Chromosome"] . "&position=" . $position_array[$j] . "&gene=" . $result_arr[0]["Gene"] . "\" target=\"_blank\">" . $position_array[$j] . "</a></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=\"" . $row_id_prefix . "_r" . "\" onclick=\"checkHighlight(this)\"></td>";
echo "</tr>";
}
echo "</table>";
echo "</div>";
echo "<div style='margin-top:10px;' align='right'>";
if (isset($improvement_status_array)) {
echo "<button onclick=\"queryAllCountsByGene('" . $dataset . "', '" . $result_arr[0]["Gene"] . "', '" . implode(";", $improvement_status_array) . "')\" style=\"margin-right:20px;\"> Download (Accession Counts)</button>";
echo "<button onclick=\"queryAllByGene('" . $dataset . "', '" . $result_arr[0]["Gene"] . "', '" . implode(";", $improvement_status_array) . "')\"> Download (All Accessions)</button>";
} else {
echo "<button onclick=\"queryAllCountsByGene('" . $dataset . "', '" . $result_arr[0]["Gene"] . "', '')\" style=\"margin-right:20px;\"> Download (Accession Counts)</button>";
echo "<button onclick=\"queryAllByGene('" . $dataset . "', '" . $result_arr[0]["Gene"] . "', '')\"> Download (All Accessions)</button>";
}
echo "</div>";
echo "<br />";
echo "<br />";
} else {
echo "<p>No Allele Catalog data available for " . $gene_array[$i] . " gene!!!</p>";
}
}
if (count($result_arr) > 0) {
echo "<br/><br/>";
echo "<div style='margin-top:10px;' align='center'>";
echo "<button onclick=\"queryAccessionInformation('" . $dataset . "')\" style=\"margin-right:20px;\">Download Accession Information</button>";
if (isset($improvement_status_array)) {
echo "<button onclick=\"queryAllCountsByMultipleGenes('" . $dataset . "', '" . implode(";", $gene_array) . "', '" . implode(";", $improvement_status_array) . "')\" style=\"margin-right:20px;\"> Download All (Accession Counts)</button>";
echo "<button onclick=\"queryAllByMultipleGenes('" . $dataset . "', '" . implode(";", $gene_array) . "', '" . implode(";", $improvement_status_array) . "')\" style=\"margin-right:20px;\"> Download All (All Accessions)</button>";
} else {
echo "<button onclick=\"queryAllCountsByMultipleGenes('" . $dataset . "', '" . implode(";", $gene_array) . "', '')\" style=\"margin-right:20px;\"> Download All (Accession Counts)</button>";
echo "<button onclick=\"queryAllByMultipleGenes('" . $dataset . "', '" . implode(";", $gene_array) . "', '')\" style=\"margin-right:20px;\"> Download All (All Accessions)</button>";
}
echo "</div>";
echo "<br/><br/>";
}
?>
<script type="text/javascript" language="javascript" src="./js/modal.js"></script>
<script type="text/javascript" language="javascript" src="./js/viewAllByGenes.js"></script>
<?php include '../footer.php'; ?>