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custom-report.php
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custom-report.php
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<?php
$format = ".".str_replace("fmt=", "", $_POST['myFormat']);
$filename = $_POST['file']??'';
if (strlen($filename)==0){
$filename="AMPDB Report";
}
?>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="shortcut icon" href="logo.png" type="image/x-icon">
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.2.3/dist/css/bootstrap.min.css" rel="stylesheet">
<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.2.3/dist/js/bootstrap.bundle.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.4/jquery.min.js"></script>
<link href="ss.css" rel="stylesheet">
<link href="ampdbTextSearch.css" rel="stylesheet">
<link href="midilizer.css" rel="stylesheet">
<title>AMPDB - Report</title>
<script>
function startDownload() {
setTimeout(function() {
var link = document.createElement('a');
link.href = '<?php if ($format == 'xml'){
echo $filename.'.xml';
} else{
echo "$filename$format";
}?>';
link.download = '<?php if ($format == 'xml'){
echo $filename.'.xml';
} else{
echo "$filename$format";
}
?>';
link.click();
}, 500);
}
</script>
</head>
<body onload="startDownload()">
<nav class="navbar navbar-expand-sm navbar-dark bg-dark fixed-top">
<div class="container-fluid">
<a class="navbar-brand fs-3" href="ampdb-home">AMPDB v1</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#mynavbar">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="mynavbar">
<ul class="navbar-nav me-auto">
<li class="nav-item">
<a class="nav-link" href="ampdb-home">Home</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Search</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="ampdb-text-search">Text Search</a></li>
<li><a class="dropdown-item" href="ampdb-specific-search">Specific Text Search</a></li>
<li><a class="dropdown-item" href="ampdb-target-organism-search">Search by Target
Organism</a></li>
<li><a class="dropdown-item" href="ampdb-pp-search">Search by Physicochemical Properties</a>
</li>
<li><a class="dropdown-item" href="ampdb-composition-search">Search by Protein
Composition</a>
</li>
<li><a class="dropdown-item" href="ampdb-activity-search">Search by Activity</a></li>
<li><a class="dropdown-item" href="ampdb-advanced-search">Advanced Search</a></li>
</ul>
</li>
<li class="nav-item">
<a class="nav-link" href="browse-all-data">Browse</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-classification">Classification</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Tools</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="https://ampdb-protein-sequence-alignment-toolbox.streamlit.app/" target="_blank">Protein Sequence Alignment Toolbox</a></li>
<li><a class="dropdown-item" href="https://ampdb-protein-feature-calculation-toolbox.streamlit.app/" target="_blank">Protein Feature Calculation Toolbox</a></li>
</ul>
<li class="nav-item">
<a class="nav-link" href="ampdb-data-stat">Statistics</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-downloads">Downloads</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-news">News/Updates</a>
</li>
<li class="nav-item">
<a class="nav-link" href="developers">Developers</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-tutorial">Tutorial</a>
</li>
<li class="nav-item">
<a class="nav-link" href="contact">Contact</a>
</li>
</ul>
<form class="d-flex" action="ampdb-quick-search-result" method="get">
<input name="term" class="form-control me-2" type="text" placeholder="Quick Search">
<input type="submit" value="Search" name="search" class="btn btn-primary">
</form>
</div>
</div>
</nav>
<?php
ini_set('max_execution_time', 1500);
require 'dbcon.php';
$ids = explode(",", $_POST["ids"]);
$colHeader = str_replace("%7C", "|", str_replace("%29", ")", str_replace("%28", "(", str_replace("+", " ", str_replace("%60", "`", str_replace("%2C", ",", str_replace("datareq=", "", $_POST["myDataset"])))))));
$format = str_replace("fmt=", "", $_POST["myFormat"]);
$tsvHeader = '';
if (strlen($colHeader) == 0) {
$colHeader = "`AMPDB_No_`, `Protein names`, `Protein families`, `Gene Names`, `Organism`, `Length`, `Protein existence`, `Sequence`, `Counts`, `Frequencies`, `missRes`, `commonRes`, `leastOccRes`, `phoAA`, `phiAA`, `basicAACount`, `acidicAACount`, `modifiedAA`, `modifiedAAfreq`, `Molecular Weight`, `Aliphatic Index`, `Instability Index`, `Hydrophobicity (GRAVY)`, `Hydrophobic Moment`, `Isoelectric Point`, `Charge (at pH 7)`, `Secondary Structure Fraction`, `Aromaticity`, `Molar Extinction Coefficient (cysteine|cystine)`, `target organism`, `peptide activity`, `enzyme`, `inhibition`, `other`, `PubMed ID`, `Entry`, `PDB`, `EMBL`, `CCDS`, `RefSeq`, `STRING`, `IntAct`, `MINT`, `DIP`, `BioGRID`, `BindingDB`, `DrugBank`, `ChEMBL`, `InterPro`, `PANTHER`, `PROSITE`, `Ensembl`, `KEGG`, `GeneTree`, `BRENDA`, `BioCyc`, `RNAct`";
$tsvHeader = $colHeader;
} else {
$tsvHeader = $colHeader;
}
$idArrLen = count($ids);
if ($format == 'tsv') {
$cc = 0;
$tsvFile = fopen("$filename.$format", "w") or die("UtO");
fwrite($tsvFile, str_replace("AMPDB_No_", "AMPDB_No_", (str_replace("Protein names", "Protein names", (str_replace("Protein families", "Protein families", (str_replace("Gene Names", "Gene names", (str_replace("Gene Names (synonym)", "Synonymous gene names", (str_replace("Organism", "Source organism", (str_replace("Length", "Length", (str_replace("Protein existence", "Protein existence", (str_replace("Proteomes", "Chromosomes & proteomes information", (str_replace("Sequence", "Sequence", (str_replace("Counts", "Counts", (str_replace("Frequencies", "Frequencies", (str_replace("missRes", "Missing Amino Acid(s)", (str_replace("commonRes", "Most Occurring Amino Acid(s)", (str_replace("leastOccRes", "Less Occurring Amino Acid(s)", (str_replace("phoAA", "Hydrophobic Amino Acid(s) Count", (str_replace("phiAA", "Hydrophilic Amino Acid(s) Count", (str_replace("basicAACount", "Basic Amino Acid(s) Count", (str_replace("acidicAACount", "Acidic Amino Acid(s) Count", (str_replace("modifiedAA", "Modified Amino Acid(s) Count", (str_replace("modifiedAAfreq", "Modified Amino Acid(s) Frequencies", (str_replace("Molecular Weight", "Molecular Mass", (str_replace("Aliphatic Index", "Aliphatic Index", (str_replace("Instability Index", "Instability Index", (str_replace("Hydrophobicity (GRAVY)", "Hydrophobicity (GRAVY)", (str_replace("Hydrophobic Moment", "Hydrophobic Moment", (str_replace("Isoelectric Point", "Isoelectric Point", (str_replace("Charge (at pH 7)", "Charge (at pH 7)", (str_replace("Secondary Structure Fraction", "Secondary Structure Fraction", (str_replace("Aromaticity", "Aromaticity", (str_replace("Molar Extinction Coefficient (cysteine|cystine)", "Molar Extinction Coefficient (cysteine|cystine)", (str_replace("target organism", "target organism", (str_replace("peptide activity", "Antimicrobial Activity", (str_replace("enzyme", "Enzymatic Activity", (str_replace("inhibition", "Inhibitory Effect", (str_replace("other", "Other Biological Activity", (str_replace("PubMed ID", "PubMed ID", (str_replace("Entry", "UniProt ID", (str_replace("PDB", "PDB", (str_replace("EMBL", "EMBL", (str_replace("CCDS", "CCDS", (str_replace("RefSeq", "RefSeq", (str_replace("STRING", "STRING ID", (str_replace("IntAct", "IntAct ID", (str_replace("MINT", "MINT ID", (str_replace("DIP", "DIP ID", (str_replace("BioGRID", "BioGRID ID", (str_replace("BindingDB", "BindingDB ID", (str_replace("DrugBank", "DrugBank ID", (str_replace("ChEMBL", "ChEMBL ID", (str_replace("InterPro", "InterPro ID", (str_replace("PANTHER", "PANTHER ID", (str_replace("PROSITE", "PROSITE ID", (str_replace("Ensembl", "Ensembl ID", (str_replace("KEGG", "KEGG ID", (str_replace("GeneTree", "GeneTree ID", (str_replace("BRENDA", "BRENDA ID", (str_replace("BioCyc", "BioCyc ID", (str_replace("RNAct", "RNAct ID", (str_replace("`", "", str_replace(",", "\t", $tsvHeader . "\n")))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))));
$arr = array();
for ($ia = 0; $ia < $idArrLen; $ia++) {
array_push($arr, $ids[$ia]);
if (($ia + 1) % 500 == 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('" . implode("','", $arr) . "')";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
fwrite($tsvFile, str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", implode("\t", $row)) . "\n"))));
}
$arr = array();
}
if ($ia + 1 == $idArrLen) {
if (($ia + 1) % 500 != 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('','" . implode("','", $arr) . "')";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
fwrite($tsvFile, str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", implode("\t", $row)) . "\n"))));
}
$arr = array();
}
}
}
fclose($tsvFile);
}
if ($format == 'json') {
$cc = 0;
$tsvFile = fopen("$filename.$format", "w") or die("UtO");
$arr = array();
$data = array();
for ($ia = 0; $ia < $idArrLen; $ia++) {
array_push($arr, $ids[$ia]);
if (($ia + 1) % 500 == 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('" . implode("','", $arr) . "')";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
$myAssArr = array();
foreach ($row as $key => $val) {
$myAssArr[str_replace("AMPDB_No_", "AMPDB_No_", (str_replace("Protein names", "Protein names", (str_replace("Protein families", "Protein families", (str_replace("Gene Names", "Gene names", (str_replace("Gene Names (synonym)", "Synonymous gene names", (str_replace("Organism", "Source organism", (str_replace("Length", "Length", (str_replace("Protein existence", "Protein existence", (str_replace("Proteomes", "Chromosomes & proteomes information", (str_replace("Sequence", "Sequence", (str_replace("Counts", "Counts", (str_replace("Frequencies", "Frequencies", (str_replace("missRes", "Missing Amino Acid(s)", (str_replace("commonRes", "Most Occurring Amino Acid(s)", (str_replace("leastOccRes", "Less Occurring Amino Acid(s)", (str_replace("phoAA", "Hydrophobic Amino Acid(s) Count", (str_replace("phiAA", "Hydrophilic Amino Acid(s) Count", (str_replace("basicAACount", "Basic Amino Acid(s) Count", (str_replace("acidicAACount", "Acidic Amino Acid(s) Count", (str_replace("modifiedAA", "Modified Amino Acid(s) Count", (str_replace("modifiedAAfreq", "Modified Amino Acid(s) Frequencies", (str_replace("Molecular Weight", "Molecular Mass", (str_replace("Aliphatic Index", "Aliphatic Index", (str_replace("Instability Index", "Instability Index", (str_replace("Hydrophobicity (GRAVY)", "Hydrophobicity (GRAVY)", (str_replace("Hydrophobic Moment", "Hydrophobic Moment", (str_replace("Isoelectric Point", "Isoelectric Point", (str_replace("Charge (at pH 7)", "Charge (at pH 7)", (str_replace("Secondary Structure Fraction", "Secondary Structure Fraction", (str_replace("Aromaticity", "Aromaticity", (str_replace("Molar Extinction Coefficient (cysteine|cystine)", "Molar Extinction Coefficient (cysteine|cystine)", (str_replace("target organism", "target organism", (str_replace("peptide activity", "Antimicrobial Activity", (str_replace("enzyme", "Enzymatic Activity", (str_replace("inhibition", "Inhibitory Effect", (str_replace("other", "Other Biological Activity", (str_replace("PubMed ID", "PubMed ID", (str_replace("Entry", "UniProt ID", (str_replace("PDB", "PDB", (str_replace("EMBL", "EMBL", (str_replace("CCDS", "CCDS", (str_replace("RefSeq", "RefSeq", (str_replace("STRING", "STRING ID", (str_replace("IntAct", "IntAct ID", (str_replace("MINT", "MINT ID", (str_replace("DIP", "DIP ID", (str_replace("BioGRID", "BioGRID ID", (str_replace("BindingDB", "BindingDB ID", (str_replace("DrugBank", "DrugBank ID", (str_replace("ChEMBL", "ChEMBL ID", (str_replace("InterPro", "InterPro ID", (str_replace("PANTHER", "PANTHER ID", (str_replace("PROSITE", "PROSITE ID", (str_replace("Ensembl", "Ensembl ID", (str_replace("KEGG", "KEGG ID", (str_replace("GeneTree", "GeneTree ID", (str_replace("BRENDA", "BRENDA ID", (str_replace("BioCyc", "BioCyc ID", (str_replace("RNAct", "RNAct ID", (str_replace("`", "", str_replace(",", "\t", $key))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))] = str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", $val))));
}
$data[] = $myAssArr;
$arr = array();
}
}
if ($ia + 1 == $idArrLen) {
if (($ia + 1) % 500 != 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('','" . implode("','", $arr) . "')";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
$myAssArr = array();
foreach ($row as $key => $val) {
$myAssArr[str_replace("AMPDB_No_", "AMPDB_No_", (str_replace("Protein names", "Protein names", (str_replace("Protein families", "Protein families", (str_replace("Gene Names", "Gene names", (str_replace("Gene Names (synonym)", "Synonymous gene names", (str_replace("Organism", "Source organism", (str_replace("Length", "Length", (str_replace("Protein existence", "Protein existence", (str_replace("Proteomes", "Chromosomes & proteomes information", (str_replace("Sequence", "Sequence", (str_replace("Counts", "Counts", (str_replace("Frequencies", "Frequencies", (str_replace("missRes", "Missing Amino Acid(s)", (str_replace("commonRes", "Most Occurring Amino Acid(s)", (str_replace("leastOccRes", "Less Occurring Amino Acid(s)", (str_replace("phoAA", "Hydrophobic Amino Acid(s) Count", (str_replace("phiAA", "Hydrophilic Amino Acid(s) Count", (str_replace("basicAACount", "Basic Amino Acid(s) Count", (str_replace("acidicAACount", "Acidic Amino Acid(s) Count", (str_replace("modifiedAA", "Modified Amino Acid(s) Count", (str_replace("modifiedAAfreq", "Modified Amino Acid(s) Frequencies", (str_replace("Molecular Weight", "Molecular Mass", (str_replace("Aliphatic Index", "Aliphatic Index", (str_replace("Instability Index", "Instability Index", (str_replace("Hydrophobicity (GRAVY)", "Hydrophobicity (GRAVY)", (str_replace("Hydrophobic Moment", "Hydrophobic Moment", (str_replace("Isoelectric Point", "Isoelectric Point", (str_replace("Charge (at pH 7)", "Charge (at pH 7)", (str_replace("Secondary Structure Fraction", "Secondary Structure Fraction", (str_replace("Aromaticity", "Aromaticity", (str_replace("Molar Extinction Coefficient (cysteine|cystine)", "Molar Extinction Coefficient (cysteine|cystine)", (str_replace("target organism", "target organism", (str_replace("peptide activity", "Antimicrobial Activity", (str_replace("enzyme", "Enzymatic Activity", (str_replace("inhibition", "Inhibitory Effect", (str_replace("other", "Other Biological Activity", (str_replace("PubMed ID", "PubMed ID", (str_replace("Entry", "UniProt ID", (str_replace("PDB", "PDB", (str_replace("EMBL", "EMBL", (str_replace("CCDS", "CCDS", (str_replace("RefSeq", "RefSeq", (str_replace("STRING", "STRING ID", (str_replace("IntAct", "IntAct ID", (str_replace("MINT", "MINT ID", (str_replace("DIP", "DIP ID", (str_replace("BioGRID", "BioGRID ID", (str_replace("BindingDB", "BindingDB ID", (str_replace("DrugBank", "DrugBank ID", (str_replace("ChEMBL", "ChEMBL ID", (str_replace("InterPro", "InterPro ID", (str_replace("PANTHER", "PANTHER ID", (str_replace("PROSITE", "PROSITE ID", (str_replace("Ensembl", "Ensembl ID", (str_replace("KEGG", "KEGG ID", (str_replace("GeneTree", "GeneTree ID", (str_replace("BRENDA", "BRENDA ID", (str_replace("BioCyc", "BioCyc ID", (str_replace("RNAct", "RNAct ID", (str_replace("`", "", str_replace(",", "\t", $key))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))] = str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", $val))));
}
$data[] = $myAssArr;
$arr = array();
}
}
}
}
fwrite($tsvFile, json_encode(array("data" => $data), JSON_PRETTY_PRINT));
fclose($tsvFile);
}
if ($format == 'xml') {
function arrayToXml($data, &$xml)
{
foreach ($data as $key => $value) {
if (is_array($value)) {
if (!is_numeric(str_replace("", "", str_replace("|", "by", str_replace("{", "", str_replace("}", "", str_replace("(", "", str_replace(")", "", str_replace(" ", "_", $key))))))))) {
$subnode = $xml->addChild(str_replace("", "", str_replace("|", "by", str_replace("{", "", str_replace("}", "", str_replace("(", "", str_replace(")", "", str_replace(" ", "_", $key))))))));
arrayToXml($value, $subnode);
} else {
arrayToXml($value, $xml);
}
} else {
$xml->addChild(str_replace("", "", str_replace("|", "by", str_replace("{", "", str_replace("}", "", str_replace("(", "", str_replace(")", "", str_replace(" ", "_", $key))))))), htmlspecialchars($value));
}
}
}
$xml = new SimpleXMLElement('<root></root>');
$xmlFilePath = $filename.'.xml';
$dom = new DOMDocument('1.0');
$dom->preserveWhiteSpace = false;
$dom->formatOutput = true;
$cc = 1;
$arr = array();
for ($ia = 0; $ia < $idArrLen; $ia++) {
array_push($arr, $ids[$ia]);
if (($ia + 1) % 500 == 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('" . implode("','", $arr) . "') LIMIT 300";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
$myAssArr = array();
foreach ($row as $key => $val) {
if ($key == 'missRes' and $val == '') {
$myAssArr[(str_replace("missRes", "Missing Amino Acid(s)", str_replace("`", "", str_replace(",", "\t", str_replace(" ", "_", $key)))))] = ' ';
} else {
$myAssArr[(str_replace("Gene Names", "Gene names", (str_replace("Organism", "Source organism", (str_replace("missRes", "Missing Amino Acid(s)", (str_replace("commonRes", "Most Occurring Amino Acid(s)", (str_replace("leastOccRes", "Less Occurring Amino Acid(s)", (str_replace("phoAA", "Hydrophobic Amino Acid(s) Count", (str_replace("phiAA", "Hydrophilic Amino Acid(s) Count", (str_replace("basicAACount", "Basic Amino Acid(s) Count", (str_replace("acidicAACount", "Acidic Amino Acid(s) Count", (str_replace("modifiedAA", "Modified Amino Acid(s) Count", (str_replace("modifiedAAfreq", "Modified Amino Acid(s) Frequencies", (str_replace("Molecular Weight", "Molecular Mass", (str_replace("peptide activity", "Antimicrobial Activity", (str_replace("enzyme", "Enzymatic Activity", (str_replace("inhibition", "Inhibitory Effect", (str_replace("other", "Other Biological Activity", (str_replace("Entry", "UniProt ID", (str_replace("PDB", "PDB", (str_replace("EMBL", "EMBL", (str_replace("CCDS", "CCDS", (str_replace("RefSeq", "RefSeq", (str_replace("STRING", "STRING ID", (str_replace("IntAct", "IntAct ID", (str_replace("MINT", "MINT ID", (str_replace("DIP", "DIP ID", (str_replace("BioGRID", "BioGRID ID", (str_replace("BindingDB", "BindingDB ID", (str_replace("DrugBank", "DrugBank ID", (str_replace("ChEMBL", "ChEMBL ID", (str_replace("InterPro", "InterPro ID", (str_replace("PANTHER", "PANTHER ID", (str_replace("PROSITE", "PROSITE ID", (str_replace("Ensembl", "Ensembl ID", (str_replace("KEGG", "KEGG ID", (str_replace("GeneTree", "GeneTree ID", (str_replace("BRENDA", "BRENDA ID", (str_replace("BioCyc", "BioCyc ID", (str_replace("RNAct", "RNAct ID", (str_replace("`", "", str_replace(",", "\t", str_replace(" ", "_", $key))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))] = str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", str_replace("'", '', $val)))));
}
}
arrayToXml($myAssArr, $xml);
$dom->loadXML($xml->asXML());
}
}
if ($ia + 1 == $idArrLen) {
if (($ia + 1) % 500 != 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('','" . implode("','", $arr) . "') LIMIT 300";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
$myAssArr = array();
foreach ($row as $key => $val) {
if ($key == 'missRes' and $val == '') {
$myAssArr[(str_replace("missRes", "Missing Amino Acid(s)", str_replace("`", "", str_replace(",", "\t", str_replace(" ", "_", $key)))))] = ' ';
} else {
$myAssArr[(str_replace("Gene Names", "Gene names", (str_replace("Organism", "Source organism", (str_replace("missRes", "Missing Amino Acid(s)", (str_replace("commonRes", "Most Occurring Amino Acid(s)", (str_replace("leastOccRes", "Less Occurring Amino Acid(s)", (str_replace("phoAA", "Hydrophobic Amino Acid(s) Count", (str_replace("phiAA", "Hydrophilic Amino Acid(s) Count", (str_replace("basicAACount", "Basic Amino Acid(s) Count", (str_replace("acidicAACount", "Acidic Amino Acid(s) Count", (str_replace("modifiedAA", "Modified Amino Acid(s) Count", (str_replace("modifiedAAfreq", "Modified Amino Acid(s) Frequencies", (str_replace("Molecular Weight", "Molecular Mass", (str_replace("peptide activity", "Antimicrobial Activity", (str_replace("enzyme", "Enzymatic Activity", (str_replace("inhibition", "Inhibitory Effect", (str_replace("other", "Other Biological Activity", (str_replace("Entry", "UniProt ID", (str_replace("PDB", "PDB", (str_replace("EMBL", "EMBL", (str_replace("CCDS", "CCDS", (str_replace("RefSeq", "RefSeq", (str_replace("STRING", "STRING ID", (str_replace("IntAct", "IntAct ID", (str_replace("MINT", "MINT ID", (str_replace("DIP", "DIP ID", (str_replace("BioGRID", "BioGRID ID", (str_replace("BindingDB", "BindingDB ID", (str_replace("DrugBank", "DrugBank ID", (str_replace("ChEMBL", "ChEMBL ID", (str_replace("InterPro", "InterPro ID", (str_replace("PANTHER", "PANTHER ID", (str_replace("PROSITE", "PROSITE ID", (str_replace("Ensembl", "Ensembl ID", (str_replace("KEGG", "KEGG ID", (str_replace("GeneTree", "GeneTree ID", (str_replace("BRENDA", "BRENDA ID", (str_replace("BioCyc", "BioCyc ID", (str_replace("RNAct", "RNAct ID", (str_replace("`", "", str_replace(",", "\t", str_replace(" ", "_", $key))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))] = str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", str_replace("'", '', $val)))));
}
}
arrayToXml($myAssArr, $xml);
$dom->loadXML($xml->asXML());
}
}
}
}
$dom->save($xmlFilePath);
}
if ($format == 'tsv') {
$cc = 0;
$tsvFile = fopen("$filename.$format", "w") or die("UtO");
fwrite($tsvFile, str_replace("AMPDB_No_", "AMPDB_No_", (str_replace("Protein names", "Protein names", (str_replace("Protein families", "Protein families", (str_replace("Gene Names", "Gene names", (str_replace("Gene Names (synonym)", "Synonymous gene names", (str_replace("Organism", "Source organism", (str_replace("Length", "Length", (str_replace("Protein existence", "Protein existence", (str_replace("Proteomes", "Chromosomes & proteomes information", (str_replace("Sequence", "Sequence", (str_replace("Counts", "Counts", (str_replace("Frequencies", "Frequencies", (str_replace("missRes", "Missing Amino Acid(s)", (str_replace("commonRes", "Most Occurring Amino Acid(s)", (str_replace("leastOccRes", "Less Occurring Amino Acid(s)", (str_replace("phoAA", "Hydrophobic Amino Acid(s) Count", (str_replace("phiAA", "Hydrophilic Amino Acid(s) Count", (str_replace("basicAACount", "Basic Amino Acid(s) Count", (str_replace("acidicAACount", "Acidic Amino Acid(s) Count", (str_replace("modifiedAA", "Modified Amino Acid(s) Count", (str_replace("modifiedAAfreq", "Modified Amino Acid(s) Frequencies", (str_replace("Molecular Weight", "Molecular Mass", (str_replace("Aliphatic Index", "Aliphatic Index", (str_replace("Instability Index", "Instability Index", (str_replace("Hydrophobicity (GRAVY)", "Hydrophobicity (GRAVY)", (str_replace("Hydrophobic Moment", "Hydrophobic Moment", (str_replace("Isoelectric Point", "Isoelectric Point", (str_replace("Charge (at pH 7)", "Charge (at pH 7)", (str_replace("Secondary Structure Fraction", "Secondary Structure Fraction", (str_replace("Aromaticity", "Aromaticity", (str_replace("Molar Extinction Coefficient (cysteine|cystine)", "Molar Extinction Coefficient (cysteine|cystine)", (str_replace("target organism", "target organism", (str_replace("peptide activity", "Antimicrobial Activity", (str_replace("enzyme", "Enzymatic Activity", (str_replace("inhibition", "Inhibitory Effect", (str_replace("other", "Other Biological Activity", (str_replace("PubMed ID", "PubMed ID", (str_replace("Entry", "UniProt ID", (str_replace("PDB", "PDB", (str_replace("EMBL", "EMBL", (str_replace("CCDS", "CCDS", (str_replace("RefSeq", "RefSeq", (str_replace("STRING", "STRING ID", (str_replace("IntAct", "IntAct ID", (str_replace("MINT", "MINT ID", (str_replace("DIP", "DIP ID", (str_replace("BioGRID", "BioGRID ID", (str_replace("BindingDB", "BindingDB ID", (str_replace("DrugBank", "DrugBank ID", (str_replace("ChEMBL", "ChEMBL ID", (str_replace("InterPro", "InterPro ID", (str_replace("PANTHER", "PANTHER ID", (str_replace("PROSITE", "PROSITE ID", (str_replace("Ensembl", "Ensembl ID", (str_replace("KEGG", "KEGG ID", (str_replace("GeneTree", "GeneTree ID", (str_replace("BRENDA", "BRENDA ID", (str_replace("BioCyc", "BioCyc ID", (str_replace("RNAct", "RNAct ID", (str_replace("`", "", str_replace(",", "\t", $tsvHeader . "\n")))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))));
$arr = array();
for ($ia = 0; $ia < $idArrLen; $ia++) {
array_push($arr, $ids[$ia]);
if (($ia + 1) % 500 == 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('" . implode("','", $arr) . "')";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
fwrite($tsvFile, str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", implode("\t", $row)) . "\n"))));
}
$arr = array();
}
if ($ia + 1 == $idArrLen) {
if (($ia + 1) % 500 != 0) {
$sql = "SELECT $colHeader FROM `master` WHERE AMPDB_No_ IN ('','" . implode("','", $arr) . "')";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
fwrite($tsvFile, str_replace("Nil", "Not found", str_replace("Nil ", "Not found", str_replace(" Nil", "Not found", str_replace(" Nil ", "Not found", implode("\t", $row)) . "\n"))));
}
$arr = array();
}
}
}
fclose($tsvFile);
}
if ($format == 'fasta') {
$cc = 0;
$tsvFile = fopen("$filename.$format", "w") or die("UtO");
$arr = array();
for ($ia = 0; $ia < $idArrLen; $ia++) {
array_push($arr, $ids[$ia]);
if (($ia + 1) % 500 == 0) {
$sql = "SELECT fasta FROM fmt WHERE id IN ('" . str_replace("AMPDB_", "", implode("','", $arr)) . "')";
$arr = array();
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
array_push($arr, $row['fasta']);
}
fwrite($tsvFile, implode("\n", $arr));
$arr = array();
}
if ($ia + 1 == $idArrLen) {
if (($ia + 1) % 500 != 0) {
$sql = "SELECT fasta FROM fmt WHERE id IN ('" . str_replace("AMPDB_", "", implode("','", $arr)) . "')";
$arr = array();
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
array_push($arr, $row['fasta']);
}
fwrite($tsvFile, implode("\n", $arr));
$arr = array();
}
}
}
fclose($tsvFile);
}
if ($format == 'txt') {
$cc = 0;
$tsvFile = fopen("$filename.$format", "w") or die("UtO");
$arr = array();
for ($ia = 0; $ia < $idArrLen; $ia++) {
array_push($arr, $ids[$ia]);
if (($ia + 1) % 500 == 0) {
$sql = "SELECT txt FROM fmt WHERE id IN ('" . str_replace("AMPDB_", "", implode("','", $arr)) . "')";
$arr = array();
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
array_push($arr, $row['txt']);
}
fwrite($tsvFile, implode("\n", $arr));
$arr = array();
}
if ($ia + 1 == $idArrLen) {
if (($ia + 1) % 500 != 0) {
$sql = "SELECT txt FROM fmt WHERE id IN ('" . str_replace("AMPDB_", "", implode("','", $arr)) . "')";
$arr = array();
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
array_push($arr, $row['txt']);
}
fwrite($tsvFile, implode("\n", $arr));
$arr = array();
}
}
}
fclose($tsvFile);
}
if ($format == 'list') {
$cc = 0;
$tsvFile = fopen("$filename.$format", "w") or die("UtO");
fwrite($tsvFile, implode("\n", $ids));
fclose($tsvFile);
}
?>
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$con->close();
?>
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