Blasterjs implementation with String #14

alslonik · 2024-04-02T13:21:30Z

Hi. I am trying to implement blasterjs via String in my web database. Here is my blast output page:

`<?php
// Include necessary files
include_once realpath("../../header.php");

// Your BLAST input parameters
$query = $_POST["query"];
$blast_db = $_POST["blast_db"];
$blast_prog = $_POST["blast_prog"];
$max_hits = $_POST["max_hits"];
$evalue = $_POST["evalue"];
$blast_matrix = $_POST["blast_matrix"];
$blast_filter = $_POST["blast_filter"];

// Define variables
$blast_res = '';
$num_input_seqs = substr_count($query, ">");

// Check for existence of blast_links.json file
$links_hash = [];
$blast_links_file = "$blast_dbs_path/blast_links.json";
if (file_exists($blast_links_file)) {
    $links_json_file = file_get_contents($blast_links_file);
    $links_hash = json_decode($links_json_file, true);
}

// Convert blast_filter checkbox value to "yes" or "no"
$blast_filter = $blast_filter == "on" ? "yes" : "no";

// Construct the BLAST command based on the selected program
if ($blast_prog == "blastn") {
    $blast_cmd = "\"$query\" | $blast_prog -db $blast_db -dust $blast_filter -evalue $evalue -num_descriptions $max_hits -num_alignments $max_hits -html -max_hsps 3";
} elseif ($blast_prog == "tblastn") {
    $blast_cmd = "\"$query\" | $blast_prog -db $blast_db -seg $blast_filter -evalue $evalue -num_descriptions $max_hits -num_alignments $max_hits -html -max_hsps 3";
} elseif (in_array($blast_prog, ["blastp", "blastx", "tblastx"])) {
    $blast_cmd = "\"$query\" | $blast_prog -db $blast_db -seg $blast_filter -evalue $evalue -matrix $blast_matrix -num_descriptions $max_hits -num_alignments $max_hits -html";
}

// Execute BLAST command
$blast_res = shell_exec('printf '.$blast_cmd);
$blast_res = str_replace('<a name=',"<a id=", $blast_res);

// Output HTML structure with BLAST results
echo $blast_res;
?>

<head>
    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" crossorigin="anonymous" />
    <!-- Include any other necessary stylesheets -->
</head>

<body>
    <!-- Your HTML content goes here -->
    <!-- Ensure that you have the necessary elements for Blaster.js -->
    <input type="file" id="blastinput" />
    <div id="blast-multiple-alignments"></div>
    <div id="blast-alignments-table"></div>
    <div id="blast-single-alignment"></div>

    <!-- Include necessary JavaScript files -->
    <script type="text/javascript" src="html2canvas.js"></script>
    <script type="text/javascript" src="blaster.min.js"></script>
    
    <script type="text/javascript">
        // Initialize Blaster.js with the Blast results
        var alignments = "<?php echo $blast_res;?>";
        
        var blasterjs = require("biojs-vis-blasterjs");
        var instance = new blasterjs({
            string: alignments,
            multipleAlignments: "blast-multiple-alignments",
            alignmentsTable: "blast-alignments-table",
            singleAlignment: "blast-single-alignment"
        });
    </script>
</body>

<!-- Include any additional scripts or JavaScript files -->
<!--<script type="text/javascript" src="fruit_genomebase/js/kinetic-v5.1.0.min.js"></script>-->
<!--<script src="fruit_genomebase/js/blast_canvas_graph.js"></script>-->


<!-- Include the output as plain text-->

<div style="margin:20px">
    <a href="blast_input_pomegranate.php"><i class='fas fa-reply' style='color:#229dff'></i> Go back to input</a>
    <a id="download_blast_table" class="float-right" style="cursor:pointer"><i class='far fa-file' style='font-size:24px;color:#229dff'></i> Download result in tabular format</a>
</div>



<?php
// Include necessary files
include_once realpath("$easy_gdb_path/footer.php");
?>

<script>
    // Your JavaScript code goes here, if any
</script>

<style>
    /* Your CSS styles go here, if any */
</style>

`
I do see the text output of blast results, but no output of blasterjs. The files are in the same directory as the blast output.php file. Also, when I put an html test for blasterjs in the same directory, it does work, but with an input file.
Any idea where am I wrong??

Thanks,
Alex

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Blasterjs implementation with String #14

Blasterjs implementation with String #14

alslonik commented Apr 2, 2024

Blasterjs implementation with String #14

Blasterjs implementation with String #14

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alslonik commented Apr 2, 2024