species_name_change PHP Code Examples

Example #1

0

Show file

File: analysis_domain.php Project: billzt/btcotton

$sql = "SELECT gene_id,domain_acc,species FROM gene2domain WHERE gene_id IN ({$id_search_string}) AND domain_db='{$domain_type}'";
$query = $connect->query($sql);
while ($row = $query->fetch_array()) {
    $gene_id = $row['gene_id'];
    $domain_acc = $row['domain_acc'];
    if (isset($data[$gene_id][$domain_acc])) {
        $data[$gene_id][$domain_acc]++;
    } else {
        $data[$gene_id][$domain_acc] = 1;
    }
    if (isset($number[$gene_id])) {
        $number[$gene_id]++;
    } else {
        $number[$gene_id] = 1;
    }
    $species[$gene_id] = species_name_change($row['species']);
}
$total_num = count($data);
require 'analysis_count_num.php';
?>

<h3>Domains in Database <?php 
echo $domain_type;
?>
</h3>

<div class="table-responsive">
    <div id="final_toolbar">
        <button id="select2analysis_btn" class="btn btn-primary" disabled>Select &amp; Re-Analysis</button>
        <button id="select2blast_btn" class="btn btn-success" disabled>Select &amp; BLAST</button>
        <button id="select2tree_btn" class="btn btn-warning" disabled>Select &amp; Phylogenetic Tree Build</button>

Example #2

0

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File: analysis_transcript_basic.php Project: billzt/btcotton

<?php

// Species
$sql = "SELECT id,species FROM gene_info WHERE id IN ({$id_search_string})";
$query = $connect->query($sql);
$data = array();
while ($row = $query->fetch_array()) {
    $gene_id = $row['id'];
    $data[$gene_id]['species'] = species_name_change($row['species']);
}
// Transcript/CDS Length
$sql = "SELECT gene_id,transcript_length,CDS_length FROM transcript_info WHERE gene_id IN ({$id_search_string}) AND principle='Y'";
$query = $connect->query($sql);
while ($row = $query->fetch_array()) {
    $gene_id = $row['gene_id'];
    $data[$gene_id]['transcript_length'] = $row['transcript_length'];
    $data[$gene_id]['CDS_length'] = isset($row['CDS_length']) ? $row['CDS_length'] : '<i>NA</i>';
}
$sql = "SELECT gene_id,GC_content FROM cds_statistics WHERE gene_id IN ({$id_search_string})";
$query = $connect->query($sql);
while ($row = $query->fetch_array()) {
    $gene_id = $row['gene_id'];
    $data[$gene_id]['GC_content'] = isset($row['GC_content']) ? $row['GC_content'] : '<abbr data-toggle="tooltip" title="Not Available"><i>NA</i></abbr>';
}
// Exon/Intron Length
$sql = "SELECT gene_id,type,COUNT(type) AS type_num, SUM(length) AS sum_length FROM exon_intron_structure\n    WHERE gene_id IN ({$id_search_string}) AND type='intron' GROUP BY gene_id,type";
$query = $connect->query($sql);
while ($row = $query->fetch_array()) {
    $gene_id = $row['gene_id'];
    $data[$gene_id]['sum_length_intron'] = $row['sum_length'];
    $data[$gene_id]['num_intron'] = $row['type_num'];

Example #3

0

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File: search_by_go.php Project: billzt/btcotton

        }
    }
    // gene id(s) -> gene name, species(s) (Print table)
    $protein_id_array = array_unique($protein_id_array);
    $gene_id_array = array_unique($gene_id_array);
    $sql = "SELECT id, species, name FROM gene_info WHERE id IN (" . implode(', ', $gene_id_array) . ")";
    $query = $connect->query($sql);
    while ($row = $query->fetch_array()) {
        $gene_id = $row['id'];
        $data[$gene_id]['name'] = $row['name'];
        $data[$gene_id]['species'] = $row['species'];
    }
    foreach ($protein_id_array as $protein_id) {
        $gene_id = preg_replace('/\\.\\d+$/', '', $protein_id);
        $gene_name = $data[$gene_id]['name'];
        $output_species = species_name_change($data[$gene_id]['species']);
        $output_go = '';
        foreach (array_keys($data[$protein_id]) as $acc) {
            $output_go .= $acc . ';';
        }
        $output_data[] = array('id' => $protein_id, 'name' => $gene_name, 'species' => $output_species, 'go' => $output_go);
    }
    file_put_contents($tmp_file, json_encode($output_data));
    ?>

<div class="table-responsive">
    <div id="final_toolbar">
        <button id="select2analysis_btn" class="btn btn-primary" disabled>Select &amp; Analysis</button>
        <button id="select2blast_btn" class="btn btn-success" disabled>Select &amp; BLAST</button>
        <button id="select2tree_btn" class="btn btn-warning" disabled>Select &amp; Phylogenetic Tree Build</button>
        <button id="select2store_btn" class="btn btn-default" disabled>Select &amp; Store</button>

Example #4

0

Show file

File: analysis_expression_fpkm.php Project: billzt/btcotton

                <?php 
}
?>
            </tr>
        </thead>
        <tbody>
        <?php 
foreach ($id_array as $input_id) {
    echo '<tr>';
    if (isset($data[$input_id])) {
        echo '<td></td>';
        $valid_id_array[] = $input_id;
        // used for drawing chart
        echo '<td>', $input_id, '</td>';
        echo '<td><a target="_blank" data-toggle="tooltip" title="Open in new window" href="/profiles/transcript/', $input_id, '.1/expression">', $input_id, '.1</a></td>';
        echo '<td><i>', species_name_change($species), '</i></td>';
        foreach ($sample_array as $sample) {
            echo '<td>';
            echo number_format($data[$input_id][$sample], 2);
            echo '</td>';
        }
    } else {
        echo '<td></td><td>', $input_id, '</td>', str_repeat('<td><abbr data-toggle="tooltip" title="Not Available"><i>NA</i></abbr></td>', count($sample_array) + 2);
    }
    echo '</tr>';
}
?>
        </tbody>
    </table>
</div>

Example #5

0

Show file

File: index_panel_expression_fpkm.php Project: billzt/btcotton

" class="panel-collapse collapse <?php 
    if ($species == 'Ghir') {
        echo 'in';
    }
    ?>
" role="tabpanel">
            <div class="panel-body">
<?php 
    foreach (array_keys($data[$species]) as $fieldset) {
        ?>
            <fieldset class="fieldset_express_fpkm">
                <legend style="font-size:120%"><?php 
        echo $fieldset;
        ?>
 (<i><?php 
        echo species_name_change($species);
        ?>
</i>)
                &nbsp; &nbsp; &nbsp; </legend>
                <div class="row"><input type="checkbox" class="check-control-all" /> <span class="bg-primary">Check All</span></div>
<?php 
        foreach (array_keys($data[$species][$fieldset]) as $category) {
            ?>
                    <div class="row has-feedback">
                        <div class="checkbox">
<?php 
            $sample_array = array_keys($data[$species][$fieldset][$category]);
            sort($sample_array);
            foreach ($sample_array as $sample) {
                ?>
                                <label class="col-md-<?php

Example #6

0

Show file

File: analysis_orthology.php Project: billzt/btcotton

$target_tax = $_POST['target_tax'];
$id_search_string = preg_replace("/',/", ".1',", $id_search_string);
$id_search_string = preg_replace("/'\$/", ".1'", $id_search_string);
$sql = "SELECT * FROM ortholog WHERE queryID IN ({$id_search_string}) AND subjectType='{$target_tax}'";
$data = array();
$query = $connect->query($sql);
while ($row = $query->fetch_array()) {
    $query_id = $row['queryID'];
    $query_id = preg_replace('/\\.\\d+$/', '', $query_id);
    $subject_id = $row['subjectID'];
    $data[$query_id][$subject_id]['queryLen'] = $row['queryLen'];
    $data[$query_id][$subject_id]['subjectLen'] = $row['subjectLen'];
    $data[$query_id][$subject_id]['queryCov'] = $row['queryCov'];
    $data[$query_id][$subject_id]['e_value'] = $row['e_value'];
    $data[$query_id][$subject_id]['identity'] = $row['identity'];
    $species[$query_id] = species_name_change($row['queryType']);
}
$total_num = count($data);
require 'analysis_count_num.php';
?>

<h3 id="target_tax_head"></h3>
<script>
    var tax = $('#target_tax').find("option:selected").text();
    $('#target_tax_head').html('Target Species: '+tax);
</script>
<div class="table-responsive">
    <div id="final_toolbar">
        <button id="select2analysis_btn" class="btn btn-primary" disabled>Select &amp; Re-Analysis</button>
        <button id="select2blast_btn" class="btn btn-success" disabled>Select &amp; BLAST</button>
        <button id="select2tree_btn" class="btn btn-warning" disabled>Select &amp; Phylogenetic Tree Build</button>

Example #7

0

Show file

File: id2geneinfo.php Project: billzt/btcotton

<?php

require '../phpInclude/function_species_name_change.php';
// short species name => full name
// connect database
require '../phpInclude/connect_db.php';
$query_id = $_POST['query_id'];
$hit_id = preg_replace('/\\.\\d+$/', '', $_POST['hit_id']);
$score = $_POST['score'];
$sql = "SELECT id,species,name,description,chromosome FROM gene_info WHERE id='{$hit_id}'";
$query = $connect->query($sql);
while ($row = $query->fetch_array()) {
    echo json_encode(array('query_id' => $query_id, 'hit_id' => $_POST['hit_id'], 'score' => $score, 'name' => $row['name'], 'desc' => $row['description'], 'species' => species_name_change($row['species']), 'chr' => $row['chromosome']));
}

Example #8

0

Show file

File: ajax_browse.php Project: billzt/btcotton

            <th data-field="id" data-sortable="true" data-formatter="IDFormatter">Gene ID</th>
            <th data-sortable="true">Gene Name</th>
            <th>Description</th>
            <th>Start</th>
            <th>End</th>
            <th>Strand</th>
            <th>Links</th>
        </tr>
    </thead>
    <tbody>
    <?php 
while ($row = $query->fetch_array()) {
    $gene_id = $row['id'];
    $gene_name = isset($row['name']) ? $row['name'] : '<abbr data-toggle="tooltip" title="Not Available"><i>NA</i></abbr>';
    $desc = isset($row['description']) ? $row['description'] : '<abbr data-toggle="tooltip" title="Not Available"><i>NA</i></abbr>';
    $output_species = species_name_change($row['species']);
    echo '<tr>';
    echo '<td></td>';
    echo '<td>', $gene_id, '</td>';
    echo '<td>', $gene_name, '</td>';
    echo '<td>', $desc, '</td>';
    echo '<td>', number_format($row['start']), '</td>';
    echo '<td>', number_format($row['end']), '</td>';
    echo '<td>', $row['strand'], '</td>';
    // Link to different databases
    echo '<td>';
    echo '<a target="_blank" data-toggle="tooltip" title="Exon-Intron Structure" href="/profiles/transcript/', $gene_id, '.1/structure"><small>Structure</small></a>; ';
    echo '<a target="_blank" data-toggle="tooltip" title="Protein Domain" href="/profiles/transcript/', $gene_id, '.1/domain"><small>Domain</small></a>; ';
    echo '<a target="_blank" data-toggle="tooltip" title="Homologous Genes in Intra/Inter Species" href="/profiles/transcript/', $gene_id, '.1/ortholog"><small>Homology</small></a>; ';
    echo '<a target="_blank" data-toggle="tooltip" title="Gene Ontology Annotation" href="/profiles/transcript/', $gene_id, '.1/go"><small>GO</small></a>; ';
    echo '<a target="_blank" data-toggle="tooltip" title="KEGG Pathway Annotation" href="/profiles/transcript/', $gene_id, '.1/kegg"><small>Pathway</small></a>; ';

Example #9

0

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File: search_by_gene_id.php Project: billzt/btcotton

$sql_restrict = "id='{$search_info}' OR ";
if (preg_match('/[^\\w\\s\\-]/', $search_info)) {
    $sql_restrict .= "name LIKE '%" . addslashes($search_info) . "%' OR description LIKE '%" . addslashes($search_info) . "%'";
} else {
    $sql_restrict .= "name LIKE '%{$search_info}%' OR description REGEXP '[[:<:]]" . $search_info . "[[:>:]]'";
}
$sql_restrict = "({$sql_restrict}) AND species='{$species}'";
// count number
$sql = "SELECT * FROM gene_info WHERE {$sql_restrict}";
$tmp_file = '../tmp/' . uniqid('search-', true);
$query = $connect->query($sql);
$total_num = $query->num_rows;
require 'search_count_num.php';
// get search results and group to JSON
while ($row = $query->fetch_array()) {
    $output_data[] = array('id' => $row['id'], 'name' => $row['name'], 'desc' => $row['description'], 'species' => species_name_change($row['species']), 'chromosome' => $row['chromosome'], 'start' => $row['start'], 'end' => $row['end'], 'strand' => $row['strand']);
}
file_put_contents($tmp_file, json_encode($output_data));
?>

<div class="table-responsive">
    <div id="final_toolbar">
        <button id="select2analysis_btn" class="btn btn-primary" disabled>Select &amp; Analysis</button>
        <button id="select2blast_btn" class="btn btn-success" disabled>Select &amp; BLAST</button>
        <button id="select2tree_btn" class="btn btn-warning" disabled>Select &amp; Phylogenetic Tree Build</button>
        <button id="select2store_btn" class="btn btn-default" disabled>Select &amp; Store</button>
    </div>
    <table data-toggle="table" class="table table-hover table-no-bordered bootstrap-table-responsive"
    data-toolbar="#final_toolbar" id="final_table"
    data-search="true" data-escape="false" data-url="../phpInclude/bootstrap_table_server_pagination.php" data-show-refresh="true"
    data-show-export="true" data-export-types="['txt', 'csv', 'excel']" data-export-data-type="all"

PHP species_name_change Examples