dara-insert.php

<?php //exit;

ini_set('display_errors', true);
require_once('config.php');
require_once($folders['lib_prefix'].'/common.php');

echo 'I am relatively healthy.', '<br />';

$filename = './t_second_rna_a14.log';

try {
    $sql = 'INSERT IGNORE INTO proteins (title, AA, alpha, beta) VALUES (?, ?, ?, ?)';
    $stmt = $dbh->prepare($sql);

    $file = file($filename);
    echo $filename;

    foreach ($file as $line) {
        $data = preg_split('/\s+/', trim($line));
        $stmt->execute($data);
    }
}
catch (Exception $e) {
    echo $e->getMessage();
}

dara-test.php

<?php

// $allFilesPath = '/WOK2/sokolova/allfiles';
$fileExt = 'int';
$fileSuffix = '00.' . $fileExt;

$inputFileName = 'rf_chi.log';

$dsn = 'mysql:dbname=dara;host=devroom';
$dbh = new PDO($dsn, 'dara', 'dara');

$name_rft = array();
$names = array();

$rf_chi_array = file($inputFileName, FILE_IGNORE_NEW_LINES ^ FILE_SKIP_EMPTY_LINES);
$rf_chi_count = count($rf_chi_array);

for ($i = 0; $i < $rf_chi_count; $i++) {
    $record = trim($rf_chi_array[$i]);
    $name_rft[$i] = preg_split('/\s+/', $record);
}

foreach ($name_rft as $rft) {
    $name = basename($rft[0], $fileSuffix);
    $names[] = $dbh->quote($name);
}

$sql = 'SELECT title, alpha, beta FROM proteins WHERE title IN (' . implode(',', $names) . ')';
$data = $dbh->query($sql)->fetchAll();

var_dump($sql, $data);

dara-update.php

<?php //exit;

ini_set('display_errors', true);
require_once('config.php');
require_once($folders['lib_prefix'].'/common.php');

echo 'I am relatively healthy.', '<br />';

$filename = 'title-mw-rg.dat';
echo $filename;

try {
    $sql = 'UPDATE proteins SET mw = ?, rg = ? WHERE title = ?';
    // $sql = 'UPDATE proteins SET mw = :mw, rg = :rg WHERE title = :title';
    $stmt = $dbh->prepare($sql);

    $file = file($filename);

    foreach ($file as $line) {
        list($title, $mw, $rg) = preg_split('/\s+/', trim($line));
        $data = array($mw, $rg, $title);

        /*
        $data = array(
            ':title' => $title,
            ':mw'    => $mw,
            ':rg'    => $rg
        );
        */ 

        $stmt->execute($data);
    }
}
catch (Exception $e) {
    echo $e->getMessage();
}

data.sql

DROP TABLE IF EXISTS proteins;

CREATE TABLE proteins (
    title CHAR(4) NOT NULL,
    AA    SMALLINT(5) UNSIGNED NOT NULL,
    alpha DECIMAL(5,2) NOT NULL,
    beta  DECIMAL(5,2) NOT NULL,
    PRIMARY KEY (title)
);

ALTER TABLE proteins
    ADD COLUMN mw DOUBLE UNSIGNED,
    ADD COLUMN rg DECIMAL(5,2) UNSIGNED,
    ADD KEY (mw),
    ADD KEY (rg)
;

INSERT INTO proteins (title, alpha, beta) VALUES
    ('1o91', 1, 1),
    ('3ihu', 1, 2),
    ('4ec6', 1, 3)
;

rf_chi.log

1o9100.int Rf 2.415 Chi 1.110
3ihu00.int Rf 2.239 Chi 1.185
2oit00.int Rf 2.361 Chi 1.159
4ec600.int Rf 2.314 Chi 1.260
9icl00.int Rf 2.156 Chi 1.207

title-mw-rg.dat

1b2m 0.2391E+05  18.71
1b7f 0.4528E+05  30.08
1c0a 0.9125E+05  31.28
1c9s 0.1906E+06  34.70
1cvj 0.1587E+06  36.24
1cx0 0.3464E+05  27.27
1ddl 0.6179E+05  29.73