Question

I want to parse a file, and store it into an Array in PHP. However, there are some rules which should the observed:

• (p=”value”) should be ignored, but the "value" should be preserved.
• - should be ignored.
• whitespaces should be ignored.
• split by \t and \n.

A sample string is :

NPD4196-2a_5_0
Geldanamycin - 0.166516 (p = 0.0068)    Alamethicin - 0.158302 (p = 0.0206)     4-Hydroxytamoxifen - 0.1429 (p = 0.0183)        Abietic acid - 0.133045 (p = 0.0203)    Caspofungin - 0.130885 (p = 0.0432)     Extract 00-303C - 0.12858 (p = 0.0356)  U73122 - 0.113274 (p = 0.0482)  Radicicol - 0.10213 (p = 0.0356)        Calcium ionophore - 0.096183 (p = 0.0262)

So, the goal is to produce a data structure like:

Array('NPD4196-2a_5_0' => Array(Array( 0 => 'Geldanamycin', 1 => '0.166516', 2 => '0.0068'), Array( ... ));

I have this written so far …

while(($line = fgets($fp)) !== false){
        $args = preg_split( '/[\t\n (=) ]+/', $line, -1, PREG_SPLIT_NO_EMPTY );
        if(count($args)){
           print_r($args);
           print "\n";
        }
}

What am I missing in other to accomplish my goal?
Thanks

Answer 1

This seems to work for one key-value pair (assuming NPD4196-2a_5_0 is the key in your example, and the second line is the value).

<?php

$fp = fopen('foo.txt', 'r');
$regex = '/(\w*)\s*-\s*([\d\.]+)\s*\(p\s*=\s*([\d\.]+)\)/';
$id = "NO ID";
$result = Array();

while(($line = fgets($fp)) !== false){
    if (!preg_match($regex, $line)) {
        $id = chop($line);
    } else {
        $all = Array();

        while (preg_match($regex, $line, $matches, PREG_OFFSET_CAPTURE)) {
            $last = end($matches);
            $line = substr($line, $last[1] + strlen($last[0]) + 1);

            $strings = Array();

            for ($i = 1; $i < 4; $i++) {
                array_push($strings, $matches[$i][0]);
            }

            array_push($all, $strings);
        }

        $result[$id] = $all;
    }
}

print_r($result);
?>

(That is a slightly edited version of David B’s regex.)

If the line doesn’t match that long RegEx pattern, it will store the line as the ID. Otherwise, it will match the RegEx, then chop off the matching part. Each iteration of the inner while loop will match one entry. Since I am grabbing the indices of the matches, the for loop is used to only add the strings to the result.

This prints:

Array
(
    [NPD4196-2a_5_0] => Array
        (
            [0] => Array
                (
                    [0] => Geldanamycin
                    [1] => 0.166516
                    [2] => 0.0068
                )

            [1] => Array
                (
                    [0] => Alamethicin
                    [1] => 0.158302
                    [2] => 0.0206
                )

            [2] => Array
                (
                    [0] => Hydroxytamoxifen
                    [1] => 0.1429
                    [2] => 0.0183
                )
...