Collect file and apply process logic

<?php

$login      = "login";      // Fill in your username / customerid
$password   = "password";   // Fill in your password
$filename   = "URL";

// Get the pricelist into an array.
$lines = file( $filename );     // personally I would suggest file_get_contents()

// Create CSV header (first row)
$fields = array(
    "sku",
    "stock"
);
// Create CSV file
$csv_file = fopen( "output.csv", "w" );
fputcsv( $csv_file, $fields );

// Loop through our array
foreach ( $lines as $line_num => $line ) {

    echo "Line #<b>{$line_num}</b> : " . htmlspecialchars( $line ) . "<br /><br />";
    $column = explode ( '"~"', $line ); // use the "~" as explode char
    echo $column[0] . " productid <BR>";
    echo $column[1] . " stock <BR>";

    // $column[1] is assumed to the stock level and contains y or n

    if( strtolower( $column[1] ) == "y") {
        $column[1] = 99;    // has stock
    } else {
        $column[1] = 0;     // wasn't a "y" so no stock for you sir
    }

    // etc
    $fields = array(
        $column[0],
        $column[1]
    );

    // stuff into a csv file
    fputcsv($csv_file, $fields);
}
// Be nice and close CSV file
fclose($csv_file);