How to encode binary to a DNA sequence - php

Question

I would like to encode a binary sequence to a DNA sequence by following this rule:
00 = A
01 = C
10 = G
11 = T
For example: 10011100 = GCTA.
I wrote a PHP script which converts my string to binary and then I convert the binary to a DNA sequence by using the str_replace function. My issue is that the DNA sequence is not correctly converted. Can someone help me?
Here's my PHP script:
<?php
// Function to convert string to bin
function strToBin($input) {
if (!is_string($input))
return false;
$ret = '';
for ($i = 0; $i < strlen($input); $i++) {
$temp = decbin(ord($input{$i}));
$ret .= str_repeat('0', 8 - strlen($temp)) . $temp;
}
return $ret;
}
$bin = strToBin('Stack');
// Try to transcript binary to DNA
$bincomb = array('00', '01', '10', '11');
$DNAtrans = array('A', 'C', 'G', 'T');
echo $transcript = str_replace($bincomb, $DNAtrans, $bin);
?>

Answer 1

The str_replace() approach doesn't work because it looks for the substrings in the order 00, 01, 10, 11. So, for example, with the binary string 1001 it replaces the inner 00 with an A, after which the string is 1A1, and no more conversions can be made.
For your function to work, you need to go through the binary string in chunks of two characters.
$bin = strToBin('Stack');
$bin = str_split($bin, 2);
$combine = array(
'00' => 'A',
'01' => 'C',
'10' => 'G',
'11' => 'T'
);
$str = '';
foreach ($bin as $item)
$str .= $combine[$item];
The string is first split into chunks of two characters, which are then looped through and their respective values appended to the result string $str.

Answer 2

In PHP, I usually do these transformations with the two-arguments implementation of strtr(), like this:
// outputs 10011100
echo strtr("GCTA", array("A" => "00", "C" => "01", "G" => "10", "T" => "11"));
The reverse is also possible:
// outputs GCTA
echo strtr("10011100", array("00" =>"A", "01" => "C", "10" => "G", "11" => "T"));