Uses the [protein_id=*] to extract the protein name.

use_protein_id_as_seq_name.php

<?php
if ($argc <= 1) {
    echo "Please supply a file name\n";
    exit(1);
}

$input = $argv[1];
$file = fopen($input, 'r');

while ($line = fgets($file)) {
    $line = trim($line, "\n");
    if (begins_with($line, '>')) {
        $line = str_replace('lcl|', '', $line);
        preg_match('/\[protein_id=(.*?)\]/', $line, $matches);
        if(count($matches) > 1) {
            $line = ">".$matches[1];
        } else {
            $parts = explode(' ', $line);
            $line = $parts[0];
        }
    }

    echo $line."\n";
}

function begins_with($string, $needle)
{
    return substr($string, 0, strlen($needle)) === $needle;
}