#
# We'll need some definitions
define('LINE_LENGTH', 60);
define('SRC', 'CGATMKRYVBHD');
define('DST', 'GCTAKMYRBVDH');
$str = '';
$seq = '';
# read in the file, a line at a time
while (!feof(STDIN)) {
$str = trim(fgets(STDIN));
if ($str[0] == '>') {
# if we're on a comment line, print the previous seq and move on
print_seq();
echo $str, "\n";
} else {
# otherwise, just append to the sequence
$seq .= $str;
}
}
print_seq();
exit;
# print the sequence out, if it exists
function print_seq()
{
global $seq;
# no time-consuming argument passing for us! :)
if ($seq != '') {
echo wordwrap(strrev(strtr(strtoupper($seq), SRC, DST)), LINE_LENGTH, "\n", true), "\n";
}
$seq = '';
}
#
# reverse complement in PHP
# contributed by Danny Sauer
# modified by anon
ob_implicit_flush(1);
ob_start(NULL, 4096);
$str = '';
$seq = '';
# read in the file, a line at a time
$stdin = STDIN;
while ($str !== '' || !feof($stdin)) {
$str = stream_get_line($stdin, 100, "\n");
if (isset($str[0]) && $str[0] === '>') {
# if we're on a comment line, print the previous seq and move on
print_seq($seq);
echo $str, "\n";
} else {
# otherwise, just append to the sequence
$seq .= $str;
}
}
print_seq($seq);
exit;
# print the sequence out, if it exists
function print_seq(&$seq)
{
if ($seq !== '') {
echo chunk_split(strrev(strtr($seq, 'ACBDGHKMNSRUTWVYacbdghkmnsrutwvy', 'TGVHCDMKNSYAAWBRTGVHCDMKNSYAAWBR')), 60, "\n");
}
$seq = '';
}
