php 统计fasta 序列长度和GC含量

<?php
$fasta = "test.fasta";
$meta  = array();
$meta  = parse_fasta($fasta);
write_res($meta);

function parse_fasta($fasta) {
$meta = array();
$file_handle = fopen($fasta, 'r');
$id = '';
$seq = '';
while (!feof($file_handle)) {
$line = fgets($file_handle);
$line = preg_replace("/\s+$/", "", $line);
if (preg_match("/^>/", $line)) {
if ($id) {
$meta[$id] = $seq;
$id = $line;
$seq = '';
} else {
$id = $line;
}
} else {
$seq .= $line;
}
}
$meta[$id] = $seq;
fclose($file_handle);
return $meta;
}

function write_res($meta) {
foreach ($meta as $key => $value) {
$len = cal_length($value);
$gc  = cal_gc($value);
echo "$key\t$value\t$len\t$gc\n";
}
}

function cal_length($seq) {
return strlen($seq);

}

function cal_gc($seq) {
$gc = array();
preg_match_all("/G|C|g|c/", $seq, $gc);
return count($gc[0]) / strlen($seq);
}

?>