最近php7的消息铺天盖地, 忍不住想尝试下。星期天看了下语法, 写个小脚本练下手;
这个脚本读取fasta 文件, 输出序列的长度和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); } ?>