最近 ghxiao 童鞋常常问我用perl处理数据的问题。今天来分享一段代码吧。

比如说,给出一个序列文件,里面都是Fasta格式的序列。 然后序列里面有一些NNNNNN的连续字符。






  • 1,CMM_开头的是该序列的ID


$/ = ">";

print "id\tstart\tend\tlen\n";  #先输出Title
	if($_ =~ /(CMM.*?)\s(.*)>/ms){ #第一个括号匹配ID。第二个匹配序列
		$id = $1;
		$seq = $2;
		$seq =~ s/\s//g; #把序列里的换行去掉。变成一列
		while ($seq =~ m/(N+)/g) { #匹配一个N或以上的字符
			$len = length($1); #返回这段匹配的长度
			$end = pos($seq); #用pos函数返回该匹配的终止位置
			$start = $end - $len + 1; #计算出起始位置
			print "$id\t$start\t$end\t$len\n"; #输出结果
运行 perl temp.pl seq.fasta >output



《 “用perl匹配字符串并返回该匹配的位置” 》 有 22 条评论

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  2. if($_ =~ /(CMM.*?)\s(.*)>/ms)


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