索引

1.统计fasta、fa和fastq文件的长度，统计fastq的reads个数，单个reads长度，reads总长度（主要是统计总长度，其他在Linux下很简单就实现了）；统计fasta文件中contig的个数，列出名称，单条的长度，以及总长度。

思路整理：这是个典型的逐行读文件，取字段，计算长度问题。

fastq简单：四行一轮，解决办法很多，可以逐行读取，逐行匹配；也可以一次读两行；输出也少，单reads长度，reads数量，reads长度总和，也没有其他有价值的信息。

fasta略微复杂：没有规律，因为序列被切成短的，只能逐行读，逐行匹配；逐行读有个问题，怎么检测结束？（这是逐行读的一个最大缺陷，你无法操纵最后一次！！！）因此，只能把最后一次放在读循环的外面，每次输出的点就在匹配title那个地方。

代码如下：

#!/usr/bin/perl
#Author:zxlee
#Function: compute the length of fastq or fasta, fa.
#usage: `perl script_name fastq/fasta/fa_file_name`, it will show the total length, also a detail file.

use strict;
use warnings;
my $infile = shift;  #give 1st default para to it, you can go on shift to get the 2st para
open IN, "<$infile" or die $!;
open OUT, ">./result_len.txt" or die $!;

our $total_len = 0;
our $seq_num = 0;
our $len;

if($infile =~ /fastq$/){
    while(<IN>){
        next if not /^@\S+/;
        my $seq = <IN>;  #your cannot use $_ here!!!
        chomp($seq);
        $seq_num += 1;
        $total_len += length($seq);
        print OUT "\nreads_len = $total_len\n" if $seq_num == 1;
    }
    print OUT "Total num of reads is $seq_num\n";
}
elsif($infile =~ /(fasta|fa)$/){ # easy way, not use "OR"
    my $chr_len = 0;
    while(<IN>){
        chomp;
        my $line = $_;
        if ($line =~ /^>(\S+)/){
            print OUT "$chr_len\n" if $chr_len != 0;
            print OUT "$1\t";
            $chr_len = 0;
        }else{
            $len = length($line) if $total_len == 0;
            $chr_len += length($line);
            $total_len += length($line);
        }
    }
    print OUT "$chr_len\n";
    print OUT "one line has $len\n";
}
print "The total length is $total_len\n";
close(IN);
close(OUT);