基因组处理

    去除基因组序列中的未定位的scaffold、Contig序列和线粒体序，主要针对NCBI提供refseq基因组序列，组装到染色体级别的物种基本都通用。将所有碱基统一成大写字母，并计算每条染色体长度，每80个字符换行。

处理脚本如下：

use strict;
open A,"$ARGV[0]";
open B,">$ARGV[1]";
open C,">$ARGV[2]";
my $help=<<USAGE;
Usage: perl $0 genome.fa new.fa chrlen.list

USAGE
die "$help",unless(@ARGV==3);

$/=">";
<A>;
my %chrlen;
while(<A>){
	chomp;
	my @line=split /\n+/,$_;
	my $seqName=shift @line;
	my $chr=(split /\s+/,((split /,/,$seqName)[0]))[-1];
	next if $chr=~ /scaffold/;
	next if $chr=~ /Contig/;
	next if $chr=~ /mitochondrion/;
	$chr="chr".$chr;
	my $seq=join "",@line;
	$seq=~s/\n//g;
	$seq=uc($seq);
	my $len=length($seq);
	$chrlen{$chr}=$len;
	$seq=~ s/(\w{80})/$1\n/g;
	if($len % 80 == 0){
		print B ">$chr\n$seq";
	}
	else{
		print B ">$chr\n$seq\n";
	}
	print C "$chr\t$chrlen{$chr}\n";
}