GC_content_hash

# usr/bin/perl -w
use strict;

unless (@ARGV==2) {                                               #@ARGV传给脚本的命令行参数列表 
    die"Usage: perl $0 <input.fa> <out.GCcontent\n";              #当命令行参数不是2的时候输出使用说明
}

my ($infile,$outfile) = @ARGV;                                    #把命令行参数赋值给输入文件和输出文件
open(IN,$infile) || die "error: can't open infile: $infile";      #打开输入文件句柄IN
open(OUT,">$outfile") || die "error: can't make outfile: $outfile"; #打开输出文件句柄OUT


#申明哈希
my %count;
my $seq;
my $line=<IN>;
chomp($line);
print OUT "$line";
while($line=<IN>)
{
	if($line !~ /^>/){
		$line=~s/[\r\n\s+]//g; 									       		                  
		$seq.=$line;
		my @array=split("",$line);		
		for(my $i=0;$i<@array;$i++){
			$count{$array[$i]}++;                              
		}
	}
	elsif($line=~/^>(.*)\n$/){

		my $len=$count{A}+$count{T}+$count{G}+$count{C};
		my $GC=( $count{G} + $count{C} );
		my $gc_count = $len ? $GC / $len : 0; #计算GC含量，如果长度为0，GC含量算0
		print OUT "\t$len\t$gc_count\n$seq\n";
		%count="";
		$seq="";
		print OUT ">$1";
	}
}

my $len=$count{A}+$count{T}+$count{G}+$count{C};
my $GC=( $count{G} + $count{C} );
my $gc_count = $len ? $GC / $len : 0;
print OUT "\t$len\t$gc_count\n$seq";

close IN;
close OUT;