circos输入数据文件格式化——depth，GC，geneskew

写了一个小脚本用来格式化数据格式，必须有正负链的深度文件，得到gtf的基因高亮区域，并且计算gc含量和geneskew：

#!/usr/bin/env perl 
use warnings;
use strict;
use Getopt::Long;

my %opt;
GetOptions(\%opt, "len=s");
$opt{len} ||= 1000;

die qq/
Usage:	perl $0 <contig.length> <ref.gtf> <ref.genome.fa> <plus.depth> <minus.depth> -len 1000(default 1000)

/ if(@ARGV < 4);

my %hash;
my %dp;
my (%gcp, %gs);
my $ci = 1;
my $cl = shift @ARGV;
open CL, $cl or die $!;
open KT, ">karyotype.txt" or die $!;
while(<CL>)
{
	chomp;
	my @tmp = split;
	print KT "chr - hs$ci $tmp[0] 0 $tmp[1] color\n";
	$hash{$tmp[0]} = "hs$ci";
	push @{$dp{$tmp[0]}}, "0";
	push @{$gcp{$tmp[0]}}, "0";
	push @{$gs{$tmp[0]}}, "0";
	$ci ++;
}
close CL;

my $j = 1;
my $gtf = shift @ARGV;
open GTF, $gtf or die $!;
open PO, ">plushighlight.txt" or die $!;
open MO, ">minushighlight.txt" or die $!;
open GID, ">geneid.txt" or die $!;
while(<GTF>)
{
	chomp;
	my @tmp = split