import gff3 file to jbrowser by chr

import_gff3_by_chr.pl

#!/usr/bin/perl -w

use strict;
use Data::Dumper;

## Written by [email protected]
# import gff3 file to jbrowser by chr
# default jbrowser installation diretory is /var/www/jbrowser/

my ($gff3_f,$outdir) = @ARGV;
my %chr;
open IN,"$gff3_f" || die $!;
while(<IN>){
	chomp;
	next if(/^#/);
	my @t = split /\t/;
	$chr{$t[0]} = 1;
}
close IN;

my @chr_gff3;
mkdir "./chr_gff3" if(! -e "./chr_gff3");
open SH,">","import_gff3.sh" || die $!;
foreach my $c (keys %chr){
	open OUT,">","./chr_gff3/$c.gff3" || die $!;
	print SH "perl /var/www/jbrowser/bin/flatfile-to-json.pl --out $outdir --gff ./chr_gff3/$c.gff3  --type mRNA   --autocomplete all --trackLabel EnsemblTrans --key 'EnsemblTrans' --getSubfeatures --className transcript  --subfeatureClasses '{\"CDS\": \"transcript-CDS\"}'  --arrowheadClass arrowhead  --urltemplate \"http://asia.ensembl.org/Homo_sapiens/Transcript/Summary?t={id}&db=core\" --maxLookback 2000\n";
	open IN,"$gff3_f" ||die $!;
	my $conti = "";
	while(<IN>){
		chomp;
		if(/^#/ && $conti eq ""){
			print OUT "$_\n";
			$conti = "####";
		}
		my @t = split /\t/;
		my $id = $t[0];
		if($t[0] eq $c){
			print OUT "$_\n";
			$conti = "";
		}
	}
	close OUT;
}
close SH;