#!/bin/perl
#use warnings;
#use strict;


my $inputfile=$ARGV[0]; #transcript
my $inputfile2=$ARGV[1];
#my $inputfile3=$ARGV[2];

open (file2,">$inputfile2.bed") or die "$!\n";

my %matrix1;my %matrix2;
my @matrixtest1;
my @matrixtest2;
my @matrixtest3;
my $var1=0;my $var=0;
my $var2=0;
my $var3=0;

open (INPUT_FILE,$inputfile);
while(my $line1=<INPUT_FILE>)
{ 
  @{$matrix1{$var}}=split(/\s/,$line1);
  if (${$matrix1{$var}}[3]>=5)
  {
  print file2 "${$matrix1{$var}}[0]\t${$matrix1{$var}}[1]\t${$matrix1{$var}}[2]\t${$matrix1{$var}}[3]\t0\t${$matrix1{$var}}[4]\n";
  }
}