#!/bin/perl
#use warnings;
#use strict;
#chr1-	56960791	56960830	-	0	32:T>G,38:G>A	ATTTTAGACATTATTTATATAATATTTATATATAAAAAT	373	1930
#chr7+	142374348	142374370	+	0	6:C>T,10:A>C	GCTACCTAAGCACAGCTAAAAG

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);
  
  print file2 "${$matrix1{$var}}[0]\t${$matrix1{$var}}[1]\t${$matrix1{$var}}[2]\t${$matrix1{$var}}[3]\t${$matrix1{$var}}[4]\t${$matrix1{$var}}[5]\t${$matrix1{$var}}[6]\n";
  
}