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

#chr7+	142374348	142374370	+	0	6:C>T,10:A>C	GCTACCTAAGCACAGCTAAAAG

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

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

my %matrix1;
my @matrix2;
my $var1=0;
my $var2=0;

open (INPUT_FILE,$inputfile);
while(my $line1=<INPUT_FILE>)  
 { @{$matrix1{$var1}}=split(/\s/,$line1);
  if ((${$matrix1{$var1}}[0]=~/chr\d{1,2}\+/) && (${$matrix1{$var1}}[3]=~/\+/))
   { @matrix2=split(/\+/,${$matrix1{$var1}}[0]);
print file2 "$matrix2[0]\t${$matrix1{$var1}}[1]\t${$matrix1{$var1}}[2]\t${$matrix1{$var1}}[3]\t${$matrix1{$var1}}[4]\t${$matrix1{$var1}}[5]\n";
    }
  elsif ((${$matrix1{$var1}}[0]=~/chr\d{1,2}\-/) && (${$matrix1{$var1}}[3]=~/\-/))
   { @matrix2=split(/\-/,${$matrix1{$var1}}[0]);
print file2 "$matrix2[0]\t${$matrix1{$var1}}[1]\t${$matrix1{$var1}}[2]\t${$matrix1{$var1}}[3]\t${$matrix1{$var1}}[4]\t${$matrix1{$var1}}[5]\n";
    }
 }

close (file2);