CTSC	chr11	-	650	E	RAB38	chr11	-	87883123	E	12	2	INTRACHR-SS-OGO-0GAP	inframe-shift

file 2 

chr11	602	63889087	HWI-ST216_106:3:67:14628:181851	-
chr11	613	69889087	HWI-ST216_106:3:24:16406:176388	+
chr11	614	80889087	HWI-ST216_106:3:21:13731:105239	+
chr11	643	94888888	HWI-ST216_111:5:22:3149:116167	+
chr11	678	98889079	HWI-ST216_106:3:5:18058:57952	+
chr11	612	108888887	HWI-ST216_106:3:8:5578:44855	+
chr5	612	63889087	HWI-ST216_106:3:67:14628:181851	-
chr3	88033200	69889087	HWI-ST216_106:3:24:16406:176388	+
chr2	88033345	80889087	HWI-ST216_106:3:21:13731:105239	+
chr1	88033376	94888888	HWI-ST216_111:5:22:3149:116167	+
chr6	88034000	98889079	HWI-ST216_106:3:5:18058:57952	+
chr7	88034123	108888887	HWI-ST216_106:3:8:5578:44855	+

##</code><code>##

#!/usr/bin/perl -w

$file1=$ARGV[0];    #First file 
$file2=$ARGV[1];    #second file 
open(TR,$file1); 
while ($line1=<TR>) 
{
chomp($line1);
@ar1 = split(/\t/,$line1);
chomp($ar1[1]);chomp($ar1[3]);
$up = $ar1[3]-500;
$dn = $ar1[3]+500; 
open(SC,$file2);
while ($line2=<SC>)
{
    chomp($line2);
    @array2 = split (/\t/, $line2);
    if ($ar1[1] eq $array2[0])
    {
for ($mm=$up;$mm<=$dn;$mm+=100)
{
$gt = $up+100;
$c ='0';    
if (($array2[1]> $up) && ($array2[1] < $gt)) 
{

    print "$up\t$gt\t$array2[1]\n";
    $c++;
}

$up=$up+50;
        
} 

}
	
    }
    
}

##</code><code>##

550	650	602 <p>
600	700	602 <p>