I have two input files :-

File 1

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    +

[download]
I want to count the number of entries in the second column of second file within 500+ (up) and 500- (down) to the number medntioned in the second column of first file.

For this, I made an script, but does not giving the desired result:- 

#!/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;
        
} 

}
    
    }
    
}

[download]

Result produced is 

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

[download]
But where is the count of 612,613, 614 etc.. these numbers are in the rage.

In reply to Sliding window perl program by genome

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.