Hello everyone!, Im new to perl and programming in general (a week!) as this question shows. I have bam files and I want to see how often strings are repeated. However, Im trying to get it to work on a txt file firstly. The thing is, I don't really want to do it as shown below. Is there a way I can code it so I dont have to specify that which I want counted? So it just tells me the frequency of every string in the tab-delimited file? And printing to another text file is preferable to STDOUT. 

#!/usr/bin/perl -w
print "Enter the name of your file, ie myfile.txt:\n";
my $val = <STDIN>;
chomp ($val);
my $cnt=0;
open (HNDL, "$val") || die "wrong filename";
while ($val = <HNDL>)
    {
      while ($val =~ /\bchr1\b/ig)
      {
        ++$cnt;
      }
    } 
print "Number of instances of 'chr1' found: $cnt\n\n";

[download]

Thank's for your time!

In reply to Counting frequency of strings in files by Cian

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.