I modified my code with ur very kind feed back but I am
getting an error like this now :- 
Can't use string("72")as an array reference while "strict refs" in use
+ at test.pl line 21, <$fh> line 2

[download]
My updated code is:- 
#!/usr/bin/perl

use strict;
use warnings;

my $qfn1 = "wah.txt";
my $qfn2 = "taj.txt";

my %positions;
{
   open(my $fh, '<', $qfn1)
      or die("Cannot open file \"$qfn1\": $!\n");

  while (<$fh>) {
   chomp; 
   my ($key, $pos) = split /\s+/;
   if (!$positions{$key}) {
     $positions{$key} = $pos;
   } else {
     my $ref = $positions{$key};
     push @$ref,$pos;
   }
}
}

my %sequences;
{
   open(my $fh, '<', $qfn2)
      or die("Cannot open file \"$qfn2\": $!\n");

   my $key;
   while (<$fh>) {
       if ( s/^>// ) {
           $key = ( split /\|/ )[1];
       }
       else {
           chomp;
           $sequences{$key} .= $_;
       }
   }
}

for my $key ( sort keys %positions ) {
   my $ref = $positions{$key};
   foreach my $value (@$ref) {
    if ( ! exists( $sequences{$key} )) {
        warn "KEY $key in File1 not found in File2\n";
        next;
    }
    if ( length( $sequences{$key} ) < $positions{$key} ) {
        warn "KEY $key: File2 string length too short for File1 positi
+on value\n";
        next;
    }
    my $index = rindex( $sequences{$key}, "ATG", $positions{$key} );
    if ( $index < 0 ) {
        warn sprintf( "KEY %s: No ATG in File2 string prior to positio
+n %d\n",
                      $key, $positions{$key} );
        next;
    }
    $index += 3 while ( ($index + 3) < $positions{$key} );
    print "$key $positions{$key} " . substr($sequences{$key}, $index, 
+3) . "\n";
}

}

[download]

In reply to Re^2: Multiple Key Problem help by ashnator
in thread Multiple Key Problem help by ashnator

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.