Hi I have got a bug in my program and I donno howto solve that. I am using the keys in File 1 to parse the file 2. Now the
problem is that when my program comes to the end of string 70th character or around, it does not report the 3 three window
characters as I am doing in the rest of my code. Can somebody help Plz ;)
Here is my code

#!/usr/bin/perl

use strict;
use warnings;

my $qfn1 = "File1.txt";
my $qfn2 = "File2.txt";

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

   while (<$fh>) {
      my ($key, $pos) = split /\s+/;
      $positions{$key} = $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 ) {
    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]

My Input file look like this:-

 
File 1:-
155369268 17 C 
169212695 70 C
269212605 90 G

File 2:-
>gi|155369268|ref|NM_001100917.1| some text
AAACAATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGAATGGGAGCTTACGGTTTTTTACG
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
>gi|169212695|ref|XM_001716884.1| some text 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCATGGGAGCTTACGGTTTTTTACG
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
>gi|269212605|ref|XM_401716884.1| some text 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCTATGAC
CTAATTGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
[download]

Output should be like this:-

155369268 7 CTA 
169212695 70 CGC
269212605 120 GGG
[download]

good bye

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