#!/usr/bin/perl

use strict;
use warnings;

$location="";
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;
      $location = $3;
   }
}

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} .= $_;
       }
   }


   if ( ! exists( $sequences{$key} )) {
       warn "KEY $key in File1 not found in File2\n";
       next;
                                      }
    my $dna = $sequences{$key};
    my $index = rindex($dna,$positions{$key});
    my $position = $index;
    my $current_base = substr($dna, $position, 1);
    my $newbase = $location;
     substr($dna,$position,1,$newbase);
      my  $Location = $position + 1;
        print "$sequences{$key}";
 } 

##</code><code>##

File 1:-
155369268 5 C 
169212695 7 T

File 2:-
>gi|155369268|ref|NM_001100917.1| After all
AAACAATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGATGAGGAGCTTACGGTTTTTTACT
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
>gi|169212695|ref|XM_001716884.1| Its the code 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT

##</code><code>##

 
>gi|155369268|ref|NM_001100917.1| After all
AAACCATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGATGAGGAGCTTACGGTTTTTTACT
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
>gi|169212695|ref|XM_001716884.1| Its the code 
AGACAATCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT