Perhaps this will help? (Sorry, I'm too lazy to use Bio::*):

#! perl -slw
use strict;
use Inline::Files;
use Data::Dump qw[ pp ];

my %seqs = map{ split "\n", $_ } <FASTA>; 
pp \%seqs;

while( my( $seq, $pos, $chr, $rep ) = split ' ', <EDITS> ) {
    substr( $seqs{ '>' . $seq }, $pos-1, 1, $rep );
}

pp \%seqs;

__FASTA__
>I
CATCAGTATAAAATGACTAGTAGCTAGATACCACAGATACGATACAACA
>II
TACCACAGATACGATACAACACATCAGTATAAAATGACTAGTAGCAGAC
__EDITS__
I   2   A   G
I   4   C   T
I   5   A   G
I   7   T   C
II  1   T   C
II  2   A   G
II  3   C   T
II  5   A   C
II  8   G   T
II  10  T   G
[download]

Output:

C:\test>1158701
{
  ">I"  => "CATCAGTATAAAATGACTAGTAGCTAGATACCACAGATACGATACAACA",
  ">II" => "TACCACAGATACGATACAACACATCAGTATAAAATGACTAGTAGCAGAC",
}

{
  ">I"  => "CGTTGGCATAAAATGACTAGTAGCTAGATACCACAGATACGATACAACA",
  ">II" => "CGTCCCATAGACGATACAACACATCAGTATAAAATGACTAGTAGCAGAC",
}
[download]