#! perl -slw
use strict;
use Inline::Files;
use Data::Dump qw[ pp ];
use constant { SEQ => 0, POS => 1, ACT => 2, REP => 3 };

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

my @edits = [ split ' ', <EDITS> ];

while( 1 ) {
    my @bits = split ' ', <EDITS>;
    if( defined $bits[ 0 ] and $bits[ 0 ] eq $edits[ 0 ][ 0 ]  ) {
        push @edits, \@bits;
        next;
    }

    for my $edit ( sort{ $b->[POS] <=> $a->[POS] } @edits ) {

        if( $edit->[ACT] eq 'I' ) {
            substr( $seqs{ '>' . $edit->[SEQ] }, $edit->[POS]-1, 0, $edit->[REP] );
        }
        elsif( $edit->[ACT] eq 'D' ) {
            substr( $seqs{ '>' . $edit->[SEQ] }, $edit->[POS]-1, 1, '' );
        }
        else { ## replace
            substr( $seqs{ '>' . $edit->[SEQ] }, $edit->[POS]-1, 1, $edit->[REP] );
        }
    }
    last unless defined $bits[ 0 ];
    @edits = \@bits;
}

pp \%seqs;

__FASTA__
>I
CATCAGTATAAAATGACTAGTAGCTAGATACCACAGATACGATACAACA
>II
TACCACAGATACGATACAACACATCAGTATAAAATGACTAGTAGCAGAC
__EDITS__
I   2   I   I
I   4   D   X
I   5   R   G
I   7   I   C
II  1   D   X
II  2   I   I
II  3   R   T
II  5   D   X
II  8   R   T
II  10  I   I