My idea is based upon using index, rindex and substr.

#!/usr/bin/perl
use strict;
use warnings;

open SEQ,  '<', 'data1.dat' or die $!;
open MASK, '<', 'data2.dat' or die $!;

while ( my $seq = <SEQ> ) {
  my $mask = <MASK>;
  my $start  =  index( $mask, 'N' );
  my $length = rindex( $mask, 'N' ) - $start + 1;

  my $lc_seq = lc substr( $seq, $start, $length );

  substr( $seq, $start, $length, $lc_seq );

  print $seq;
}

[download]

Updates:

  1. Important notice from kirillm. My solution doesn't cover all possible cases.
  2. fixed calculation error
  3. see my other post for my updated code.

In reply to Re: Lower-casing Substrings and Iterating Two Files together by linuxer
in thread Lower-casing Substrings and Iterating Two Files together by neversaint

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