This is a reverse problem to my earlier posting. What I need to do is to recover the substrings back to the string with gap (N) for those non-dotted substrings. This is the working code I have: 


#!/usr/bin/perl -w
use strict;
my $s1 = 'GATTACGAGTGGCGCTCGTGTAACGGCA';

my @ar  =  ('GATTACG','GCGCTCG','AACGGCA');  #21 (0,11,21)
my @ar2 =  ('GATTACG','TTACGAG','CGTGTAA');  #16
my @ar3 =  ('TACGAGT','GTGGCGC','GCTCGTG');  #17
my @ar4 =  ('GG','GG');

print append_n($s1,\@ar),"\n";
print append_n($s1,\@ar2),"\n";
print append_n($s1,\@ar3),"\n";
print append_n($s1,\@ar4),"\n";

sub append_n
{
      my ( $str, $array ) = @_;
      my $nstring = "N" x length($str);

      foreach my $sbstr ( @$array )
      {
       my $pos = index $str, $sbstr;
       substr ($nstring, $pos, length ($sbstr)) = $sbstr;
      }   

      return $nstring;
  }

[download]


The code gives a correct result, except for the case where there are duplicates in the arrays (@ar4). It only returns one instance instead of all. So here is the result: 
GATTACGNNNNGCGCTCGNNNAACGGCA  #correct
GATTACGAGNNNNNNNCGTGTAANNNNN  #correct
NNNTACGAGTGGCGCTCGTGNNNNNNNN  #correct
NNNNNNNNNNGGNNNNNNNNNNNNNNNN  #wrong

[download]
supposedly it should return :NNNNNNNNNNGGNNNNNNNNNNNNGGNN
Is there a way to overcome this bug?
Regards,
Edward

In reply to Recovering Substrings to String with Gap by monkfan

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