Extract masked positions in fasta file. Question on [biosupport.se](https://biosupport.se/p/327/)

extract_masked.pl

#!/usr/bin/env perl

use strict;
use warnings;

=pod

=head1

         FILE: extract_masked.pl

        USAGE: ./extract_masked.pl fasta_file.fas

  DESCRIPTION: Question on biosupport.se (https://biosupport.se/p/327/), 11/22/2013:
               "Does anyone know of a quick way to extract the positions for a particular mask from a fasta file?
               So for example if I wanted to extract the position for all missing sites for chr 1 and this is
               coded as "." in my fasta file - how can I generate a bed file with the list of these positions?
               Input:

               chr1
               AAAAA.NNNNCCCCTTTT..A

               output:
               <chr> <start_pos (index="" start="" 0)=""> <end_pos>
               chr1: 5 5
               chr1: 18 19
               Thank you in advance."

        NOTES: Mostly untested, and with plenty of room for improvments. Caveat emptor!

       AUTHOR: Johan Nylander (JN), [email protected]

      COMPANY: BILS/NRM

      VERSION: 1.0

      CREATED: 11/22/2013

     REVISION: ---

=cut

## Specify search symbol 
my $char = '.'; # Character to search for

## Print first line in output to standard out
print STDOUT '<chr> <start_pos (index="" start="" 0)=""> <end_pos>', "\n";

## Parse FASTA format manually from standard in. Assuming that sequences might be on separate lines.
## Also assuming that the fasta header given as example above ("chr1") actually should be (">chr1")!
local $/ = '>';
while(<>) {
    chomp;
    next if(/^\s*$/);
    my ($header, @record) = split /\n/;
    my $seq = '';
    foreach my $line (@record) {
        $seq .= $line;
    }
    #print STDERR ">$header\n$seq\n";

    ## Get positions of $char in sequence
    my @positions = ();
    my $offset = 0;
    my $position = index($seq, $char, $offset);
    while ($position != -1) {
        push(@positions, $position);
        $offset = $position + 1;
        $position = index($seq, $char, $offset);
    }

    ## Print only start and stop of continuous occurrences of $char.
    ## Mind you - plenty of room for improvment in this section!
    if ((scalar(@positions) == length($seq)) or (scalar(@positions) == 0)) {
        ## Skip records with no chars, or records with all chars...
    }
    else {
        my $x = -1;
        my $first = '';
        my $didfirst = 0;
        foreach my $val (@positions) {
            $x++;
            my $y = $x + 1;
            if ( ($positions[$y] - $val) == 1 ) {
                if ($first) {
                    print STDOUT "\n";
                }
                else {
                    print STDOUT "$header $val ";
                    $didfirst = 1;
                }
            }
            else {
                if ($didfirst) {
                    print STDOUT "$val\n";
                    $didfirst = 0;
                }
                else {
                    print STDOUT "$header: $val $val\n";
                    $first = '';
                }
            }
        }
    }
}
__END__