Question

I have this file

427 A   C   A/C 12
436 G   C   G/C 12
445 C   T   C/T 12
447 A   G   A/G 9
451 T   C   T/C 5
456 A   G   A/G 12
493 G   A   G/A 12

I wanted to read the first column and find all other ids which are differences less than 10.

427 A   C   A/C 12  436
436 G   C   G/C 12  427,445
445 C   T   C/T 12  436,447,451
447 A   G   A/G 9   445,451,456
451 T   C   T/C 5   445,447,456
456 A   G   A/G 12  451,447
493 G   A   G/A 12

The last column should be like the above. All id’s which are + or – 10 bases apart from that specific id. For example for 436, the boundaries are {426 – 446} other id’s which are in that range are 427 and 445 so i displayed them in 6th column..

Answer 1

Here’s one way using Perl:

use strict;
use warnings;

open my $fh, '<', 'dataFile.txt' or die $!;
chomp( my @data = <$fh> );
close $fh;

my @IDs = map /(\d+)/, @data;

for (@data) {
    my ($id) = /(\d+)/;
    print "$_\t"
      . ( join ',', grep { abs $id - $_  < 11 and $id != $_ } @IDs )
      . "\n";
}

Output:

427 A   C   A/C 12  436
436 G   C   G/C 12  427,445
445 C   T   C/T 12  436,447,451
447 A   G   A/G 9   445,451,456
451 T   C   T/C 5   445,447,456
456 A   G   A/G 12  447,451
493 G   A   G/A 12