One option is to use a module that implements interval sets. CPAN has many; I can't tell which is to be recommended. Here's an example using Set::IntSpan. 

#! /usr/bin/perl

use strict;
use warnings;

use Set::IntSpan;

my $seq_len = 150;
my (%seqs, %ranges);

for (<>) {
    m/^(\d+)\s+(\d+)\.\.(\d+)/ or next;

    $seqs{$1} //= [ $1 +0, $1 + $seq_len-1 ];

    $ranges{$2,$3} //= [ $2, $3 ];
}

my $S = Set::IntSpan->new([ values %seqs ]);
printf "Total seq coverage: %d\n", $S->size;

for (@ranges{ sort keys %ranges }) {
    my $window = [ $_->[0], $_->[1] + $seq_len-1 ];

    my $T = $S->intersect([ $window ]);

    printf "range [%d..%d]  window [%d..%d]  %s  covers %d\n",
                    @$_, @$window, $T->run_list, $T->size;
}
__END__
Total seq coverage: 1251
range [1..1524]  window [0..1673]  46-195,403-552,800-981,1008-1157,14
+07-1556  covers 782
range [2052..3260]  window [2051..3409]  2360-2509,2967-3135,3170-3319
+  covers 469

[download]

To me it looks like there's a bug in that module (ver 1.19): documentation promises the operands are not affected, yet intersect method appears to modify $window. Hm.

In reply to Re: find the coverage of sequence in a particular range by oiskuu
in thread find the coverage of sequence in a particular range by Anonymous Monk

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