I have some segments start and end position on a reference sequence, I
want to calculate the uncoverage region for the reference;

for example: reference sequence length= 100,

name [start,end]
segment 1 [1,20]
segment 2 [2,28]
segment 3 [50,100]
segment 4 [5,38]

so uncover region = [38,49]


now I already have %pos{start}=end structure for those segment
position, could somebody give a good method?


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Hi Lemon,

On Tue, 13 Sep 2011 04:54:40 -0700 (PDT)
Lemon <lemon027 [at] gmail.com> wrote:

> I have some segments start and end position on a reference sequence, I
> want to calculate the uncoverage region for the reference;
>
> for example: reference sequence length=3D 100,
>
> name [start,end]
> segment 1 [1,20]
> segment 2 [2,28]
> segment 3 [50,100]
> segment 4 [5,38]
>
> so uncover region =3D [38,49]
>
>
> now I already have %pos{start}=3Dend structure for those segment
> position, could somebody give a good method?
>

I suggest you merge overlapping segments into big meta-segments using a sor=
ted
array, one by one, and then see the uncovered regions between two adjacent
meta-segments.

Regards,

Shlomi Fish

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On Tue, 13 Sep 2011 04:54:40 -0700, Lemon wrote:

> I have some segments start and end position on a reference sequence, I
> want to calculate the uncoverage region for the reference;
>
> for example: reference sequence length=3D 100,
>
> name [start,end]
> segment 1 [1,20]
> segment 2 [2,28]
> segment 3 [50,100]
> segment 4 [5,38]
>
> so uncover region =3D [38,49]
>
>
> now I already have %pos{start}=3Dend structure for those segment positi=
on,
> could somebody give a good method?

By the usual definition the uncovered region is [39,49]. Here's an
approach:

$ cat differ
#!/usr/local/bin/perl
use strict;
use warnings;

use Set::IntSpan; # http://search.cpan.org/perldoc?Set%3A%3AIntSpan

my ($diff, [at] sets) =3D map { Set::IntSpan->new( $_ ) }
qw(1-100 1-20 2-28 50-100 5-38);
$diff -=3D $_ for [at] sets;
print "$diff\n";

$ ./differ
39-49

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