Dear All,

More of a conceptual problem than a Perl problem per se.

I am parsing the output of a program (non-perl and not editable) that compares two DNA sequences. The results are given as sets of 2-D co-ordinates.

e.g. 

[
    ['NM_144963','2713','4091'],
    ['NM_144963','1949','2712']
];

[download]
where field 1 is the name
field2 is the start coordinate
and field3 is the end coordinate

A simple sort allows me to sort the above and calculate the coverage 

    my @sorted = sort {($a->[1] <=>$b->[1]) || ($a->[2] <=> $b->[2])}@
+array;
    my $coverage = 0;
    for (@sorted){
        $coverage += $_->[2] - $_->[1] +1;
    }
    printf "cover = %.1f%% \n", $coverage/$length *100;

[download]
All well and good for the above case. But parts of my data are overlapping e.g. 
[
    ['NM_176827','618','710'],
    ['NM_176827','621','710'],
    ['NM_176827','622','692'],
    ['NM_176827','629','710']
]

[download]
Here my code breaks down and I cannot for the life of me think of a data structure that will allow adequately deal with both cases (i.e a collection of distinct hits, a collection of overlapping hits) or worse a combination of the two.

When they overlap I need to pick the longest hit. (i.e. the first array above).

Am I just having a brain metldown today - Can someone point me in the direction of an obvious solution. Thanks a lot

A.A.

In reply to Comparing 2-D co-ordinates by aging acolyte

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