Re^2: Counting problem!

Thank you so much for your help, There is another question that I would like to know if I want to get out put with more details what should I do, cause In some part of my data I have similar coordinates which make problem with script they look like :


__DATA__
chr1    101  105   X     X     -
chr1    101  105   X     X     -
chr1    101  105   X     X     -
chr1    101  105   X     X     -
chr1    102  108   X     X     -
chr1    106  111   X     X     -
chr1    106  111   X     X     -
chr1    112  113   X     X     -
chr1    113  115   X     X     -
chr2    114  118   X     X     -
chr2    114  118   X     X     -
chr2    114  118   X     X     -
chr2    114  118   X     X     -
chr2    119  121   X     X     -
chr2    120  123   X     X     -
chr3    125  130   X     X     -
chr3    125  130   X     X     -
chr3    131  132   X     X     -

then I want to get output like this :

output :

ID_1    chr1   101   105   4
ID_1    chr1   102   106   1
ID_1    chr1   106   111   2
ID_2    chr1   112   113   1
ID_3    chr1   113   115   1
ID_1    chr2   114   118   1
ID_2    chr2   119   123   1
ID_2    chr2   119   123   1
ID_1    chr3   125   130   2
ID_2    chr3   131   132   1
[download]

which it counts the number of similar coordinates as well and show them individually instead of total counting by merging them.

Comment on Re^2: Counting problem! Download Code

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Re^3: Counting problem! by JavaFan (Canon) on Mar 22, 2012 at 19:35 UTC
I tried to make sense of your output, but failed. Probably the fourth column of the second row was typoed, and should read 108. But I've no idea why the first three output lines all have the same value in the first column. However, to count, that's trivial. Make a hash key from the primary key of your data, and just, uhm, count. You know, add one each time you see the same thing: `$counts{$key,$start,$end}++;` [download]	[reply] [d/l]

Replies are listed 'Best First'.

Re^3: Counting problem!
by JavaFan (Canon) on Mar 22, 2012 at 19:35 UTC

However, to count, that's trivial. Make a hash key from the primary key of your data, and just, uhm, count. You know, add one each time you see the same thing:

    $counts{$key,$start,$end}++;
[download]

[reply]
[d/l]