Hi Davide,

The summary_size is just the number of bins to aggregate the data over. It can be greater than (end - start) because UCSC allows this, and so we allow it too since we copy their method.

Kanwei

On Tue, Mar 8, 2011 at 2:23 AM, Davide Cittaro <davide.cittaro@ifom-ieo-campus.it> wrote:
Hello James, 

On Mar 8, 2011, at 1:23 AM, James Taylor wrote:

Davide, see bx.bbi.bigwig_file.BigWigFile


I'm trying to... :-)

Implemented in Cython, there is also some BigBed support with a common class (bbi_file) for the indexing and aggregation pieces.

This is currently read only. Also, not tested exhaustively on different types of bigwig, but I believe we have most cases correct.

read only is fine for me (at least at the moment). I see the method to get data from a bigwig file is BigWigFile.query(), is it?
What is the summary_size one must specify? Data are returned as statistics of the region between chr:start-end, the number of statistics is given by summary_size. In my mind the summary_size could be the number of "chunks" between start and end. Unfortunately I see that I can specify summary_size > (end - start) hence I don't know what summary_size is :-)

d



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