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.citt...@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
>
>
>
> /*
> Davide Cittaro, PhD
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: davide.citt...@ifom-ieo-campus.it
> */
>
>
>
>
>
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