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 :-)
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