Hi all, Probably this is not the best place to ask about bx-python, but since most of bx developers are galaxy developers, it may be worth trying... I just want to know the status of bigwig support in bx. I need to handle bigwig as input data and I previously wrapped kent binaries with python subprocess. I wanted to make it more pythonic and started reading bigwig docs. If bx already has support for an iterator similar to bx.wiggle.Reader (I need to transfer all the chromosome in another data structure) I won't read docs further :-) Thanks d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */ -- /* Davide Cittaro Next Generation Sequencing and Affymetrix data analyst Cogentech - Consortium for genomic technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Davide, see bx.bbi.bigwig_file.BigWigFile 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. Input is welcome! On Mar 7, 2011, at 5:14 PM, Davide Cittaro wrote:
Hi all, Probably this is not the best place to ask about bx-python, but since most of bx developers are galaxy developers, it may be worth trying... I just want to know the status of bigwig support in bx. I need to handle bigwig as input data and I previously wrapped kent binaries with python subprocess. I wanted to make it more pythonic and started reading bigwig docs. If bx already has support for an iterator similar to bx.wiggle.Reader (I need to transfer all the chromosome in another data structure) I won't read docs further :-)
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.cittaro@ifom-ieo-campus.it */
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
/* Davide Cittaro, PhD
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
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participants (3)
-
Davide Cittaro -
James Taylor -
Kanwei Li