about bx-python and bigwig

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about bx-python and bigwig

Davide Cittaro
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: [hidden email]
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--
/*
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: [hidden email]
*/




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Re: about bx-python and bigwig

James Taylor-2
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 :-)



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Re: about bx-python and bigwig

Davide Cittaro
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
*/





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Re: about bx-python and bigwig

Kanwei Li
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 <[hidden email]> 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
*/





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Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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