API: Getting DNase-seq cut data from BAM files

At the heart of the pyDNase package is the BAMHandler class, which provides an interfact to the cut data in a BAM file corresponding to a DNase-seq dataset. The interface is extremely simple:

>>> import pyDNase
>>> reads = pyDNase.BAMHandler("pyDNase/test/data/example.bam")
>>> reads["chr6,170863500,170863532,+"]
{'+': [0,0,0,0,1,0,0,1,1,2,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,1,1,0,0,0],
'-': [0,10,1,0,1,0,4,9,0,1,0,2,1,0,0,0,0,0,3,0,6,3,0,0,0,1,1,1,3,0,3,6]}

As you can see, querying the BAMHandler object returns a dictionary containing arrays with cut count on the positive reference strand (+), and cuts on the negative reference strand (-). If you wanted to look at the cuts with reference to something on the opposite strand, you can rotate the data 180 degrees by passing a “-” flag,

>>> reads["chr6,170863500,170863532,-"]
{'+': [6,3,0,3,1,1,1,0,0,0,3,6,0,3,0,0,0,0,0,1,2,0,1,0,9,4,0,1,0,1,10,0],
'-': [0,0,0,1,1,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,2,1,1,0,0,1,0,0,0,0]}

By default, the BAMHandler caches lookups in 1000bp chunks. You can alter this behaviour at instanstiation. The BAMHandler also gives an interface to the Footprint Occupancy Score (FOS).

class pyDNase.BAMHandler(filePath, caching=True, chunkSize=1000, ATAC=False)

The object that provides the interface to DNase-seq data help in a BAM file

FOS(interval, bgsize=35)

Calculates the Footprint Occupancy Score (FOS) for a Genomicinterval. See Neph et al. 2012 (Nature) for full details.

Args:

interval (GenomicInterval): The interval that you want the FOS for

Kwargs:

bgsize (int): The size of the flanking region to use when calculating the FOS (default: 35)

Returns:

A float with the FOS - returns -1 if it can’t calculate it

__getitem__(vals)

Wrapper for get_cut_values

__init__(filePath, caching=True, chunkSize=1000, ATAC=False)

Initializes the BAMHandler with a BAM file

Args:

filePath (str): the path of a sorted, indexed BAM file from a DNase-seq experiment

Kwargs:

chunkSize (int): and int of the size of the regions to load if caching (default: 1000) caching (bool): enables or disables read caching (default: True)

Raises:

IOError