UTR-motifs.py

"""
Illustrates how to use pybedtools to count motifs along sliding windows 
of UTRs from a GFF file.

This uses example data shipped with pybedtools.
"""

import pybedtools


def renamer(f):
    # BEDTools sees the featuretype of a GFF file as the "name" when using
    # makewindows, so we need to set the featuretype to be the ID.  Or whatever
    # GFF attribute is of interest.
    if f[2] == 'UTR':
        f[2] = f['ID']
        return f


# Prepare the UTRs file
utrs = pybedtools.example_bedtool('gdc.gff')\
    .each(renamer)

# 20-bp windows, labeled by their name and an integer
windows = pybedtools.BedTool().window_maker(b=utrs, w=20, i='srcwinnum' )

motifs = pybedtools.example_bedtool('gdc.bed')

# Count up the number of features in each window.
# Last column of this file will have the number of motifs hitting that window
results = windows.intersect(motifs, c=True)

BEDTools makewindows doesn't keep strand information, so if you need strand then you need a different strategy:

def stranded_windows(f, n=5):
    name = f['ID']
    for i, start in enumerate(range(0, len(f) - n, n)):
        f.start = start
        f.stop = start + n
        f.attrs['ID'] = '%s_%s' % (name, i)
        yield f

windows = pybedtools.example_bedtool('gdc.gff')\
    .filter(lambda x: x[2] == 'UTR')\
    .split(stranded_windows)