Comments (3)
This is a limitation of the BEDTools syntax and the Python language . . . the way around it is to provide a dictionary of kwargs:
a.genome_coverage(bg=True, **{'5': True})
Ugly, but it works. Don't forget you'll also need a genome
(or g
if you have a file) kwarg for genome_coverage
to work.
from pybedtools.
Ah, thanks! Chromosome sizes are optional. I believe you fixed it recently.
In [12]: b = a.genome_coverage(bg=True, **{'5':True})
In [13]: b.head(3)
chr1 0 1 32
chr1 277 278 60
chr1 278 279 66
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Ah right, I missed you're using a BAM. Glad it works!
from pybedtools.
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