pybedtools.featurefuncs.three_prime

pybedtools.featurefuncs.three_prime(feature, upstream=500, downstream=500, add_to_name=None, genome=None)

Returns the 3’-most coordinate, plus upstream and downstream bp; adds the string add_to_name to the feature’s name if provided (e.g., “_polyA_site”)

Parameters:

featurepybedtools.Interval instance

upstream, downstreaint

Number of bp upstream or downstream of the strand-specific stop position of the feature to include. Default is 500 for both upstream and downstream so that the returned feature is 1kb centered on the 5’ end of the feature. Unstranded features (where strand=”.”) are treated as plus-strand features.

add_to_namestr or None

If not None, append the string suffix to the name field of the feature (for example “_TSS”).

genomedict or None

If not None, then ensure that the start/stop positions are within the boundaries of the chromosome.