def __init__(self, gtf_file, landmarks=ALL_LANDMARKS, use_strand=True, **kwargs):
super(DistToClosestLandmarkExtractor, self).__init__(gtf_file, **kwargs)
self._gtf_file = gtf_file
self.landmarks = extract_landmarks(gtf_file, landmarks=landmarks)
self.columns = landmarks # column names. Reqired for concating distances into array
self.use_strand = use_strand
# set index to chromosome and strand - faster access
self.landmarks = {k: v.set_index(["seqname", "strand"])
for k, v in six.iteritems(self.landmarks)}
def test_extract_landmarks(gtf):
"""Run for all the extractors
"""
ldm = extract_landmarks(gtf)
assert isinstance(ldm, dict)