def _get_splice_site_coordinates(self, t, start, end, exon_i):
"""Returns distance from exon."""
left_diff, right_diff = TranscriptProviderUtils.determine_closest_distance_from_exon(start, end, exon_i, t)
if abs(left_diff) < abs(right_diff):
dist_from_exon = left_diff * -1
if dist_from_exon > -1: dist_from_exon = -1
elif abs(right_diff) < abs(left_diff):
dist_from_exon = right_diff * -1
if dist_from_exon < 1: dist_from_exon = 1
else:
dist_from_exon = 0
if t.get_strand() == "-":
dist_from_exon *= -1
return dist_from_exon
def _get_splice_site_coordinates(self, t, start, end, exon_i):
"""Returns distance from exon."""
left_diff, right_diff = TranscriptProviderUtils.determine_closest_distance_from_exon(
start, end, exon_i, t)
if abs(left_diff) < abs(right_diff):
dist_from_exon = left_diff * -1
if dist_from_exon > -1: dist_from_exon = -1
elif abs(right_diff) < abs(left_diff):
dist_from_exon = right_diff * -1
if dist_from_exon < 1: dist_from_exon = 1
else:
dist_from_exon = 0
if t.get_strand() == "-":
dist_from_exon *= -1
return dist_from_exon
def _extract_exon_info(self, position, tx):
"""
Create basic information about the given position relative to the transcript.
:param int position: in genomic space
:param Transcript tx:
:return tuple:
[0]: closest exon index of the position (0-based),
[1]: whether the distance was left in genomic space (false for overlap)
[2]: whether the position overlaps an exon
"""
exon_index = TranscriptProviderUtils.determine_closest_exon(tx, position, position)
if exon_index is None:
return exon_index, None, None, None
left_distance, right_distance = TranscriptProviderUtils.determine_closest_distance_from_exon(position, position,
exon_index, tx)
is_in_exon = (left_distance <= 0) and (right_distance >= 0)
is_diff_is_positive = (left_distance > 0) and (right_distance > 0)
is_negative_strand = (tx.get_strand() == "-")
return exon_index, is_diff_is_positive, is_in_exon, is_negative_strand
def _extract_exon_info(self, position, tx):
"""
Create basic information about the given position relative to the transcript.
:param int position: in genomic space
:param Transcript tx:
:return tuple:
[0]: closest exon index of the position (0-based),
[1]: whether the distance was left in genomic space (false for overlap)
[2]: whether the position overlaps an exon
"""
exon_index = TranscriptProviderUtils.determine_closest_exon(tx, position, position)
if exon_index is None:
return exon_index, None, None, None
left_distance, right_distance = TranscriptProviderUtils.determine_closest_distance_from_exon(position, position,
exon_index, tx)
is_in_exon = (left_distance <= 0) and (right_distance >= 0)
is_diff_is_positive = (left_distance > 0) and (right_distance > 0)
is_negative_strand = (tx.get_strand() == "-")
return exon_index, is_diff_is_positive, is_in_exon, is_negative_strand
def test_determine_closest_distance_from_exon_in_exon(self):
tx = self.retrieve_test_transcript_MAPK1()
# Right in exon 1
left_diff, right_diff = TranscriptProviderUtils.determine_closest_distance_from_exon(22162000, 22162005, 1, tx)
self.assertTrue(left_diff < 0 and right_diff > 0, "left distance should be negative while right distance should be positive.")
