def test_deletion_in_exon(self, egfr_evidence):
bpp = BreakpointPair(
Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-8)
bpp = BreakpointPair(
Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='GTAC',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-4)
def test_deletion_across_intron(self, egfr_evidence):
# 55240539_55240621 55323947_55324313
bpp = BreakpointPair(
Breakpoint('7', 55240610, orient=ORIENT.LEFT),
Breakpoint('7', 55323950, orient=ORIENT.RIGHT),
untemplated_seq='GTAC',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-10)
# 55210998_55211181 55218987_55219055
bpp = BreakpointPair(
Breakpoint('7', 55211180, orient=ORIENT.LEFT),
Breakpoint('7', 55218990, orient=ORIENT.RIGHT),
untemplated_seq='',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-4 + -135, -4)
def test_insertion_at_exon_start(self, egfr_evidence):
# 55238868_55238906
bpp = BreakpointPair(
Breakpoint('7', 55233130, orient=ORIENT.LEFT),
Breakpoint('7', 55238868, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(6)
def test_indel_in_intron(self, egfr_evidence):
# 55238868_55238906
bpp = BreakpointPair(
Breakpoint('7', 5523700, orient=ORIENT.LEFT),
Breakpoint('7', 5523751, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-44)
def test_insertion_at_exon_start_mixed(self, egfr_evidence):
# EXON 15: 55232973-55233130
# EXON 16: 55238868-55238906
# EXON 17: 55240676-55240817
bpp = BreakpointPair(
Breakpoint('7', 55238867, orient=ORIENT.LEFT),
Breakpoint('7', 55238868, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(6)
def egfr_distance(self, pos1, pos2):
return TranscriptomeEvidence.distance(self.evidence, pos1, pos2)