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)