def test_mixed_protocol_fusions_different_sequence(self):
genome_ev = BreakpointPair(Breakpoint('1', 1),
Breakpoint('1', 10),
opposing_strands=True,
data={
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: 'a',
COLUMNS.protocol: PROTOCOL.GENOME,
COLUMNS.transcript1: None,
COLUMNS.transcript2: None,
COLUMNS.fusion_cdna_coding_start: 1,
COLUMNS.fusion_cdna_coding_end: 10
})
trans_ev = BreakpointPair(Breakpoint('1', 50),
Breakpoint('1', 60),
opposing_strands=True,
data={
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: 'b',
COLUMNS.protocol: PROTOCOL.TRANS,
COLUMNS.transcript1: None,
COLUMNS.transcript2: None,
COLUMNS.fusion_cdna_coding_start: 1,
COLUMNS.fusion_cdna_coding_end: 10
})
self.assertFalse(
pairing.inferred_equivalent(genome_ev, trans_ev, self.TRANSCRIPTS))
def test_mixed_protocol_fusions_same_sequence_diff_translation(
self, genomic_event1, genomic_event2, transcripts
):
genome_ev = BreakpointPair(
Breakpoint('1', 1),
Breakpoint('1', 10),
opposing_strands=True,
**{
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: 'a',
COLUMNS.protocol: PROTOCOL.GENOME,
COLUMNS.transcript1: None,
COLUMNS.transcript2: None,
COLUMNS.fusion_cdna_coding_start: 1,
COLUMNS.fusion_cdna_coding_end: 10,
},
)
trans_ev = BreakpointPair(
Breakpoint('1', 50),
Breakpoint('1', 60),
opposing_strands=True,
**{
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: 'a',
COLUMNS.protocol: PROTOCOL.TRANS,
COLUMNS.transcript1: None,
COLUMNS.transcript2: None,
COLUMNS.fusion_cdna_coding_start: 1,
COLUMNS.fusion_cdna_coding_end: 50,
},
)
assert not pairing.inferred_equivalent(genome_ev, trans_ev, transcripts)
def test_mixed_protocol_one_predicted_one_mismatch(self):
genome_ev = BreakpointPair(
Breakpoint('1', 350, orient=ORIENT.LEFT),
Breakpoint('1', 400, orient=ORIENT.RIGHT),
opposing_strands=False,
data={
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: None,
COLUMNS.protocol: PROTOCOL.GENOME,
COLUMNS.transcript1: self.ust1.name,
COLUMNS.transcript2: None,
},
)
trans_ev = BreakpointPair(
Breakpoint('1', 350, orient=ORIENT.LEFT),
Breakpoint('1', 400, orient=ORIENT.RIGHT),
opposing_strands=False,
data={
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: None,
COLUMNS.protocol: PROTOCOL.TRANS,
COLUMNS.transcript1: self.ust1.name,
COLUMNS.transcript2: None,
},
)
self.assertTrue(
pairing.equivalent(genome_ev, trans_ev, self.TRANSCRIPTS))
self.assertTrue(
pairing.equivalent(trans_ev, genome_ev, self.TRANSCRIPTS))
genome_ev.data[COLUMNS.transcript2] = self.ust1.name
genome_ev.data[COLUMNS.transcript1] = None
trans_ev.data[COLUMNS.transcript2] = self.ust1.name
trans_ev.data[COLUMNS.transcript1] = None
self.assertTrue(
pairing.inferred_equivalent(genome_ev, trans_ev, self.TRANSCRIPTS))
self.assertTrue(
pairing.inferred_equivalent(trans_ev, genome_ev, self.TRANSCRIPTS))
def test_mixed_protocol_one_predicted_one_mismatch(
self, genomic_event1, genomic_event2, transcripts, unspliced_transcript1
):
genome_ev = BreakpointPair(
Breakpoint('1', 350, orient=ORIENT.LEFT),
Breakpoint('1', 400, orient=ORIENT.RIGHT),
opposing_strands=False,
**{
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: None,
COLUMNS.protocol: PROTOCOL.GENOME,
COLUMNS.transcript1: unspliced_transcript1.name,
COLUMNS.transcript2: None,
},
)
trans_ev = BreakpointPair(
Breakpoint('1', 350, orient=ORIENT.LEFT),
Breakpoint('1', 400, orient=ORIENT.RIGHT),
opposing_strands=False,
**{
COLUMNS.event_type: SVTYPE.DEL,
COLUMNS.call_method: CALL_METHOD.CONTIG,
COLUMNS.fusion_sequence_fasta_id: None,
COLUMNS.protocol: PROTOCOL.TRANS,
COLUMNS.transcript1: unspliced_transcript1.name,
COLUMNS.transcript2: None,
},
)
assert pairing.equivalent(genome_ev, trans_ev, transcripts)
assert pairing.equivalent(trans_ev, genome_ev, transcripts)
genome_ev.data[COLUMNS.transcript2] = unspliced_transcript1.name
genome_ev.data[COLUMNS.transcript1] = None
trans_ev.data[COLUMNS.transcript2] = unspliced_transcript1.name
trans_ev.data[COLUMNS.transcript1] = None
assert pairing.inferred_equivalent(genome_ev, trans_ev, transcripts)
assert pairing.inferred_equivalent(trans_ev, genome_ev, transcripts)