def test_genome_protocol_by_split(self, genomic_event1, genomic_event2, transcripts, distances):
genomic_event1.call_method = CALL_METHOD.SPLIT
genomic_event2.call_method = CALL_METHOD.SPLIT
assert pairing.equivalent(genomic_event1, genomic_event2, distances=distances)
distances[CALL_METHOD.FLANK] = 100
distances[CALL_METHOD.SPLIT] = 10
genomic_event1.break1.start = 11
genomic_event1.break1.end = 20
assert not pairing.equivalent(genomic_event1, genomic_event2, distances=distances)
def test_genome_protocol_by_split(self):
self.gev1.call_method = CALL_METHOD.SPLIT
self.gev2.call_method = CALL_METHOD.SPLIT
self.assertTrue(
pairing.equivalent(self.gev1, self.gev2, distances=self.distances))
self.distances[CALL_METHOD.FLANK] = 100
self.distances[CALL_METHOD.SPLIT] = 10
self.gev1.break1.start = 11
self.gev1.break1.end = 20
self.assertFalse(
pairing.equivalent(self.gev1, self.gev2, distances=self.distances))
def test_genome_protocol_by_contig(self):
self.gev1.call_method = CALL_METHOD.CONTIG
self.gev2.call_method = CALL_METHOD.CONTIG
self.distances[CALL_METHOD.CONTIG] = 0
self.distances[CALL_METHOD.SPLIT] = 10
self.assertTrue(
pairing.equivalent(self.gev1, self.gev2, distances=self.distances))
self.gev1.break1.start = 2
self.gev1.break1.end = 20
self.assertFalse(
pairing.equivalent(self.gev1, self.gev2, distances=self.distances))
def test_genome_protocol_by_contig(
self, genomic_event1, genomic_event2, transcripts, distances
):
genomic_event1.call_method = CALL_METHOD.CONTIG
genomic_event2.call_method = CALL_METHOD.CONTIG
distances[CALL_METHOD.CONTIG] = 0
distances[CALL_METHOD.SPLIT] = 10
assert pairing.equivalent(genomic_event1, genomic_event2, distances=distances)
genomic_event1.break1.start = 2
genomic_event1.break1.end = 20
assert not pairing.equivalent(genomic_event1, genomic_event2, distances=distances)
def test_mixed_protocol_fusions_same_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: None,
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: None,
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.equivalent(genome_ev, trans_ev, self.TRANSCRIPTS))
genome_ev.data[COLUMNS.fusion_sequence_fasta_id] = 'a'
trans_ev.data[COLUMNS.fusion_sequence_fasta_id] = 'a'
self.assertTrue(
pairing.inferred_equivalent(genome_ev, trans_ev, self.TRANSCRIPTS))
def test_useq_uncertainty(self):
event1 = BreakpointPair(Breakpoint('1', 157540650, orient='L'),
Breakpoint('1', 157540877, orient='R'),
event_type='deletion',
call_method='contig',
untemplated_seq='GCCTGGCCGCA')
event2 = BreakpointPair(Breakpoint('1', 157540661, orient='L'),
Breakpoint('1', 157540877, orient='R'),
event_type='deletion',
call_method='spanning reads')
self.assertTrue(pairing.equivalent(event1, event2))
def test_useq_uncertainty2(self):
event1 = BreakpointPair(Breakpoint('1', 32, orient='L'),
Breakpoint('1', 61, orient='R'),
event_type='deletion',
call_method='contig',
untemplated_seq='A')
event2 = BreakpointPair(Breakpoint('1', 24, orient='L'),
Breakpoint('1', 61, orient='R'),
event_type='deletion',
call_method='contig',
untemplated_seq='TTTTTTTTT')
self.assertTrue(pairing.equivalent(event1, event2))
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)
def test_genome_protocol_ns_orient(self):
self.gev2.break1.orient = ORIENT.LEFT
self.gev1.break2.orient = ORIENT.RIGHT
self.assertTrue(
pairing.equivalent(self.gev1, self.gev2, self.TRANSCRIPTS))
def test_genome_protocol_diff_event_type(self):
self.gev2.data[COLUMNS.event_type] = SVTYPE.DEL
self.gev1.data[COLUMNS.event_type] = SVTYPE.INS
self.assertFalse(
pairing.equivalent(self.gev1, self.gev2, self.TRANSCRIPTS))
def test_genome_protocol_diff_strand(self):
self.gev2.break1.strand = STRAND.POS
self.gev1.break1.strand = STRAND.NEG
self.assertFalse(
pairing.equivalent(self.gev1, self.gev2, self.TRANSCRIPTS))
def test_genome_protocol_diff_chrom(self):
self.gev2.break1.chr = '2'
self.assertFalse(
pairing.equivalent(self.gev1, self.gev2, self.TRANSCRIPTS))
def test_genome_protocol_ns_orient(self, genomic_event1, genomic_event2, transcripts):
genomic_event2.break1.orient = ORIENT.LEFT
genomic_event1.break2.orient = ORIENT.RIGHT
assert pairing.equivalent(genomic_event1, genomic_event2, transcripts)
def test_genome_protocol_diff_event_type(self, genomic_event1, genomic_event2, transcripts):
genomic_event2.data[COLUMNS.event_type] = SVTYPE.DEL
genomic_event1.data[COLUMNS.event_type] = SVTYPE.INS
assert not pairing.equivalent(genomic_event1, genomic_event2, transcripts)
def test_genome_protocol_diff_strand(self, genomic_event1, genomic_event2, transcripts):
genomic_event2.break1.strand = STRAND.POS
genomic_event1.break1.strand = STRAND.NEG
assert not pairing.equivalent(genomic_event1, genomic_event2, transcripts)
def test_genome_protocol_diff_chrom(self, genomic_event1, genomic_event2, transcripts):
genomic_event2.break1.chr = '2'
assert not pairing.equivalent(genomic_event1, genomic_event2, transcripts)
