def test_filter_by_annotations_one_transcript(self):
self.gev1.data[COLUMNS.gene1] = None
self.gev1.data[COLUMNS.gene2] = 'XYS'
self.gev1.data[COLUMNS.transcript1] = None
self.gev1.data[COLUMNS.transcript2] = 'XYSZ'
self.gev2.data[COLUMNS.gene1] = 'XYZ'
self.gev2.data[COLUMNS.gene2] = 'XYS'
self.gev2.data[COLUMNS.transcript1] = 'XYZA'
self.gev2.data[COLUMNS.transcript2] = 'XYSB'
result, removed = filter_by_annotations([self.gev1, self.gev2], self.best_transcripts)
bpp = result[0]
self.assertEqual(self.gev2, bpp)
def test_filter_by_annotations_one_best_transcripts(self):
self.gev1.data[COLUMNS.gene1] = 'XYZ'
self.gev1.data[COLUMNS.gene2] = 'ABC'
self.gev1.data[COLUMNS.transcript1] = 'XYZB'
self.gev1.data[COLUMNS.transcript2] = 'ABCA'
self.gev2.data[COLUMNS.gene1] = 'XYZ'
self.gev2.data[COLUMNS.gene2] = 'ABC'
self.gev2.data[COLUMNS.transcript1] = 'XYZA'
self.gev2.data[COLUMNS.transcript2] = 'ABCB'
result, removed = filter_by_annotations([self.gev1, self.gev2], self.best_transcripts)
bpp = result[0]
self.assertEqual(self.gev1, bpp)
self.assertEqual('XYZB', bpp.data[COLUMNS.transcript1])
def test_filter_by_annotations_no_transcripts(self):
self.gev1.data[COLUMNS.gene1] = None
self.gev1.data[COLUMNS.gene2] = None
self.gev1.data[COLUMNS.transcript1] = None
self.gev1.data[COLUMNS.transcript2] = None
self.gev2.data[COLUMNS.gene1] = None
self.gev2.data[COLUMNS.gene2] = None
self.gev2.data[COLUMNS.transcript1] = None
self.gev2.data[COLUMNS.transcript2] = None
self.gev1.break1.strand = STRAND.POS
result, removed = filter_by_annotations([self.gev1, self.gev2], self.best_transcripts)
bpp = result[0]
self.assertEqual(None, bpp.data[COLUMNS.transcript1])
def test_filter_by_annotations_two_best_transcripts(self):
self.gev1.data[COLUMNS.gene1] = 'ABC'
self.gev1.data[COLUMNS.gene2] = 'ABC'
self.gev1.data[COLUMNS.transcript1] = 'ABCA'
self.gev1.data[COLUMNS.transcript2] = 'ABCA'
self.gev2.data[COLUMNS.gene1] = 'ABC'
self.gev2.data[COLUMNS.gene2] = 'ABC'
self.gev2.data[COLUMNS.transcript1] = 'ABCD'
self.gev2.data[COLUMNS.transcript2] = 'ABCD'
result, removed = filter_by_annotations([self.gev1, self.gev2], self.best_transcripts)
bpp = result[0]
print(bpp.data)
self.assertEqual(self.gev1, bpp)
self.assertEqual('ABCA', bpp.data[COLUMNS.transcript1])
def test_filter_by_annotations_two_transcripts(self):
self.gev1.data[COLUMNS.gene1] = 'XYZ'
self.gev1.data[COLUMNS.gene2] = 'XYS'
self.gev1.data[COLUMNS.transcript1] = 'XYZB'
self.gev1.data[COLUMNS.transcript2] = 'XYSZ'
self.gev2.data[COLUMNS.gene1] = 'XYZ'
self.gev2.data[COLUMNS.gene2] = 'XYS'
self.gev2.data[COLUMNS.transcript1] = 'XYZA'
self.gev2.data[COLUMNS.transcript2] = 'XYSB'
bpps, removed = filter_by_annotations([self.gev1, self.gev2], self.best_transcripts)
print(bpps)
bpp = bpps[0]
print(bpp, bpp.data)
self.assertEqual(self.gev2, bpp)
self.assertEqual('XYZA', bpp.data[COLUMNS.transcript1])
def test_filter_by_annotations_one_best_transcripts(
self, genomic_event1, genomic_event2, best_transcripts):
genomic_event1.data[COLUMNS.gene1] = 'XYZ'
genomic_event1.data[COLUMNS.gene2] = 'ABC'
genomic_event1.data[COLUMNS.transcript1] = 'XYZB'
genomic_event1.data[COLUMNS.transcript2] = 'ABCA'
genomic_event2.data[COLUMNS.gene1] = 'XYZ'
genomic_event2.data[COLUMNS.gene2] = 'ABC'
genomic_event2.data[COLUMNS.transcript1] = 'XYZA'
genomic_event2.data[COLUMNS.transcript2] = 'ABCB'
result, removed = filter_by_annotations(
[genomic_event1, genomic_event2], best_transcripts)
bpp = result[0]
assert bpp == genomic_event1
assert bpp.data[COLUMNS.transcript1] == 'XYZB'
def test_filter_by_annotations_two_fusion_cdna(self):
self.gev1.data[COLUMNS.gene1] = 'XYZ'
self.gev1.data[COLUMNS.gene2] = 'XYS'
self.gev1.data[COLUMNS.transcript1] = 'XYZB'
self.gev1.data[COLUMNS.transcript2] = 'XYSZ'
self.gev2.data[COLUMNS.gene1] = 'XYZ'
self.gev2.data[COLUMNS.gene2] = 'XYS'
self.gev2.data[COLUMNS.transcript1] = 'XYZB'
self.gev2.data[COLUMNS.transcript2] = 'XYSZ'
self.gev1.data[COLUMNS.fusion_cdna_coding_start] = 1
self.gev1.data[COLUMNS.fusion_cdna_coding_end] = 20
self.gev2.data[COLUMNS.fusion_cdna_coding_start] = 1
self.gev2.data[COLUMNS.fusion_cdna_coding_end] = 40
result, removed = filter_by_annotations([self.gev1, self.gev2], self.best_transcripts)
bpp = result[0]
self.assertEqual(self.gev2, bpp)
def test_filter_by_annotations_two_best_transcripts(
self, genomic_event1, genomic_event2, best_transcripts):
genomic_event1.data[COLUMNS.gene1] = 'ABC'
genomic_event1.data[COLUMNS.gene2] = 'ABC'
genomic_event1.data[COLUMNS.transcript1] = 'ABCA'
genomic_event1.data[COLUMNS.transcript2] = 'ABCA'
genomic_event2.data[COLUMNS.gene1] = 'ABC'
genomic_event2.data[COLUMNS.gene2] = 'ABC'
genomic_event2.data[COLUMNS.transcript1] = 'ABCD'
genomic_event2.data[COLUMNS.transcript2] = 'ABCD'
result, removed = filter_by_annotations(
[genomic_event1, genomic_event2], best_transcripts)
bpp = result[0]
print(bpp.data)
assert bpp == genomic_event1
assert bpp.data[COLUMNS.transcript1] == 'ABCA'
def test_filter_by_annotations_no_transcripts(self, genomic_event1,
genomic_event2,
best_transcripts):
genomic_event1.data[COLUMNS.gene1] = None
genomic_event1.data[COLUMNS.gene2] = None
genomic_event1.data[COLUMNS.transcript1] = None
genomic_event1.data[COLUMNS.transcript2] = None
genomic_event2.data[COLUMNS.gene1] = None
genomic_event2.data[COLUMNS.gene2] = None
genomic_event2.data[COLUMNS.transcript1] = None
genomic_event2.data[COLUMNS.transcript2] = None
genomic_event1.break1.strand = STRAND.POS
result, removed = filter_by_annotations(
[genomic_event1, genomic_event2], best_transcripts)
bpp = result[0]
assert bpp.data[COLUMNS.transcript1] is None
def test_filter_by_annotations_two_transcripts(self, genomic_event1,
genomic_event2,
best_transcripts):
genomic_event1.data[COLUMNS.gene1] = 'XYZ'
genomic_event1.data[COLUMNS.gene2] = 'XYS'
genomic_event1.data[COLUMNS.transcript1] = 'XYZB'
genomic_event1.data[COLUMNS.transcript2] = 'XYSZ'
genomic_event2.data[COLUMNS.gene1] = 'XYZ'
genomic_event2.data[COLUMNS.gene2] = 'XYS'
genomic_event2.data[COLUMNS.transcript1] = 'XYZA'
genomic_event2.data[COLUMNS.transcript2] = 'XYSB'
bpps, removed = filter_by_annotations([genomic_event1, genomic_event2],
best_transcripts)
print(bpps)
bpp = bpps[0]
print(bpp, bpp.data)
assert bpp == genomic_event2
assert bpp.data[COLUMNS.transcript1] == 'XYZA'
def test_filter_by_annotations_two_fusion_cdna(self, genomic_event1,
genomic_event2,
best_transcripts):
genomic_event1.data[COLUMNS.gene1] = 'XYZ'
genomic_event1.data[COLUMNS.gene2] = 'XYS'
genomic_event1.data[COLUMNS.transcript1] = 'XYZB'
genomic_event1.data[COLUMNS.transcript2] = 'XYSZ'
genomic_event2.data[COLUMNS.gene1] = 'XYZ'
genomic_event2.data[COLUMNS.gene2] = 'XYS'
genomic_event2.data[COLUMNS.transcript1] = 'XYZB'
genomic_event2.data[COLUMNS.transcript2] = 'XYSZ'
genomic_event1.data[COLUMNS.fusion_cdna_coding_start] = 1
genomic_event1.data[COLUMNS.fusion_cdna_coding_end] = 20
genomic_event2.data[COLUMNS.fusion_cdna_coding_start] = 1
genomic_event2.data[COLUMNS.fusion_cdna_coding_end] = 40
result, removed = filter_by_annotations(
[genomic_event1, genomic_event2], best_transcripts)
bpp = result[0]
assert bpp == genomic_event2
