def crossmap_to_internal_setup(coordinate_system, selector_model=None):
if coordinate_system == "g":
crossmap = Genomic()
return {
"crossmap_function": crossmap.genomic_to_coordinate,
"point_function": get_point_value,
}
elif coordinate_system == "c":
crossmap = Coding(
selector_model["exon"],
selector_model["cds"][0],
selector_model["inverted"],
)
return {
"crossmap_function": crossmap.coding_to_coordinate,
"point_function": point_to_x_coding,
"inverted": selector_model["inverted"],
}
elif coordinate_system == "n":
crossmap = Coding(
selector_model["exon"],
(selector_model["exon"][0][0], selector_model["exon"][-1][-1]),
selector_model["inverted"],
)
return {
"crossmap_function": crossmap.coding_to_coordinate,
"point_function": point_to_x_coding,
"inverted": selector_model["inverted"],
}
def test_Coding_no_utr_degenerate_return():
"""UTRs may be missing."""
crossmap = Coding([(10, 11)], (10, 11))
assert crossmap.coordinate_to_coding(8, True) == (-2, 0, -1, -2)
assert crossmap.coordinate_to_coding(9, True) == (-1, 0, -1, -1)
assert crossmap.coordinate_to_coding(11, True) == (1, 0, 1, 1)
assert crossmap.coordinate_to_coding(12, True) == (2, 0, 1, 2)
def test_Coding_protein():
"""Protein positions."""
crossmap = Coding(_exons, _cds)
# Boundary between 5' UTR and CDS.
invariant(
crossmap.coordinate_to_protein, 31,
crossmap.protein_to_coordinate, (-1, 3, 0, -1, 0))
invariant(
crossmap.coordinate_to_protein, 32,
crossmap.protein_to_coordinate, (1, 1, 0, 0, 0))
# Intron boundary.
invariant(
crossmap.coordinate_to_protein, 34,
crossmap.protein_to_coordinate, (1, 3, 0, 0, 0))
invariant(
crossmap.coordinate_to_protein, 35,
crossmap.protein_to_coordinate, (1, 3, 1, 0, 0))
# Boundary between CDS and 3' UTR.
invariant(
crossmap.coordinate_to_protein, 42,
crossmap.protein_to_coordinate, (2, 3, 0, 0, 0))
invariant(
crossmap.coordinate_to_protein, 43,
crossmap.protein_to_coordinate, (1, 1, 0, 1, 0))
def crossmap_to_hgvs_setup(coordinate_system, selector_model=None, degenerate=False):
"""
Returns a crossmap instance able to convert from the internal system
to the to hgvs system.
"""
if coordinate_system == "g":
crossmap = Genomic()
return {
"crossmap_function": crossmap.coordinate_to_genomic,
"point_function": genomic_to_point,
}
elif coordinate_system == "c":
crossmap = Coding(
selector_model["exon"], selector_model["cds"][0], selector_model["inverted"]
)
return {
"crossmap_function": crossmap.coordinate_to_coding,
"point_function": coding_to_point,
"degenerate": degenerate,
"inverted": selector_model["inverted"],
}
elif coordinate_system == "n":
crossmap = NonCoding(selector_model["exon"], selector_model["inverted"])
return {
"crossmap_function": crossmap.coordinate_to_noncoding,
"point_function": noncoding_to_point,
"inverted": selector_model["inverted"],
}
else:
raise Exception("Unsupported coordinate system: {}.".format(coordinate_system))
return crossmap
def test_Coding_inverted_degenerate():
"""Degenerate upstream and downstream positions are silently corrected."""
crossmap = Coding([(10, 20)], (11, 19), True)
degenerate_equal(
crossmap.coding_to_coordinate, 20,
[(-1, -1, -1, -1), (-2, 0, -1, -1), (1, -2, 0, -1), (1, -10, 1, -1)])
degenerate_equal(
crossmap.coding_to_coordinate, 9,
[(1, 1, 1, 1), (2, 0, 1, 1), (8, 2, 0, 1), (-1, 10, -1, 1)])
def test_Coding_inverted_no_utr_degenerate():
"""UTRs may be missing."""
crossmap = Coding([(10, 11)], (10, 11), True)
degenerate_equal(
crossmap.coding_to_coordinate, 11,
[(1, -1, 0, -1), (-1, 0, -1, -1), (1, -2, 1, -1)])
degenerate_equal(
crossmap.coding_to_coordinate, 9,
[(1, 1, 0, 1), (1, 0, 1, 1), (-1, 2, -1, 1)])
def test_Coding_no_utr3_inverted():
"""A 3' UTR may be missing."""
crossmap = Coding([(10, 20)], (10, 15), True)
# Direct transition from CDS to downstream.
invariant(
crossmap.coordinate_to_coding, 10,
crossmap.coding_to_coordinate, (5, 0, 0, 0))
invariant(
crossmap.coordinate_to_coding, 9,
crossmap.coding_to_coordinate, (5, 1, 0, 1))
def test_Coding_no_utr5_inverted():
"""A 5' UTR may be missing."""
crossmap = Coding([(10, 20)], (15, 20), True)
# Direct transition from upstream to CDS.
invariant(
crossmap.coordinate_to_coding, 20,
crossmap.coding_to_coordinate, (1, -1, 0, -1))
invariant(
crossmap.coordinate_to_coding, 19,
crossmap.coding_to_coordinate, (1, 0, 0, 0))
def test_Coding_small_utr3_inverted():
"""A 5' UTR may be of lenght one."""
crossmap = Coding([(10, 20)], (11, 15), True)
# Transition from CDS to 3' UTR to downstream.
invariant(
crossmap.coordinate_to_coding, 11,
crossmap.coding_to_coordinate, (4, 0, 0, 0))
invariant(
crossmap.coordinate_to_coding, 10,
crossmap.coding_to_coordinate, (1, 0, 1, 0))
invariant(
crossmap.coordinate_to_coding, 9,
crossmap.coding_to_coordinate, (1, 1, 1, 1))
def test_Coding_small_utr5_inverted():
"""A 5' UTR may be of lenght one."""
crossmap = Coding([(10, 20)], (15, 19), True)
# Transition from upstream to 5' UTR to CDS.
invariant(
crossmap.coordinate_to_coding, 20,
crossmap.coding_to_coordinate, (-1, -1, -1, -1))
invariant(
crossmap.coordinate_to_coding, 19,
crossmap.coding_to_coordinate, (-1, 0, -1, 0))
invariant(
crossmap.coordinate_to_coding, 18,
crossmap.coding_to_coordinate, (1, 0, 0, 0))
def test_Coding_small_utr5():
"""A 5' UTR may be of lenght one."""
crossmap = Coding([(10, 20)], (11, 15))
# Transition from upstream to 5' UTR to CDS.
invariant(
crossmap.coordinate_to_coding, 9,
crossmap.coding_to_coordinate, (-1, -1, -1, -1))
invariant(
crossmap.coordinate_to_coding, 10,
crossmap.coding_to_coordinate, (-1, 0, -1, 0))
invariant(
crossmap.coordinate_to_coding, 11,
crossmap.coding_to_coordinate, (1, 0, 0, 0))
def test_Coding_small_utr3():
"""A 5' UTR may be of lenght one."""
crossmap = Coding([(10, 20)], (15, 19))
# Transition from CDS to 3' UTR to downstream.
invariant(
crossmap.coordinate_to_coding, 18,
crossmap.coding_to_coordinate, (4, 0, 0, 0))
invariant(
crossmap.coordinate_to_coding, 19,
crossmap.coding_to_coordinate, (1, 0, 1, 0))
invariant(
crossmap.coordinate_to_coding, 20,
crossmap.coding_to_coordinate, (1, 1, 1, 1))
def test_Coding():
"""Forward oriented coding transcript."""
crossmap = Coding(_exons, _cds)
# Boundary between 5' and CDS.
invariant(
crossmap.coordinate_to_coding, 31,
crossmap.coding_to_coordinate, (-1, 0, -1, 0))
invariant(
crossmap.coordinate_to_coding, 32,
crossmap.coding_to_coordinate, (1, 0, 0, 0))
# Boundary between CDS and 3'.
invariant(
crossmap.coordinate_to_coding, 42,
crossmap.coding_to_coordinate, (6, 0, 0, 0))
invariant(
crossmap.coordinate_to_coding, 43,
crossmap.coding_to_coordinate, (1, 0, 1, 0))
def test_Coding_regions_inverted():
"""The CDS can start or end on a region boundary."""
crossmap = Coding([(10, 21), (30, 40), (49, 60)], (30, 40), True)
# Upstream odd length intron between two regions.
invariant(
crossmap.coordinate_to_coding, 44,
crossmap.coding_to_coordinate, (-1, 5, -1, 0))
invariant(
crossmap.coordinate_to_coding, 43,
crossmap.coding_to_coordinate, (1, -4, 0, 0))
# Downstream odd length intron between two regions.
invariant(
crossmap.coordinate_to_coding, 25,
crossmap.coding_to_coordinate, (10, 5, 0, 0))
invariant(
crossmap.coordinate_to_coding, 24,
crossmap.coding_to_coordinate, (1, -4, 1, 0))
def to_cds_coordinate(variants, sequences, selector_model):
"""
Converts the locations to cds equivalent.
:param variants: Variants with locations in the coordinate system.
:param selector_model:
:param crossmap:
"""
exons, cds = _get_exons_and_cds(selector_model)
crossmap = Coding(selector_model["exon"], cds, selector_model["inverted"])
if selector_model.get("inverted"):
variants = reverse_variants(variants, sequences)
splice_site_hits = _get_splice_site_hits(variants, exons, cds)
coordinate_variants = to_exon_positions(variants, exons, cds)
cds_variants = []
for variant in coordinate_variants:
cds_variants.append(
variant_to_cds_coordinate(variant, sequences, selector_model, crossmap)
)
return cds_variants, splice_site_hits
def test_Coding_inverted_degenerate_return():
"""Degenerate upstream and downstream positions may be returned."""
crossmap = Coding([(10, 20)], (11, 19), True)
assert crossmap.coordinate_to_coding(20, True) == (-2, 0, -1, -1)
assert crossmap.coordinate_to_coding(9, True) == (2, 0, 1, 1)
def test_Coding_inverted_degenerate_no_return():
"""Degenerate internal positions do not exist."""
crossmap = Coding([(10, 20), (30, 40)], (10, 40), True)
assert (crossmap.coordinate_to_coding(25) ==
crossmap.coordinate_to_coding(25, True))