def test_Genomic():
"""Genomic positions are coordinates incremented by one."""
crossmap = Genomic()
invariant(
crossmap.coordinate_to_genomic, 0, crossmap.genomic_to_coordinate, 1)
invariant(
crossmap.coordinate_to_genomic, 98, crossmap.genomic_to_coordinate, 99)
def test_MultiLocus_offsets_odd_inverted():
"""Offets exacly between two loci are assigned to the upstream locus."""
multi_locus = MultiLocus([(1, 3), (6, 8)], True)
invariant(
multi_locus.to_position, 4, multi_locus.to_coordinate, (1, 2, 0))
invariant(
multi_locus.to_position, 3, multi_locus.to_coordinate, (2, -1, 0))
def test_MultiLocus_adjacent_loci():
"""Positions are continuous when loci are adjacent."""
multi_locus = MultiLocus([(1, 3), (3, 5)])
invariant(
multi_locus.to_position, 2, multi_locus.to_coordinate, (1, 0, 0))
invariant(
multi_locus.to_position, 3, multi_locus.to_coordinate, (2, 0, 0))
def test_MultiLocus_offsets_even_inverted():
"""Offsets are assigned to the nearest locus."""
multi_locus = MultiLocus([(1, 3), (7, 9)], True)
invariant(
multi_locus.to_position, 5, multi_locus.to_coordinate, (1, 2, 0))
invariant(
multi_locus.to_position, 4, multi_locus.to_coordinate, (2, -2, 0))
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_NonCoding_inverted():
"""Forward oriented noncoding transcript."""
crossmap = NonCoding(_exons, inverted=True)
# Boundary between upstream and transcript.
invariant(
crossmap.coordinate_to_noncoding, 72,
crossmap.noncoding_to_coordinate, (1, -1, -1))
invariant(
crossmap.coordinate_to_noncoding, 71,
crossmap.noncoding_to_coordinate, (1, 0, 0))
# Boundary between downstream and transcript.
invariant(
crossmap.coordinate_to_noncoding, 5,
crossmap.noncoding_to_coordinate, (22, 0, 0))
invariant(
crossmap.coordinate_to_noncoding, 4,
crossmap.noncoding_to_coordinate, (22, 1, 1))
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 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_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_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_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_Locus_inverted():
"""Reverse orientent Lovus."""
locus = Locus((30, 35), True)
invariant(locus.to_position, 35, locus.to_coordinate, (0, -1))
invariant(locus.to_position, 34, locus.to_coordinate, (0, 0))
invariant(locus.to_position, 33, locus.to_coordinate, (1, 0))
invariant(locus.to_position, 31, locus.to_coordinate, (3, 0))
invariant(locus.to_position, 30, locus.to_coordinate, (4, 0))
invariant(locus.to_position, 29, locus.to_coordinate, (4, 1))
def test_Locus():
"""Forward orientent Lovus."""
locus = Locus((30, 35))
invariant(locus.to_position, 29, locus.to_coordinate, (0, -1))
invariant(locus.to_position, 30, locus.to_coordinate, (0, 0))
invariant(locus.to_position, 31, locus.to_coordinate, (1, 0))
invariant(locus.to_position, 33, locus.to_coordinate, (3, 0))
invariant(locus.to_position, 34, locus.to_coordinate, (4, 0))
invariant(locus.to_position, 35, locus.to_coordinate, (4, 1))
def test_MultiLocus_inverted():
"""Reverse oriented MultiLocus."""
multi_locus = MultiLocus(_locations, True)
# Boundary between upstream and the first locus.
invariant(
multi_locus.to_position, 72, multi_locus.to_coordinate, (0, -1, -1))
invariant(
multi_locus.to_position, 71, multi_locus.to_coordinate, (0, 0, 0))
# Internal locus.
invariant(
multi_locus.to_position, 35, multi_locus.to_coordinate, (8, -1, 0))
invariant(
multi_locus.to_position, 34, multi_locus.to_coordinate, (8, 0, 0))
invariant(
multi_locus.to_position, 33, multi_locus.to_coordinate, (9, 0, 0))
invariant(
multi_locus.to_position, 31, multi_locus.to_coordinate, (11, 0, 0))
invariant(
multi_locus.to_position, 30, multi_locus.to_coordinate, (12, 0, 0))
invariant(
multi_locus.to_position, 29, multi_locus.to_coordinate, (12, 1, 0))
# Boundary between the last locus and downstream.
invariant(
multi_locus.to_position, 5, multi_locus.to_coordinate, (21, 0, 0))
invariant(
multi_locus.to_position, 4, multi_locus.to_coordinate, (21, 1, 1))
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))