def _locate_codons_in_orf(sequence, orf, snv):
'It locates the snv in the orf coordinate system'
query_name = sequence.name
orf_seq = orf.qualifiers['dna']
subject_name = 'subject'
subject_fhand = NamedTemporaryFile(suffix='.fasta')
subject_fhand.write('>%s\n%s\n' % (subject_name, orf_seq))
subject_fhand.flush()
parameters = {'subject':subject_fhand.name}
aligner = create_runner(tool='water', parameters=parameters)
result_fhand = aligner(sequence)['water']
relations = build_relations_from_aligment(result_fhand,
query_name=sequence.name,
subject_name=subject_name)
#print relations
coord = CoordSystem(relations=[relations])
# snv .positions
snv_pos = snv.location.start.position
try:
snv_in_orf = coord.transform(from_mol=query_name, to_mol=subject_name,
position=snv_pos)
except RuntimeError:
snv_in_orf = None
#print snv_in_orf_start, snv_in_orf_end
orf_start = 0
orf_end = len(orf.qualifiers['dna']) - 1
orf_start_limit_in_seq = coord.transform(from_mol=subject_name,
to_mol=query_name,
position=orf_start)
orf_end_limit_in_seq = coord.transform(from_mol=subject_name,
to_mol=query_name,
position=orf_end)
if snv_in_orf is None:
# it can be utr3, utr5, or None
if snv_pos < orf_start_limit_in_seq:
position = 'utr5'
elif snv_pos > orf_end_limit_in_seq:
position = 'in utr3'
else:
position = None
codon_start = None
snv_in_orf = None
else:
start_codon_pos = snv_in_orf % 3
codon_start = snv_in_orf - start_codon_pos
position = 'orf'
return (position, codon_start, snv_in_orf)
def test_merge_overlaping_segments(self):
'It test the segment merging'
coord = CoordSystem(relations=[])
limits = [(0, 2)]
expected = [(0, 2)]
assert coord._merge_overlaping_segments(limits) == expected
limits = [(0, 2), (4, 6)]
expected = [(0, 2), (4, 6)]
assert coord._merge_overlaping_segments(limits) == expected
limits = [(0, 2), (4, 6), (0, 8)]
expected = [(0, 8)]
assert coord._merge_overlaping_segments(limits) == expected
def test_transformation(self):
'It test the transformation between fragments'
coord = CoordSystem(relations=[])
assert coord._transform_pos((1, 10), (2, 11), 2) == 3
assert coord._transform_pos((1, 10), (11, 2), 2) == 10
assert coord._transform_pos((0, 12), (16, 4), 2) == 14
#if we deal with CodonPosition we get the right answer and type
result = coord._transform_pos((2, 7), (CodonPosition(2, 1),
CodonPosition(4, 0)), 4)
expected = CodonPosition(3, 0)
assert result == expected
assert type(result) == type(expected)
result = coord._transform_pos((CodonPosition(2, 1),
CodonPosition(4, 0)),
(2, 7), CodonPosition(3, 1))
expected = 5
assert result == expected
assert type(result) == type(expected)
result = coord._transform_pos((CodonPosition(4, 0),
CodonPosition(2, 1)),
(2, 7), CodonPosition(3, 2))
expected = 3
assert result == expected
assert type(result) == type(expected)
def test_basic_coord(self):
'It tests the basic coordinate transformations'
#geno 111
# 0123456789012
#geno2 1234567890123
#geno3 1111111
# 6543210987654
#
#cdna 0123 4567
#
#prot 00 011
# 01 201
coord = CoordSystem(relations=[{'geno': [(2, 5), (8, 11)],
'cdna': [(0, 3), (4, 7)]}])
assert coord.transform(from_mol='cdna', to_mol='geno', position=6) == 10
assert coord.transform(from_mol='cdna', to_mol='geno', position=0) == 2
#more than two
coord = CoordSystem(relations=[{'geno': [(0, 12)], 'geno2': [(1, 13)]},
{'geno': [(2, 5), (8, 11)],
'cdna':[(0, 3), (4, 7)]},])
assert coord.transform(from_mol='geno', to_mol='cdna', position=3) == 1
assert coord.transform(from_mol='cdna', to_mol='geno', position=6) == 10
assert coord.transform(from_mol='geno', to_mol='geno2',
position=1) == 2
#with proteins
coord = CoordSystem(relations=[{'geno': [(0, 12)], 'geno2': [(1, 13)]},
{'geno': [(2, 5), (8, 11)],
'cdna':[(0, 3), (4, 7)]},
{'cdna':[(2, 6)],
'prot':[(CodonPosition(0, 0), CodonPosition(1, 1))]}])
assert coord.transform(from_mol='geno', to_mol='cdna', position=3) == 1
assert coord.transform(from_mol='cdna', to_mol='geno', position=6) == 10
assert coord.transform(from_mol='geno', to_mol='geno2',
position=11) == 12
assert coord.transform(from_mol='geno', to_mol='prot',
position=5) == 1
assert coord.transform(from_mol='prot', to_mol='geno',
position=2) == 8
#geno 111
# 0123456789012
#geno3 1111111
# 6543210987654
#reversed
coord = CoordSystem(relations=[{'geno': [(0, 12)], 'geno3': [(16, 4)]}])
assert coord.transform(from_mol='geno', to_mol='geno3',
position=2) == 14
#geno 111
# 0123456789012
#cdna 876 543210
#prot 54 3210
coord = CoordSystem(relations=[{'geno': [(1, 3), (6, 11)],
'cdna':[(8, 6), (5, 0)]},
{'cdna':[(2, 7)],
'prot':[(CodonPosition(0, 0), CodonPosition(1, 2))]}])
assert coord.transform(from_mol='geno', to_mol='prot',
position=2) == 5
def test_intersec_segments(self):
'It test the segment intersection'
coord = CoordSystem(relations=[])
limits1 = [(0, 2)]
limits2 = [(2, 8)]
expected = [(0, 1), (2, 2), (3, 8)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(1, 10)]
limits2 = [(5, 6)]
expected = [(1, 4), (5, 6), (7, 10)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(1, 10)]
limits2 = [(1, 10)]
expected = [(1, 10)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(1, 10)]
limits2 = [(2, 9)]
expected = [(1, 1), (2, 9), (10, 10)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(4, 12)]
limits2 = [(6, 8)]
expected = [(4, 5), (6, 8), (9, 12)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(4, 8)]
limits2 = [(6, 12)]
expected = [(4, 5), (6, 8), (9, 12)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(0, 8)]
limits2 = [(0, 12)]
expected = [(0, 8), (9, 12)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(0, 8)]
limits2 = [(2, 8)]
expected = [(0, 1), (2, 8)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(0, 2)]
limits2 = [(3, 8)]
expected = [(0, 2), (3, 8)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(0, 2)]
limits2 = [(4, 8)]
expected = [(0, 2), (4, 8)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(0, 12)]
limits2 = [(2, 5), (8, 11)]
expected = [(0, 1), (2, 5), (6, 7), (8, 11), (12, 12)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(12, 0)]
limits2 = [(12, 0)]
expected = [(12, 0)]
assert coord._intersec_segments(limits1, limits2) == expected
limits1 = [(12, 6), (5, 0)]
limits2 = [(13, 7)]
expected = [(13, 13), (12, 7), (6, 6), (5, 0)]
assert coord._intersec_segments(limits1, limits2) == expected
#cdna 876 543210
#prot 54 3210
limits1 = [(8, 6), (5, 0)]
limits2 = [(7, 2)]
expected = [(8, 8), (7, 6), (5, 2), (1, 0)]
assert coord._intersec_segments(limits1, limits2) == expected