def test_mix_of_string_and_Polymorphisms_in_list():
sites = [Polymorphism(316,0,'C'), '316.1A']
seq = sites2seq(sites, region=(314,318))
assert seq == 'CCCACT'
# reverse the order
sites = ['316.1A', Polymorphism(316,0,'C')]
seq = sites2seq(sites, region=(314,318))
assert seq == 'CCCACT'
def test_more_than_two_gapped_segments():
sets = [ [(16024,16365),(73,340),(577,1000)],
[(16024,16365),(16300,340),(577,1000)], # overlapping segments
]
for s in sets:
should_cover = Coverage(*s)
seq = sites2seq('', region=should_cover)
covers = calc_coverage(seq)
print "should cover: '%s' - does cover: '%s'" % (should_cover, covers)
assert should_cover == covers
def test_gapped_variant_segments():
should_cover = Coverage((16024,16365),(73,340))
variants = ['16311 263 311',
'16024 73', # little bit tricky - first site from second chunk is variant
# '16365', # impossible, middle site is a variant
]
for v in variants:
seq = sites2seq(v, region=should_cover)
covers = calc_coverage(seq)
print "should cover: '%s' - does cover: '%s'" % (should_cover, covers)
assert should_cover == covers
def test_gapped_rcrs_segments():
ranges = [ [(16024,16365), (73,340) ],
[(16024,16569), (73,340) ],
[(16024,16569), (73,577) ],
[(16024,16400), (1,577) ],
]
for pair in ranges:
should_cover = Coverage(*pair)
seq = sites2seq('', region=should_cover)
covers = calc_coverage(seq)
print "should cover: '%s' - does cover: '%s'" % (should_cover, covers)
assert should_cover == covers
def test_single_rcrs_segment():
ranges = [(16024,16365),
(73,340),
(16000,340),
(16000,577),
(577,15992),
(16000,16569),
]
for item in ranges:
should_cover = Coverage(item)
seq = sites2seq('', region=should_cover)
covers = calc_coverage(seq)
print "should cover: '%s' - does cover: '%s'" % (should_cover, covers)
assert should_cover == covers
def test_single_variant_segments():
should_cover = Coverage((16024,16365))
variants = ['16311',
'16223 16265T',
'16223 16260 16270 16287 16311',
'16148 16172 16187 16188G 16189 16209 16223 16230 16311 16320',
'16024', # tricky, first site is a variant
'16365', # tricky, last site is a variant
'16024 16365', # tricky, both first and last sites are variants
'16363 16364 16365', # tricky, last few sites are variants
]
for v in variants:
seq = sites2seq(v, region=should_cover)
covers = calc_coverage(seq)
print "should cover: '%s' - does cover: '%s'" % (should_cover, covers)
assert should_cover == covers
def test_all_range_argument():
assert sites2seq('', region='all') == rCRS
def test_coding_range_argument():
assert sites2seq('', region='coding') == rCRS[576:15992]
def test_HVR1toHVR2_range_argument():
assert sites2seq('', region='HVR1to2') == rCRS[16023:]+rCRS[:340]
def test_sites_outside_region_snp():
assert sites2seq('73G') == rCRS[16023:16365]
def test_single_site_as_string_in_list():
sites = ['16129-']
seq = sites2seq(sites)
assert '-' in seq
def test_insertion_in_custom_range():
assert 'GCAT' == sites2seq('1.1C', region=[1,2,3])
def test_deletion_at_start_of_custom_range():
assert '-AT' == sites2seq('1-', region=[1,2,3])
def test_single_substition_in_correct_place():
# rCRS string is 0-based count
# rCRS as DNA sequence is 1-based
# the the numbering discrepancy
assert 'A' == sites2seq('16129A', region='all')[16128]
def test_two_sites_as_Polymorphisms_in_list():
sites = [Polymorphism(316,0,'C'), Polymorphism(316,1,'A')]
seq = sites2seq(sites, region=(314,318))
assert seq == 'CCCACT'
def test_two_sites_as_string_in_list():
sites = ['316C', '316.1A']
seq = sites2seq(sites, region=(314,318))
assert seq == 'CCCACT'
def test_two_sites_in_string():
sites = '316C 316.1A'
seq = sites2seq(sites, region=range(314,319))
assert seq == 'CCCACT'
def test_single_site_as_Polymorphism_in_list():
sites = [Polymorphism(16129,0,'-')]
seq = sites2seq(sites)
assert '-' in seq
def test_custom_range():
assert 'GAG' == sites2seq('', region=[1,5,9])
def test_single_site_as_string():
sites = '16129-'
seq = sites2seq(sites)
assert '-' in seq
def test_two_insertions_in_custom_range():
assert 'GCAGT' == sites2seq('1.1C 2.1G', region=[1,2,3])
def test_default_sequence_range_is_HVR1():
assert sites2seq('') == rCRS[16023:16365]
assert sites2seq('', region=(16024,16365)) == rCRS[16023:16365]
def test_deletion_in_middle_of_custom_range():
assert 'G-T' == sites2seq('2-', region=[1,2,3])
def test_rCRS_argument_returns_rCRS():
assert sites2seq('rCRS') == rCRS[16023:16365]
def test_sites_outside_region_del():
assert sites2seq('489d') == rCRS[16023:16365]
def test_HVR2_range_argument():
assert sites2seq('', region='HVR2') == rCRS[72:340]
def test_sites_outside_region_ins():
assert sites2seq('315.1C') == rCRS[16023:16365]
def test_HVR1andHVR2_range_argument():
assert sites2seq('', region='HVR1and2') == rCRS[16023:16365]+rCRS[72:340]