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