def recombination_map(self, map_name=None):
"""
Returns an :class:`msprime.RecombinationMap` instance representing the
recombination map for this chromosome. If ``map_name`` is provided,
return the corresponding recombination map; if not, use the default
recombination map for this species.
"""
if map_name is None:
map_name = self.default_genetic_map
genetic_map = genetic_maps.get_genetic_map(self.species, map_name)
return genetic_map.get_chromosome_map(self.name)
def test_multiple_threads_downloading(self):
gm = genetic_maps.get_genetic_map("drosophila_melanogaster", "Comeron2012_dm6")
gm.download()
saved = gm.is_cached
try:
# Trick the download code into thinking there's several happening
# concurrently
gm.is_cached = lambda: False
with self.assertWarns(UserWarning):
gm.download()
finally:
gm.is_cached = saved
def recombination_map(self, map_name=None):
"""
Returns an :class:`msprime.RecombinationMap` instance representing the
recombination map for this chromosome. If ``map_name`` is provided,
return the corresponding recombination map; if not, use the default
recombination map for this species.
"""
if map_name is None:
map_name = self.default_genetic_map
genetic_map = genetic_maps.get_genetic_map(self.species, map_name)
if genetic_map.contains_chromosome_map(self.name):
ret = genetic_map.get_chromosome_map(self.name)
else:
warnings.warn(
"Warning: recombination map not found for chromosome: '{}'"
" on map: '{}', substituting a zero"
"-recombination map.".format(self.name, map_name))
ret = msprime.RecombinationMap.uniform_map(self.length, 0)
return ret
def test_known_get_chromosome_map(self):
default_map = homo_sapiens.genome.default_genetic_map
HapmapII_GRCh37 = genetic_maps.get_genetic_map("homo_sapiens",
default_map)
recombination_map = HapmapII_GRCh37.get_chromosome_map("chr1")
self.assertIsInstance(recombination_map, msprime.RecombinationMap)
def test_unknown_get_chromosome_map(self):
default_map = homo_sapiens.genome.default_genetic_map
HapmapII_GRCh37 = genetic_maps.get_genetic_map("homo_sapiens",
default_map)
with self.assertRaises(ValueError):
HapmapII_GRCh37.get_chromosome_map("jibberish")
def test_get_genetic_map(self):
default_map = homo_sapiens.genome.default_genetic_map
HapmapII_GRCh37 = genetic_maps.get_genetic_map("homo_sapiens",
default_map)
self.assertIsInstance(HapmapII_GRCh37, genetic_maps.GeneticMap)