def get_genetic_map_tarball():
"""
Returns a genetic map in hapmap format in a tarball as a bytes object.
"""
with tempfile.TemporaryDirectory() as map_dir:
for j in range(1, 10):
# TODO Have a way to put in different maps??
with open(os.path.join(map_dir, "prefix_chr{}.txt".format(j)),
"w") as f:
print("Chromosome Position(bp) Rate(cM/Mb) Map(cM)",
file=f)
print("chr1 55550 2.981822 0.000000", file=f)
print("chr1 82571 2.082414 0.080572", file=f)
print("chr1 88169 0 0.092229", file=f)
# For the tarfile to be in the right format, we must be in the right directory.
with genetic_maps.cd(map_dir):
# Now tar up this map_directory
with tempfile.TemporaryFile('wb+') as tmp_file:
with tarfile.open(fileobj=tmp_file, mode="w:gz") as tar_file:
for filename in os.listdir("."):
tar_file.add(filename)
# Read back the tarball
tmp_file.seek(0)
tarball = tmp_file.read()
return tarball
def get_maps(self, tarball):
maps = {}
with tempfile.TemporaryFile('wb+') as f:
f.write(tarball)
f.seek(0)
with tarfile.open(fileobj=f, mode='r') as tar_file:
with tempfile.TemporaryDirectory() as extract_dir:
with genetic_maps.cd(extract_dir):
tar_file.extractall()
for fn in os.listdir(extract_dir):
maps[fn] = msprime.RecombinationMap.read_hapmap(fn)
return maps
def get_genetic_map_tarball(custom_file_f=None, filter=None):
"""
Returns a genetic map in hapmap format in a tarball as a bytes object.
:param func custom_file_f: A function that accepts a single parameter
(a folder name), which may be used to create additional files under
the given folder. All files in the folder will be included in the
returned tarball.
:param func filter: A function which is passed as the ``filter`` argument
to ``TarFile.add()``. This function can be used to change the info
field for each file in the returned tarball. See tarfile documentation
for more details.
"""
with tempfile.TemporaryDirectory() as map_dir:
for j in range(1, 10):
# TODO Have a way to put in different maps??
with open(os.path.join(map_dir, "prefix_chr{}.txt".format(j)),
"w") as f:
print("Chromosome Position(bp) Rate(cM/Mb) Map(cM)",
file=f)
print("chr1 55550 2.981822 0.000000", file=f)
print("chr1 82571 2.082414 0.080572", file=f)
print("chr1 88169 0 0.092229", file=f)
if custom_file_f is not None:
# Do arbitrary things under map_dir.
custom_file_f(map_dir)
# For the tarfile to be in the right format, we must be in the right directory.
with genetic_maps.cd(map_dir):
# Now tar up this map_directory
with tempfile.TemporaryFile('wb+') as tmp_file:
with tarfile.open(fileobj=tmp_file, mode="w:gz") as tar_file:
for filename in os.listdir("."):
tar_file.add(filename, filter=filter)
# Read back the tarball
tmp_file.seek(0)
tarball = tmp_file.read()
return tarball