def load_population_from_file(archive_path, extract_path="."):
"""Load a population from a snapshot.
Load a population from a snapshot,
which should be stored in a .tar archive.
archive_path - path to archive
extract_path - path to directory where files will be extracted
"""
popn_archive = tarfile.open(archive_path)
clone_fname = mut_fname = param_fname = anlt_fname = None
# get filenames for extraction
# NB this may break if filenames in save_population_to_file() are changed
members_to_extract = []
for member in popn_archive.getmembers():
if member.name.startswith('clones_'):
clone_fname = "{}/{}".format(extract_path, member.name)
members_to_extract.append(member)
elif member.name.startswith('mutations_'):
mut_fname = "{}/{}".format(extract_path, member.name)
members_to_extract.append(member)
elif member.name.startswith('params_'):
param_fname = "{}/{}".format(extract_path, member.name)
members_to_extract.append(member)
elif member.name.startswith('anlt_'):
anlt_fname = "{}/{}".format(extract_path, member.name)
members_to_extract.append(member)
fnames = [clone_fname, mut_fname, param_fname, anlt_fname]
if not all(fnames):
raise Exception("population archive is missing required files")
# extract snapshot files
popn_archive.extractall(path=extract_path, members=members_to_extract)
popn_archive.close()
# load parameters, mutations and clones
t_curr, opt, popn_params = load_parameters_from_file(param_fname)
analytics = Analytics.init_from_file(anlt_fname)
all_muts, mutation_map = load_muts_from_file(opt, mut_fname)
root_clone = load_clones_from_file(opt, mutation_map, clone_fname)
# construct population from parameter set,
# clone tree and mutation dictionary
new_popn = Population.init_from_file(opt, analytics, popn_params,
root_clone, all_muts)
# now delete the individual snapshot files,
# as we will always load popn from an archive
for fname in fnames:
delete_local_file(fname)
return t_curr, opt, new_popn
