def lkh_assemble(reads: List[Tuple[str, str]], scores: np.ndarray) -> Tuple[
List[str], float, int]:
"""
starting lkh run (i.e. calling make_new_lkh_run)
parses the output tour and creates a List[Node]
which is used for the assemble_tour method to assemble the contigs
:param reads:
:param scores:
:return:
"""
filtered_reads_lengths = [len(x[1]) for i, x in enumerate(reads)]
read_strings = [x[1] for i, x in enumerate(reads)]
manipulated_scores = manipulate_scores2atsp(scores, filtered_reads_lengths)
create_full_atsp_via_scores('/home/andreas/GDrive/workspace/atspsa/footest', manipulated_scores)
start_time_tsp = time.time()
run_lkh('/home/andreas/GDrive/workspace/atspsa/footest.par')
end_time_tsp = time.time()
tour = parser.parse_tour('/home/andreas/GDrive/workspace/atspsa/footest.tour')
with open('/home/andreas/GDrive/workspace/atspsa/footest.tour', 'r') as f:
tsp_value = int(
[x.split('COMMENT : Length = ')[1] for x in f.readlines() if x.startswith('COMMENT : Length = ')][0]) - sum(
filtered_reads_lengths)
tsp_contigs = assemble_tour(scores, read_strings, tour)
print(tsp_contigs)
# compare_tours(tour, scores)
print(end_time_tsp - start_time_tsp)
return tsp_contigs, end_time_tsp - start_time_tsp, tsp_value
def make_new_lkh_run(filename: str, scores: np.ndarray, circular=False) -> None: #TODO delete?
"""
creates files for and runs LKH
:param filename:
:param scores:
:param circular:
:return:
"""
create_full_atsp_via_scores_with_big_M(filename, scores, circular)
run_lkh(filename + '.par')
return
