def assemble(fasta_file: str, score_file: str, tsp_bool=True, ap_bool=True):
"""
method for assembly via atsp/LKH or Hungarian Alogrithm
:param fasta_file:
:param score_file:
:param tsp:
:param ap:
:return:
"""
# read scores, reads
nr_of_reads, scores = read_score_file.read_score_file(score_file)
reads_with_id = parser.parse_fasta_with_id(fasta_file)
print('Fasta file read.')
# detect inclusions
# inclusions = look_for_included_reads([read[1] for i, read in enumerate(reads)], scores)
# reduce the scores matrix
# reduced_scores = remove_included_reads_in_scores(scores, inclusions)
# TSP
if tsp_bool:
lkh_contigs, lkh_time, lkh_value = lkh_assemble(reads_with_id, scores)
else:
lkh_contigs, lkh_time, lkh_value = [], -1.0, -1
if ap_bool:
# Assignment problem
reads_str_only = [read[1] for i, read in enumerate(reads_with_id)]
ap_contigs, ap_time, ap_value = munkres(reads_str_only, scores)
else:
ap_contigs, ap_time, ap_value = [], -1.0, -1
with open(score_file.split('.score')[0] + '.assembly', 'w') as f:
f.write('LKH: Circular: {}\nLKH_Contigs:\n'.format(circular))
f.write('\n'.join(lkh_contigs))
f.write('\nLKH_Objective_Value: {}\n'.format(lkh_value))
f.write('LKH_Time: {}\n'.format(lkh_time))
f.write('Assignment Problem:\nAP_Contigs:\n')
f.write('\n'.join(ap_contigs))
f.write('\nAP_Objective_Value: {}'.format(ap_value))
f.write('\nAP_Time: {}'.format(ap_time))
def create_full_atsp(file: str, circular=False) -> None:
current_file = file.split('.score')[0] + '_full'
print(current_file)
nr_of_reads, scores = read_score_file.read_score_file(file)
scores[scores < MINIMAL_OVERLAP_SCORE] = -BIG_M_WEIGHT
createtsp.write_full_atsp(current_file, nr_of_reads, scores, circular)
