def run_msa(queries, input_state):
args = input_state.args
if args['subsample'] != 1:
if args['subsample'] < 1:
subsample_size = int(args['subsample']*len(queries))
elif args['subsample'] > 1:
subsample_size = int(min(len(queries),args['subsample']))
if args['random_subset']:
# Randomize order and take first _subsample_size_ sequences, then reorder
query_ids = [x for x in range(len(queries))]
shuffle(query_ids)
query_ids = sorted(query_ids[0:subsample_size])
queries = list([queries[i] for i in query_ids])
else:
if args['subsample_start'] < 1:
start = int(args['subsample_start']*len(queries))
else:
start = int(args['subsample_start'])
queries = list([queries[i] for i in range(start,start+subsample_size)])
if args['random_order']:
shuffle(queries)
msa_driver = MultipleSequenceDriver(queries, input_state)
# Build composite
msa_driver.build_composite()
# Align sequences (iteratively if given in params)
msa_driver.align()
# Build resultant consensus
consensus_object = msa_driver.build_consensus(args['thresh'],args['type'])
# Write MSA and consensus to file
consensus_fact = ConsensusFilterFactory(msa_driver,consensus_object)
consensus_fact.write(fname=args['build'])
msa.add_consensus(threshold, msa.build_consensus(float(threshold)))
print("Consensus at threshold " + threshold + ": " + msa.get_consensus(threshold).consensus)
if args["newick"]:
if args["threshold"]:
generate_consensus_newick(msa, msa.get_consensus(float(args["threshold"])), args["newick"])
else:
generate_consensus_newick(msa, list(msa.consensuses.values())[0], args["newick"])
if args["scores"]:
generate_score_and_conserved_chars_file(msa, args["scores"])
if args["k"]:
threshold, k = msa.find_conservation_boundary()
print(
"At threshold %.2f, average conservation and proportion of conserved characters are both %.2f%%"
% (threshold, k * 100)
)
if args["newbuild"]:
# consensus_object = msa.build_consensus(args['threshold'],args['type'])
# Write MSA and consensus to file
consensus_fact = ConsensusFilterFactory(msa, msa.get_consensus(threshold))
consensus_fact.write(fname=args["newbuild"])
status_message("Consensus statistics computation complete ", "OK")
except (IOError, KeyboardInterrupt, IndexError) as e:
print(str(e))