def pattern_selection(project_directory, **kwargs):
logger = logging.getLogger(__name__)
logger.info("BEGIN Pattern Selection")
args = _set_parameters(**kwargs)
start_time = time.time()
_check_inputs(args['max_loci'], args['required_loci'],
args['exclude_loci'])
history = History(project_directory.make_new_file(
"history", "pattern_selection_history"),
"Pattern_Selection",
project_directory.timestamp,
param_dict=args)
preprocessing_history = History(
project_directory.get_parent_subdirectory_file(
"history", "preprocessing_history_{}.txt".format(
project_directory.get_parent_directory_timestamp())),
"Preprocessing",
exists=True)
# Get JSON file path from preprocessing step
json_file = preprocessing_history.get_path("PATTERN JSON")
variant_matrix = preprocessing_history.get_path("VARIANT SITE MATRIX FILE")
sep = {
'comma': ",",
"space": " ",
"tab": "\t"
}[preprocessing_history.get_parameter("SEP")]
# Get flag file path from preprocessing step
flag_file = preprocessing_history.get_path("PRIMER ZONE FLAGS")
primer_zone_size = preprocessing_history.get_parameter("PZ_SIZE")
history.add_path("PATTERN JSON", json_file)
logger.info("Reading from pattern JSON: %s", json_file)
# Read in pattern JSON
patterns = Patterns()
patterns.load_patterns(json_file)
if len(args['exclude_loci']):
patterns.remove_sites(args['exclude_loci'])
if len(args['required_loci']):
patterns.add_required_sites(args['required_loci'])
if len(args['exclude_strains']):
patterns.remove_strains(args['exclude_strains'])
patterns.set_resolution(args['res'], args['stop_at_res'])
best_set = _get_minimum_spanning_set(
patterns, args['reps'], args['max_loci'], args['max_res'],
args['n_threads'], int(preprocessing_history.get_parameter("PZ_SIZE")))
haplotype_file = project_directory.make_new_file("minimum_spanning_set",
".haplotype", "csv")
amplicon_json = project_directory.make_new_file("minimum_spanning_set",
".amplicons", "json")
haplotype_matrix = project_directory.make_new_file("minimum_spanning_set",
"haplotypes", "csv")
amplicon_matrix = project_directory.make_new_file("minimum_spanning_set",
"amplicons", "csv")
pattern_matrix = project_directory.make_new_file("minimum_spanning_set",
"patterns", "csv")
summary_file = project_directory.make_new_file("summary", "summary")
haplotype = Haplotype(patterns, best_set, flag_file, primer_zone_size,
variant_matrix, sep)
haplotype.write_haplotype(haplotype_file)
history.add_path("Haplotype File", haplotype_file)
haplotype.write_json(amplicon_json)
history.add_path("Amplicon JSON", amplicon_json)
haplotype.write_summary(summary_file)
history.add_path("Summary", summary_file)
haplotype.write_output(haplotype_matrix, pattern_matrix, amplicon_matrix)
history.add_path("Haplotype Matrix", haplotype_matrix)
history.add_path("Amplicon Matrix", amplicon_matrix)
history.add_path("Pattern Matrix", pattern_matrix)
logger.info("FINISHED Pattern Selection")
run_time = time.time() - start_time
history.add_other("Run Time", run_time)
history.write()
