good_genomes = args.good_genomes.split(",")
if args.trim_names:
good_genomes = [
genome_name.split(args.trimmer_char, 1)[0]
for genome_name in good_genomes
]
for genome_name in list(genomes.keys()):
if genome_name not in good_genomes:
del genomes[genome_name]
if args.bad_genomes != "":
bad_genomes = args.bad_genomes.split(",")
if args.trim_names:
bad_genomes = [
genome_name.split(args.trimmer_char, 1)[0]
for genome_name in bad_genomes
]
for genome_name in list(genomes.keys()):
if genome_name in bad_genomes:
del genomes[genome_name]
if args.filter_duplications:
remove_duplications(genomes=genomes)
result = get_assembly_points(genomes=genomes)
logger.info(
"Writing output to file \"{file_name}\"".format(file_name=args.output))
camsa_io.write_assembly_points(assembly_points=result,
destination=args.output,
output_setup=args.o_format,
delimiter=args.o_delimiter)
logger.info("Elapsed time: {el_time}".format(
el_time=str(datetime.datetime.now() - start_time)))
print("# NOTE: this is not a valid config, but rather a summary of the utilized options", file=destination)
print(parser.format_values(), file=destination)
for pairs_path in args.points:
full_path = os.path.abspath(os.path.expanduser(pairs_path))
base_name = os.path.basename(full_path)
shutil.copyfile(src=full_path, dst=os.path.join(input_report_dir, base_name))
# "merged" subdir of the report
# will contain assembly points, that constitute the merged assembly
merged_report_dir = os.path.join(args.output_dir, "merged")
camsa_io.remove_dir(dir_path=merged_report_dir)
os.makedirs(merged_report_dir)
merged_report_points_path = os.path.join(merged_report_dir, "merged.camsa.points")
with open(merged_report_points_path, "wt") as destination:
camsa_io.write_assembly_points(destination=destination,
assembly_points=[ap for ap in merged_assembly_points if ap.participates_in_merged],
output_setup=args.o_merged_format)
# "comparative" subdir of the report
# will contain assembly points divided into subgroups based in the agreement in input assemblies
comparative_report_dir = os.path.join(args.output_dir, "comparative")
camsa_io.remove_dir(dir_path=comparative_report_dir)
subgroups_report_dir = os.path.join(comparative_report_dir, "subgroups")
camsa_io.remove_dir(comparative_report_dir)
os.makedirs(comparative_report_dir)
os.makedirs(subgroups_report_dir)
for group in grouped_assemblies:
comparative_report_group_points_path = os.path.join(subgroups_report_dir, "{group_name}.camsa.points".format(group_name=".".join(group.name)))
with open(comparative_report_group_points_path, "wt") as destination:
camsa_io.write_assembly_points(assembly_points=group.aps,
destination=destination,
ch.setFormatter(logging.Formatter(args.c_logging_formatter_entry))
logger.info("Starting the converting process")
paths = []
for file_name in args.agouti:
logger.info("Processing file \"{file_name}\"".format(file_name=file_name))
with open(file_name, "rt") as source:
for line in source:
line = line.strip()
if len(line) == 0 or line.startswith("#") or line.startswith(">"):
continue
path = line.split(args.i_delimiter)
if args.source is not None:
source = args.source
else:
source = os.path.basename(file_name)
source = os.path.splitext(source)[0]
paths.append((source, path))
logger.info("A total of {paths_cnt} paths were extracted from {file_cnt} files"
"".format(paths_cnt=len(paths), file_cnt=len(args.agouti)))
assembly_points = []
for source, path in paths:
if len(path) <= 1:
logger.warning("Encountered a path of length <= 1 {{{path}}}; skipping"
"".format(path=",".join(path)))
continue
assembly_points.extend(get_assembly_points(agouti_path=path, source=source, oriented=args.oriented))
logger.info("Writing output to file \"{file_name}\"".format(file_name=args.output))
camsa_io.write_assembly_points(assembly_points=assembly_points, destination=args.output, output_setup=args.o_format, delimiter=args.o_delimiter)
logger.info("Elapsed time: {el_time}".format(el_time=str(datetime.datetime.now() - start_time)))
data = line.split("\t", 8)
if Component.is_scaffold_component(data[4]):
logger.debug(
"Processing a non-gap data line: {line}".format(line=line))
component = ScaffoldComponent.from_agp_data(data=data)
else:
logger.debug(
"Processing a gap data line: {line}".format(line=line))
component = GapComponent.from_agp_data(data=data)
objects[component.object_id].append(component)
for object_id in objects.keys():
logger.debug(
"Processing object {object_id}".format(object_id=object_id))
objects[object_id] = sorted(
objects[object_id],
key=lambda component: (component.object_beg, component.object_end))
components = objects[object_id]
camsa_points = object_as_camsa_points(object_as_components=components,
extra_data=args)
assembly_points.extend(camsa_points)
logger.info("Writing CAMSA formatted assembly poitns to {file}".format(
file=args.output.name))
camsa_io.write_assembly_points(assembly_points=assembly_points,
destination=args.output,
output_setup=args.o_format)
logger.info("Finished the conversion.")
logger.info("Elapsed time: {el_time}".format(
el_time=str(datetime.datetime.now() - start_time)))
full_path = os.path.abspath(os.path.expanduser(pairs_path))
base_name = os.path.basename(full_path)
shutil.copyfile(src=full_path,
dst=os.path.join(input_report_dir, base_name))
# "merged" subdir of the report
# will contain assembly points, that constitute the merged assembly
merged_report_dir = os.path.join(args.output_dir, "merged")
camsa_io.remove_dir(dir_path=merged_report_dir)
os.makedirs(merged_report_dir)
merged_report_points_path = os.path.join(merged_report_dir,
"merged.camsa.points")
with open(merged_report_points_path, "wt") as destination:
camsa_io.write_assembly_points(destination=destination,
assembly_points=[
ap for ap in merged_assembly_points
if ap.participates_in_merged
],
output_setup=args.o_merged_format)
# "comparative" subdir of the report
# will contain assembly points divided into subgroups based in the agreement in input assemblies
comparative_report_dir = os.path.join(args.output_dir, "comparative")
camsa_io.remove_dir(dir_path=comparative_report_dir)
subgroups_report_dir = os.path.join(comparative_report_dir, "subgroups")
camsa_io.remove_dir(comparative_report_dir)
os.makedirs(comparative_report_dir)
os.makedirs(subgroups_report_dir)
for group in grouped_assemblies:
comparative_report_group_points_path = os.path.join(
subgroups_report_dir, "{group_name}.camsa.points".format(
group_name=".".join(group.name)))