help="Directory with families of species")
"""
parser.add_argument("-o", "--output_file", action="store", dest="output", default="stdout",
help="Output file. Default: stdout")
"""
args = parser.parse_args()
# run after scripts/expansion/compare_cluster.py
# out_fd = sys.stdout if args.output == "stdout" else open(args.output, "w")
species_syn_dict = TwoLvlDict()
for species in args.species_list:
species_syn_dict[species] = read_synonyms_dict("%s%s/all.t" % (args.species_dir, species))
species_syn_dict.write("families_all_species.t", absent_symbol=".")
not_assembled = species_syn_dict.filter_by_line(is_assembled)
species_syn_dict.write("correctly_assembled_families_species.t", absent_symbol=".")
assembled_ids = IdSet(species_syn_dict.sl_keys())
assembled_ids.write("assembled_families.ids")
not_assembled_ids = IdSet(not_assembled.sl_keys())
not_assembled_ids.write("non_assembled_families.ids")
"""
if args.output != "stdout":
out_fd.close()
"""
default="stdout",
help="Output file. Default: stdout")
args = parser.parse_args()
out_fd = sys.stdout if args.output == "stdout" else open(args.output, "w")
species_syn_dict = TwoLvlDict()
for species in args.species_list:
species_syn_dict[species] = read_synonyms_dict("%s%s/all.t" %
(args.species_dir, species))
species_syn_dict.write("families_all_species.t", absent_symbol=".")
nonassembled = species_syn_dict.filter_by_line(filter_nonassembled)
species_syn_dict.write("correctly_assembled_families_species.t",
absent_symbol=".")
nonassembled.write("not_assembled_families_in_all_species.t",
absent_symbol=".")
complicated_families_dict = nonassembled.filter_by_line(
filter_splited_to_several_fam)
complicated_families_dict.write("complicated_families.t", absent_symbol=".")
complicated_families_syn_dict = SynDict()
complicated_families_syn_ids = IdSet()
sl_keys = list(complicated_families_dict.sl_keys())
for sl_key in sl_keys:
sp_set = set()
for species in complicated_families_dict: