def test_is_comment_string(self):
# a sting is considered a comment if it non empty first char is "#"
self.assertTrue(GRIMMReader.is_comment_string("#"))
self.assertTrue(GRIMMReader.is_comment_string(" #"))
self.assertTrue(GRIMMReader.is_comment_string("# "))
self.assertTrue(GRIMMReader.is_comment_string(" # "))
self.assertTrue(GRIMMReader.is_comment_string("# aaa "))
self.assertFalse(GRIMMReader.is_comment_string("a# "))
self.assertTrue(GRIMMReader.is_comment_string(" ## "))
logger.setLevel(args.c_logging_level)
logger.addHandler(ch)
logger.info(full_description)
logger.info(parser.format_values())
ch.setFormatter(logging.Formatter(args.c_logging_formatter_entry))
logger.info("Starting the converting process")
genomes = defaultdict(list)
for file_name in args.grimm:
logger.info(
"Processing file \"{file_name}\"".format(file_name=file_name))
with open(file_name, "rt") as source:
current_genome = None
for line in source:
line = line.strip()
if len(line) == 0 or GRIMMReader.is_comment_string(
data_string=line):
continue
if GRIMMReader.is_genome_declaration_string(data_string=line):
current_genome = GRIMMReader.parse_genome_declaration_string(
data_string=line).name
if args.trim_names:
current_genome = current_genome.split(
args.trimmer_char, 1)[0]
elif current_genome is not None:
current_chromosome = []
chr_type, blocks = GRIMMReader.parse_data_string(
data_string=line)
genomes[current_genome].append((chr_type, blocks))
if args.good_genomes != "":
good_genomes = args.good_genomes.split(",")
if args.trim_names:
ch.setLevel(args.c_logging_level)
logger.setLevel(args.c_logging_level)
logger.addHandler(ch)
logger.info(full_description)
logger.info(parser.format_values())
ch.setFormatter(logging.Formatter(args.c_logging_formatter_entry))
logger.info("Starting the converting process")
genomes = defaultdict(list)
for file_name in args.grimm:
logger.info("Processing file \"{file_name}\"".format(file_name=file_name))
with open(file_name, "rt") as source:
current_genome = None
for line in source:
line = line.strip()
if len(line) == 0 or GRIMMReader.is_comment_string(data_string=line):
continue
if GRIMMReader.is_genome_declaration_string(data_string=line):
current_genome = GRIMMReader.parse_genome_declaration_string(data_string=line).name
if args.trim_names:
current_genome = current_genome.split(args.trimmer_char, 1)[0]
elif current_genome is not None:
current_chromosome = []
chr_type, blocks = GRIMMReader.parse_data_string(data_string=line)
genomes[current_genome].append((chr_type, blocks))
if args.good_genomes != "":
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: