def __init__(self, config, logger):
self.config = config
self.logger = logger
self.start_time = datetime.now()
# set/create output directory
create_output_directory(config)
log_file = os.path.join(config.WORK_DIR, "application.log")
log_file_handler = FileHandler(log_file, mode="w")
if config.DEBUG:
log_file_handler.setFormatter(
Formatter(
"%(asctime)s %(levelname)8s %(message)s [%(module)s %(lineno)d]",
datefmt='%Y/%m/%d %H:%M:%S'))
else:
log_file_handler.setFormatter(
Formatter("%(asctime)s %(message)s",
datefmt='%Y/%m/%d %H:%M:%S'))
self.logger.addHandler(log_file_handler)
self.logger.info(
"DFAST pipeline started. (version {})".format(dfast_version))
self.logger.info("Results will be generated into '{}'.".format(
config.WORK_DIR))
# initializing query genome.
self.genome = Genome(config)
self.ltg = LocusTagGenerator(self.genome, config)
self.fu = FeatureUtil(self.genome, config)
self.sa = StructuralAnnotation(self.genome, config)
self.fa = FunctionalAnnotation(self.genome, config)
self.ddbj = DDBJsubmission(self.genome, config)
self.genbank = GenBankSubmission(self.genome, config)
def fix_origin(input_file, output_file=None, offset=0, logger=None):
if logger is None:
logger = getLogger(__name__)
if __name__ != '__main__':
loglevel_bkup = logger.level
logger.setLevel(WARNING)
logger.warning("[WARNING] Trying to locate a dnaA gene to fix the sequence origin of the chromosome. DO NOT APPLY THIS TO A DRAFT GENOME.")
config = Config()
config.GENOME_FASTA = input_file
config.FUNCTIONAL_ANNOTATION[0]["options"]["offset"] = offset
tmp_dir = tempfile.mkdtemp()
config.WORK_DIR = tmp_dir
logger.info("A temporary working directory was created in {}".format(config.WORK_DIR))
genome = Genome(config)
sa = StructuralAnnotation(genome, config)
fa = FunctionalAnnotation(genome, config)
sa.execute()
fa.execute()
if output_file:
f = open(output_file, "w")
logger.info("The origin-fixed genome fasta file is written to {}.".format(output_file))
else:
f = sys.stdout
SeqIO.write(list(genome.seq_records.values()), f, "fasta")
shutil.rmtree(config.WORK_DIR)
logger.info("The temporary working {} was cleaned up.".format(config.WORK_DIR))
if __name__ != '__main__':
logger.setLevel(loglevel_bkup)
class Pipeline():
def __init__(self, config, logger):
self.config = config
self.logger = logger
self.start_time = datetime.now()
# set/create output directory
create_output_directory(config)
log_file = os.path.join(config.WORK_DIR, "application.log")
log_file_handler = FileHandler(log_file, mode="w")
if config.DEBUG:
log_file_handler.setFormatter(
Formatter(
"%(asctime)s %(levelname)8s %(message)s [%(module)s %(lineno)d]",
datefmt='%Y/%m/%d %H:%M:%S'))
else:
log_file_handler.setFormatter(
Formatter("%(asctime)s %(message)s",
datefmt='%Y/%m/%d %H:%M:%S'))
self.logger.addHandler(log_file_handler)
self.logger.info(
"DFAST pipeline started. (version {})".format(dfast_version))
self.logger.info("Results will be generated into '{}'.".format(
config.WORK_DIR))
# initializing query genome.
self.genome = Genome(config)
self.ltg = LocusTagGenerator(self.genome, config)
self.fu = FeatureUtil(self.genome, config)
self.sa = StructuralAnnotation(self.genome, config)
self.fa = FunctionalAnnotation(self.genome, config)
self.ddbj = DDBJsubmission(self.genome, config)
self.genbank = GenBankSubmission(self.genome, config)
def execute(self):
self.sa.execute() # execute structural annotation
self.fu.execute() # feature adjustment: sort, remove_partial, (merge)
self.fa.execute() # functional annotation
self.ltg.execute() # assigning locus_tags
self.genome.add_source_features() # set source feature
# writing result files.
write_results(self.genome, self.config)
GenomeStat.execute(self.genome)
self.ddbj.create_submission_file()
self.genbank.create_submission_file()
if self.config.DEBUG:
self.genome.to_pickle(
os.path.join(self.config.WORK_DIR, "genome.pickle"))
end_time = datetime.now()
running_time = end_time - self.start_time
running_time = running_time.total_seconds()
h, remainder = divmod(running_time, 3600)
m, s = divmod(remainder, 60)
self.logger.info("DFAST pipeline completed!")
self.logger.info("Total running time: {0:.0f}h{1:.0f}m{2:.0f}s".format(
h, m, s))
def cleanup(self):
self.sa.cleanup()
self.fa.cleanup()
shutil.rmtree(os.path.join(self.config.WORK_DIR, "input"))