except AttributeError:
return os.path.basename(fast5_fpath).replace(".fast5", "")
else:
return filename_payload
# end try
# end def get_checkstr
from src.platform import get_logfile_path
from src.printlog import get_full_time, printlog_info, printlog_error
from src.printlog import printlog_error_time, log_info, printn, printlog_info_time
import logging
logfile_path = get_logfile_path("barapost-binning", outdir_path)
logging.basicConfig(filename=logfile_path,
format='%(levelname)s: %(asctime)s %(message)s',
datefmt='%Y-%m-%d %H:%M:%S',
level=logging.INFO,
filemode='w')
log_info(sys.platform)
log_info(sys.implementation)
log_info(sys.version)
print("|=== barapost-binning.py (version {}) ===|\n".format(__version__))
log_info("barapost-binning.py (version {})".format(__version__))
print(get_full_time() + " - Start working\n")
log_info("Start working.")
# Some possible warnings:
print("Error: unable to create result directory `{}`".format(
outdir_path))
print(str(oserr))
platf_depend_exit(1)
# end try
# end if
from src.filesystem import create_result_directory
from src.filesystem import is_fastq, is_fasta
from src.platform import get_logfile_path
from src.check_connection import check_connection
from src.printlog import get_full_time, printlog_info, log_info
import logging
logging.basicConfig(filename=get_logfile_path("prober", outdir_path),
format='%(levelname)s: %(asctime)s %(message)s',
datefmt='%Y-%m-%d %H:%M:%S',
level=logging.INFO,
filemode='w')
log_info(sys.platform)
log_info(sys.implementation)
log_info(sys.version)
# If there are any fastq input files -- import fastq record generator
if any(filter(is_fastq, fq_fa_list)):
from src.fastq import fastq_packets
# end if
# If there are any fasta input files -- import fasta record generator
if any(filter(is_fasta, fq_fa_list)):
"""\nMaybe, the reason is that output directory generated by `barapost-prober.py`
isn't named `barapost_result` and you have forgotten to specify it with `-r` option?"""
)
# end if
platf_depend_exit(1)
# end if
# end if
del db_exists, acc_file_exists
# Generate path to log file:
from src.platform import get_logfile_path
from src.printlog import get_full_time, printn, printlog_info, printlog_info_time
from src.printlog import printlog_error, printlog_error_time, log_info, printlog_warning
import logging
logging.basicConfig(filename=get_logfile_path("barapost-local",
tax_annot_res_dir),
format='%(levelname)s: %(asctime)s %(message)s',
datefmt='%Y-%m-%d %H:%M:%S',
level=logging.INFO,
filemode='w')
log_info(sys.platform)
log_info(sys.implementation)
log_info(sys.version)
print("|=== barapost-local.py (version {}) ===|\n".format(__version__))
log_info("barapost-local.py (version {})".format(__version__))
print(get_full_time() + "- Start working\n")
log_info("Start working.")
# |===== Proceed =====|