diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py
index 015eeae83963b813bf0c3266376a2dde7607f5a1..d9989ef72dc4eb6979c9245fbf894c8835564bb3 100644
--- a/PanACoTA/subcommands/prepare.py
+++ b/PanACoTA/subcommands/prepare.py
@@ -43,10 +43,11 @@ def main(cmd, NCBI_species, NCBI_taxid, outdir, threads, no_refseq, only_mash, l
Main method, constructing the draft dataset for the given species
verbosity:
- - defaut 0 : stdout contains INFO, stderr contains ERROR.
- - 1: stdout contains INFO, stderr contains WARNING and ERROR
- - 2: stdout contains (DEBUG), DETAIL and INFO, stderr contains WARNING and ERROR
- - >=15: Add DEBUG in stdout
+ - defaut 0 : stdout contains INFO, stderr contains ERROR, .log contains INFO and more, .log.err contains warning and more
+ - 1: same as 0 + WARNING in stderr
+ - 2: same as 1 + DETAILS in stdout + DETAILS in .log.details
+ - >=15: same as 2 + Add DEBUG in stdout + create .log.debug with everything from info to debug
+
Parameters
----------
@@ -74,10 +75,10 @@ def main(cmd, NCBI_species, NCBI_taxid, outdir, threads, no_refseq, only_mash, l
lower limit of distance between 2 genomes to keep them
verbose : int
verbosity:
- default (0): info in stdout, error and more in stderr
- 1 = add warnings in stderr
- 2 = like 1 + add DETAIL to stdout (by default only INFO)
- >15: add debug to stdout
+ - defaut 0 : stdout contains INFO, stderr contains ERROR, .log contains INFO and more, .log.err contains warning and more
+ - 1: same as 0 + WARNING in stderr
+ - 2: same as 1 + DETAILS in stdout + DETAILS in .log.details
+ - >=15: same as 2 + Add DEBUG in stdout + create .log.debug with everything from info to debug
quiet : bool
True if nothing must be sent to stdout/stderr, False otherwise
@@ -113,10 +114,8 @@ def main(cmd, NCBI_species, NCBI_taxid, outdir, threads, no_refseq, only_mash, l
if verbose >= 15:
level = logging.DEBUG
logfile_base = os.path.join(outdir, "PanACoTA_prepare_{}").format(species_linked)
- logfile_base = utils.init_logger(logfile_base, level, name='', details=True,
- verbose=verbose, quiet=quiet)
- logger = logging.getLogger('')
- keyargs = {'section': 'refseq', 'file_format': 'fasta', 'output': '/Users/aperrin/Softwares/gem-hub_src/PanACoTA/104099-out', 'parallel': 1, 'group': 'bacteria', 'species_taxid': '104099'}
+ logfile_base, logger = utils.init_logger(logfile_base, level, 'prepare', details=True,
+ verbose=verbose, quiet=quiet)
logger.info("Command used\n \t > " + cmd)
message = f"'PanACoTA prepare' will run on {threads} "
@@ -235,7 +234,7 @@ def build_parser(parser):
"of 'N' stretches, put this value to this option."))
helper = parser.add_argument_group('Others')
helper.add_argument("-v", "--verbose", dest="verbose", action="count", default=0,
- help="Increase verbosity in stdout/stderr.")
+ help="Increase verbosity in stdout/stderr and log files.")
helper.add_argument("-q", "--quiet", dest="quiet", action="store_true", default=False,
help=("Do not display anything to stdout/stderr. log files will "
"still be created."))
@@ -310,7 +309,7 @@ def check_args(parser, args):
if args.cutn == 0 or args.cutn == 5:
message = (" !! Your genomes will be split when sequence contains at "
"least {}'N' at a stretch. If you want to change this threshold, use "
- "'--cutn' option (0 if you do not want to cut)").format(args.cutn)
+ "'--cutn n' option (n=0 if you do not want to cut)").format(args.cutn)
print(colored(message, "yellow"))
# Warn user about selection of genomes thresholds
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 0f2b5a4c7e7218dbd9d7804d38b5ac06967169f0..f438fde78c5d4d7c99e209d3225d92d80d25241b 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -56,10 +56,11 @@ def init_logger(logfile_base, level, name, details=False, verbose=0, quiet=False
if we need to name the logger (used for tests)
verbose : int
be more verbose:
- default (0): info in stdout, error and more in stderr
+ default (0): info in stdout, error and more in stderr ;
+ info and more in *.log ; warning and more in *.log.err
1 = add warnings in stderr
- 2 = like 1 + add DETAIL to stdout (by default only INFO)
- >15: add debug to stdout
+ 2 = like 1 + add details to stdout (by default only INFO) + add details to *.log.details
+ >15: add debug to stdout and create *.log.debug with all levels
quiet : bool
True if nothing must be sent to stdout/stderr, False otherwise
"""
@@ -171,7 +172,7 @@ def init_logger(logfile_base, level, name, details=False, verbose=0, quiet=False
err_handler.setLevel(logging.ERROR) # write all messages >= ERROR
err_handler.setFormatter(formatter_stream)
logger.addHandler(err_handler) # add handler to logger
- return logfile
+ return logfile, logger
class LessThanFilter(logging.Filter):