def main(cmdlineargs=None, default_outfile=sys.stdout):
"""
Main function that sets up a processing pipeline and runs it.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
start_time = time.time()
parser = get_option_parser()
if cmdlineargs is None:
cmdlineargs = sys.argv[1:]
options, args = parser.parse_args(args=cmdlineargs)
# Setup logging only if there are not already any handlers (can happen when
# this function is being called externally such as from unit tests)
if not logging.root.handlers:
setup_logging(stdout=bool(options.output), quiet=options.quiet or options.report == 'minimal')
if options.quiet and options.report:
parser.error("Options --quiet and --report cannot be used at the same time")
paired = determine_paired_mode(options)
assert paired in (False, 'first', 'both')
if paired == 'first':
# legacy mode
assert options.pair_filter is None
pair_filter_mode = 'first'
elif options.pair_filter is None:
# default
pair_filter_mode = 'any'
else:
# user-provided behavior
pair_filter_mode = options.pair_filter
try:
is_interleaved_input, is_interleaved_output = determine_interleaved(options, args)
input_filename, input_paired_filename, quality_filename = input_files_from_parsed_args(args,
paired, is_interleaved_input)
pipeline = pipeline_from_parsed_args(options, paired, pair_filter_mode, quality_filename, is_interleaved_output)
outfiles = open_output_files(options, default_outfile, is_interleaved_output)
except CommandLineError as e:
parser.error(e)
return # avoid IDE warnings below
if options.cores < 0:
parser.error('Value for --cores cannot be negative')
cores = available_cpu_count() if options.cores == 0 else options.cores
if cores > 1:
if (
ParallelPipelineRunner.can_output_to(outfiles)
and quality_filename is None
and not options.colorspace
and options.format is None
):
runner = ParallelPipelineRunner(pipeline, cores, options.buffer_size)
else:
logger.error('Running in parallel is currently not supported for '
'the given combination of command-line parameters.\nThese '
'options are not supported: --info-file, --rest-file, '
'--wildcard-file, --untrimmed-output, '
'--untrimmed-paired-output, --too-short-output, '
'--too-short-paired-output, --too-long-output, '
'--too-long-paired-output, --format, --colorspace')
sys.exit(1)
else:
runner = pipeline
try:
runner.set_input(input_filename, file2=input_paired_filename,
qualfile=quality_filename, colorspace=options.colorspace,
fileformat=options.format, interleaved=is_interleaved_input)
runner.set_output(outfiles)
except (seqio.UnknownFileType, IOError) as e:
parser.error(e)
implementation = platform.python_implementation()
opt = ' (' + implementation + ')' if implementation != 'CPython' else ''
logger.info("This is cutadapt %s with Python %s%s", __version__,
platform.python_version(), opt)
logger.info("Command line parameters: %s", " ".join(cmdlineargs))
logger.info("Processing reads on %d core%s in %s mode ...",
cores, 's' if cores > 1 else '',
{False: 'single-end', 'first': 'paired-end legacy', 'both': 'paired-end'}[pipeline.paired])
if pipeline.should_warn_legacy:
logger.warning('\n'.join(textwrap.wrap('Legacy mode is '
'enabled. Read modification and filtering options *ignore* '
'the second read. To switch to regular paired-end mode, '
'provide the --pair-filter=any option or use any of the '
'-A/-B/-G/-U/--interleaved options.')))
try:
stats = runner.run()
# cProfile.runctx('stats=runner.run()', globals(), locals(), 'profile_main.prof')
runner.close()
except KeyboardInterrupt:
print("Interrupted", file=sys.stderr)
sys.exit(130)
except IOError as e:
if e.errno == errno.EPIPE:
sys.exit(1)
raise
except (seqio.FormatError, seqio.UnknownFileType, EOFError) as e:
sys.exit("cutadapt: error: {0}".format(e))
elapsed = time.time() - start_time
if not options.quiet:
# send statistics to stderr if result was sent to stdout
stat_file = sys.stderr if options.output is None else None
with redirect_standard_output(stat_file):
if options.report == 'minimal':
print_minimal_report(stats, elapsed, options.gc_content / 100)
else:
print_report(stats, elapsed, options.gc_content / 100)
def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):
"""
Main function that sets up a processing pipeline and runs it.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
start_time = time.time()
parser = get_argument_parser()
if cmdlineargs is None:
cmdlineargs = sys.argv[1:]
args, leftover_args = parser.parse_known_args(args=cmdlineargs)
# log to stderr if results are to be sent to stdout
log_to_stdout = args.output is not None and args.output != "-" and args.paired_output != "-"
# Setup logging only if there are not already any handlers (can happen when
# this function is being called externally such as from unit tests)
if not logging.root.handlers:
setup_logging(logger,
stdout=log_to_stdout,
quiet=args.quiet,
minimal=args.report == 'minimal',
debug=args.debug)
profiler = setup_profiler_if_requested(args.profile)
if args.quiet and args.report:
parser.error(
"Options --quiet and --report cannot be used at the same time")
if args.colorspace:
parser.error(
"These colorspace-specific options are no longer supported: "
"--colorspace, -c, -d, --double-encode, -t, --trim-primer, "
"--strip-f3, --maq, --bwa, --no-zero-cap. "
"Use Cutadapt 1.18 or earlier to work with colorspace data.")
paired = determine_paired(args)
assert paired in (False, True)
# Print the header now because some of the functions below create logging output
log_header(cmdlineargs)
if leftover_args:
warn_if_en_dashes(cmdlineargs)
parser.error("unrecognized arguments: " + " ".join(leftover_args))
if args.cores < 0:
parser.error('Value for --cores cannot be negative')
cores = available_cpu_count() if args.cores == 0 else args.cores
file_opener = FileOpener(compression_level=args.compression_level,
threads=0 if cores == 1 else None)
if sys.stderr.isatty() and not args.quiet:
progress = Progress()
else:
progress = DummyProgress()
try:
is_interleaved_input = args.interleaved and len(args.inputs) == 1
input_filename, input_paired_filename = setup_input_files(
args.inputs, paired, is_interleaved_input)
check_arguments(args, paired)
pipeline = pipeline_from_parsed_args(args, paired, file_opener)
outfiles = open_output_files(args, default_outfile, file_opener)
infiles = InputFiles(input_filename,
file2=input_paired_filename,
interleaved=is_interleaved_input)
runner = setup_runner(pipeline, infiles, outfiles, progress, cores,
args.buffer_size)
except CommandLineError as e:
parser.error(str(e))
return # avoid IDE warnings below
logger.info("Processing reads on %d core%s in %s mode ...", cores,
's' if cores > 1 else '', {
False: 'single-end',
True: 'paired-end'
}[pipeline.paired])
try:
with runner as r:
stats = r.run()
except KeyboardInterrupt:
print("Interrupted", file=sys.stderr)
sys.exit(130)
except BrokenPipeError:
sys.exit(1)
except (dnaio.FileFormatError, dnaio.UnknownFileFormat, EOFError) as e:
sys.exit("cutadapt: error: {}".format(e))
elapsed = time.time() - start_time
if args.report == 'minimal':
report = minimal_report
else:
report = full_report
logger.log(REPORT, '%s', report(stats, elapsed, args.gc_content / 100))
if profiler is not None:
import pstats
profiler.disable()
pstats.Stats(profiler).sort_stats('time').print_stats(20)
def main(cmdlineargs, default_outfile=sys.stdout.buffer) -> Statistics:
"""
Set up a processing pipeline from the command-line arguments, run it and return
a Statistics object.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
start_time = time.time()
parser = get_argument_parser()
args, leftover_args = parser.parse_known_args(args=cmdlineargs)
# log to stderr if results are to be sent to stdout
log_to_stdout = args.output is not None and args.output != "-" and args.paired_output != "-"
# Setup logging only if there are not already any handlers (can happen when
# this function is being called externally such as from unit tests)
if not logging.root.handlers:
setup_logging(logger,
stdout=log_to_stdout,
quiet=args.quiet,
minimal=args.report == 'minimal',
debug=args.debug)
log_header(cmdlineargs)
profiler = setup_profiler_if_requested(args.profile)
if args.quiet and args.report:
parser.error(
"Options --quiet and --report cannot be used at the same time")
if leftover_args:
warn_if_en_dashes(cmdlineargs)
parser.error("unrecognized arguments: " + " ".join(leftover_args))
if args.cores < 0:
parser.error('Value for --cores cannot be negative')
cores = available_cpu_count() if args.cores == 0 else args.cores
file_opener = FileOpener(compression_level=args.compression_level,
threads=0 if cores == 1 else None)
if sys.stderr.isatty() and not args.quiet:
progress = Progress()
else:
progress = DummyProgress()
paired = determine_paired(args)
assert paired in (False, True)
try:
is_interleaved_input = args.interleaved and len(args.inputs) == 1
input_filename, input_paired_filename = setup_input_files(
args.inputs, paired, is_interleaved_input)
check_arguments(args, paired)
adapters, adapters2 = adapters_from_args(args)
pipeline = pipeline_from_parsed_args(args, paired, file_opener,
adapters, adapters2)
adapter_names = [a.name for a in adapters] # type: List[str]
adapter_names2 = [a.name for a in adapters2] # type: List[str]
outfiles = open_output_files(args, default_outfile, file_opener,
adapter_names, adapter_names2)
inpaths = InputPaths(input_filename,
path2=input_paired_filename,
interleaved=is_interleaved_input)
runner = setup_runner(pipeline, inpaths, outfiles, progress, cores,
args.buffer_size, file_opener)
except CommandLineError as e:
logger.debug("Command line error. Traceback:", exc_info=True)
parser.error(str(e))
return
logger.info("Processing reads on %d core%s in %s mode ...", cores,
's' if cores > 1 else '', {
False: 'single-end',
True: 'paired-end'
}[pipeline.paired])
try:
with runner as r:
stats = r.run()
except KeyboardInterrupt:
print("Interrupted", file=sys.stderr)
sys.exit(130)
except BrokenPipeError:
sys.exit(1)
except (dnaio.FileFormatError, dnaio.UnknownFileFormat, EOFError) as e:
logger.debug("Command line error. Traceback:", exc_info=True)
sys.exit("cutadapt: error: {}".format(e))
elapsed = time.time() - start_time
if args.report == 'minimal':
report = minimal_report
else:
report = full_report
logger.log(REPORT, '%s', report(stats, elapsed, args.gc_content / 100))
if profiler is not None:
import pstats
profiler.disable()
pstats.Stats(profiler).sort_stats('time').print_stats(20)
return stats
def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):
"""
Main function that sets up a processing pipeline and runs it.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
start_time = time.time()
parser = get_argument_parser()
if cmdlineargs is None:
cmdlineargs = sys.argv[1:]
args = parser.parse_args(args=cmdlineargs)
# log to stderr if results are to be sent to stdout
log_to_stdout = args.output is not None and args.output != "-" and args.paired_output != "-"
# Setup logging only if there are not already any handlers (can happen when
# this function is being called externally such as from unit tests)
if not logging.root.handlers:
setup_logging(stdout=log_to_stdout,
quiet=args.quiet,
minimal=args.report == 'minimal',
debug=args.debug)
if args.profile:
import cProfile
profiler = cProfile.Profile()
profiler.enable()
if args.quiet and args.report:
parser.error(
"Options --quiet and --report cannot be used at the same time")
if args.colorspace:
parser.error(
"These colorspace-specific options are no longer supported: "
"--colorspace, -c, -d, --double-encode, -t, --trim-primer, "
"--strip-f3, --maq, --bwa, --no-zero-cap. "
"Use Cutadapt 1.18 or earlier to work with colorspace data.")
paired = determine_paired_mode(args)
assert paired in (False, True)
# Print the header now because some of the functions below create logging output
log_header(cmdlineargs)
try:
is_interleaved_input, is_interleaved_output = determine_interleaved(
args)
input_filename, input_paired_filename = input_files_from_parsed_args(
args.inputs, paired, is_interleaved_input)
pipeline = pipeline_from_parsed_args(args, paired,
is_interleaved_output)
outfiles = open_output_files(args, default_outfile,
is_interleaved_output)
except CommandLineError as e:
parser.error(e)
return # avoid IDE warnings below
if args.cores < 0:
parser.error('Value for --cores cannot be negative')
cores = available_cpu_count() if args.cores == 0 else args.cores
if cores > 1:
if ParallelPipelineRunner.can_output_to(outfiles):
runner_class = ParallelPipelineRunner
runner_kwargs = dict(n_workers=cores, buffer_size=args.buffer_size)
else:
logger.error(
'Running in parallel is currently not supported for '
'the given combination of command-line parameters.\nThese '
'options are not supported: --info-file, --rest-file, '
'--wildcard-file, --untrimmed-output, '
'--untrimmed-paired-output, --too-short-output, '
'--too-short-paired-output, --too-long-output, '
'--too-long-paired-output, --format\n'
'Also, demultiplexing is not supported.\n'
'Omit --cores/-j to continue.')
return # avoid IDE warnings below
else:
runner_class = SerialPipelineRunner
runner_kwargs = dict()
infiles = InputFiles(input_filename,
file2=input_paired_filename,
interleaved=is_interleaved_input)
try:
runner = runner_class(pipeline, infiles, outfiles, **runner_kwargs)
except (dnaio.UnknownFileFormat, IOError) as e:
parser.error(e)
return # avoid IDE warnings below
logger.info("Processing reads on %d core%s in %s mode ...", cores,
's' if cores > 1 else '', {
False: 'single-end',
True: 'paired-end'
}[pipeline.paired])
try:
stats = runner.run()
runner.close()
except KeyboardInterrupt:
print("Interrupted", file=sys.stderr)
sys.exit(130)
except IOError as e:
if e.errno == errno.EPIPE:
sys.exit(1)
raise
except (dnaio.FileFormatError, dnaio.UnknownFileFormat, EOFError) as e:
sys.exit("cutadapt: error: {}".format(e))
elapsed = time.time() - start_time
if args.report == 'minimal':
report = minimal_report
else:
report = full_report
logger.log(REPORT, '%s', report(stats, elapsed, args.gc_content / 100))
if args.profile:
import pstats
profiler.disable()
pstats.Stats(profiler).sort_stats('time').print_stats(20)