def main(args=None):
if args is None:
args = sys.argv[1:]
# Set the default level
bioconvert.logger.level = "ERROR"
# Changing the log level before argparse is run
try:
bioconvert.logger.level = args[args.index("-l") + 1]
except:
pass
try:
bioconvert.logger.level = args[args.index("--level") + 1]
except:
pass
try:
bioconvert.logger.level = args[args.index("-v") + 1]
except:
pass
try:
bioconvert.logger.level = args[args.index("--verbosity") + 1]
except:
pass
allow_indirect_conversion = False
try:
args.index("--allow-indirect-conversion")
allow_indirect_conversion = True
except:
pass
try:
args.index("-a")
allow_indirect_conversion = True
except:
pass
arg_parser = argparse.ArgumentParser(
prog="bioconvert",
description="""Convertor infer the
formats from the first command. We do
not scan the input file. Therefore
users must ensure that their input
format files are properly
formatted.""",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
Bioconvert contains tens of converters whose list is available as follows:
bioconvert --help
Each conversion has its own sub-command and dedicated help. For instance:
bioconvert fastq2fasta --help
Because the subcommand contains the format, extensions are not important
for the conversion itself. This would convert the test.txt file (fastq
format) into a fasta file:
bioconvert fastq2fasta test.txt test.fasta
Users must ensure that their input format files are properly formatted.
If there is a conversion from A to B and another for B to C, you can also
perform indirect conversion using -a argument (experimental). This command
shows all possible indirect conversions:
bioconvert --help -a
Please visit http://bioconvert.readthedocs.org for more information about the
project or formats available.
Bioconvert is an open source collaborative project. Please feel free to
join us at https://github/biokit/bioconvert
""")
registry = Registry()
subparsers = arg_parser.add_subparsers(
help='sub-command help',
dest='command',
)
max_converter_width = 2 + max(
[len(in_fmt) for in_fmt, _, _, _ in registry.iter_converters()])
# show all possible conversion
for in_fmt, out_fmt, converter, path in \
sorted(registry.iter_converters(allow_indirect_conversion)):
sub_parser_name = "{}2{}".format(in_fmt.lower(), out_fmt.lower())
if converter:
link_char = '-'
if len(converter.available_methods) <= 1:
help_details = ""
else:
help_details = " (%i methods)" % len(
converter.available_methods)
else: #if path:
link_char = '~'
if len(path) == 3:
help_details = " (w/ 1 intermediate)"
else:
help_details = " (w/ %i intermediates)" % (len(path) - 2)
help_text = '%sto%s> %s%s' % (
(in_fmt + ' ').ljust(max_converter_width, link_char),
link_char,
out_fmt,
help_details,
)
sub_parser = subparsers.add_parser(
sub_parser_name,
help=help_text,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
# aliases=["{}_to_{}".format(in_fmt.lower(), out_fmt.lower()), ],
epilog="""Bioconvert is an open source collaborative project.
Please feel free to join us at https://github/biokit/bioconvert
""",
)
if converter:
converter.add_argument_to_parser(sub_parser=sub_parser)
elif path:
for a in ConvBase.get_common_arguments():
a.add_to_sub_parser(sub_parser)
arg_parser.add_argument(
"-v",
"--verbosity",
default=bioconvert.logger.level,
help="Set the outpout verbosity.",
choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
)
arg_parser.add_argument(
"--dependency-report",
action="store_true",
default=False,
help="Output all bioconvert dependencies in json and exit")
arg_parser.add_argument("-a",
"--allow-indirect-conversion",
action="store_true",
help="Show all possible indirect conversions "
"(labelled as intermediate) (EXPERIMENTAL)")
arg_parser.add_argument("--version",
action="store_true",
default=False,
help="Show version")
arg_parser.add_argument(
"--conversion-graph",
nargs="?",
default=None,
choices=[
"cytoscape",
"cytoscape-all",
],
)
try:
args = arg_parser.parse_args(args)
except SystemExit as e:
# parsing ask to stop, maybe a normal exit
if e.code == 0:
raise e
# Parsing failed, trying to guess command
from bioconvert.core.levenshtein import wf_levenshtein as lev
sub_command = None
args_i = 0
while sub_command is None and args_i < len(args):
if args[args_i][0] != '-' and (
args_i == 0 or args[args_i - 1] != '-v'
and args[args_i - 1] != '--verbose'
and args[args_i - 1] != '--conversion-graph'):
sub_command = args[args_i]
args_i += 1
if sub_command is None:
# No sub_command found, so letting the initial exception be risen
raise e
conversions = []
for in_fmt, out_fmt, converter, path in registry.iter_converters(
allow_indirect_conversion):
conversion_name = "{}2{}".format(in_fmt.lower(), out_fmt.lower())
conversions.append((lev(conversion_name,
sub_command), conversion_name))
matches = sorted(conversions)[:5]
if matches[0][0] == 0:
# sub_command was ok, problem comes from elswhere
raise e
arg_parser.exit(
e.code, '\n\nYour converter {}() was not found. \n'
'Here is a list of possible matches: {} ... '
'\nYou may also add the -a argument to enfore a '
'transitive conversion. The whole list is available using\n\n'
' bioconvert --help -a \n'.format(
sub_command, ', '.join([v for _, v in matches])))
if args.version:
print("{}".format(bioconvert.version))
sys.exit(0)
if args.dependency_report:
print(
json.dumps(
get_known_dependencies_with_availability(as_dict=True),
sort_keys=True,
indent=4,
))
sys.exit(0)
if args.conversion_graph:
if args.conversion_graph.startswith("cytoscape"):
all_converter = args.conversion_graph == "cytoscape-all"
print(
json.dumps(
graph.create_graph_for_cytoscape(
all_converter=all_converter),
indent=4,
))
sys.exit(0)
if args.command is None:
msg = 'No converter specified. You can list converter by doing bioconvert --help'
arg_parser.error(msg)
if not (getattr(args, "show_methods", False) or args.input_file):
arg_parser.error('Either specify an input_file (<INPUT_FILE>) or '
'ask for available methods (--show-method)')
if not args.allow_indirect_conversion and \
ConvMeta.split_converter_to_extensions(args.command) not in registry:
arg_parser.error('The conversion %s is not available directly, '
'you have to accept that we chain converter to do'
' so (--allow-indirect-conversion or -a)' %
args.command)
args.raise_exception = args.raise_exception or args.verbosity == "DEBUG"
# Set the logging level
bioconvert.logger.level = args.verbosity
# Figure out whether we have several input files or not
# Are we in batch mode ?
import glob
if args.batch:
filenames = glob.glob(args.input_file)
else:
filenames = [args.input_file]
for filename in filenames:
args.input_file = filename
try:
analysis(args)
except Exception as e:
if args.raise_exception:
raise e
else:
bioconvert.logger.error(e)
sys.exit(1)
def analysis(args):
in_fmt, out_fmt = ConvMeta.split_converter_to_extensions(args.command)
# do we want to know the available methods ? If so, print info and quit
if getattr(args, "show_methods", False):
class_converter = Registry()[(in_fmt, out_fmt)]
print("Methods available: {}".format(
class_converter.available_methods))
print("\nPlease see http://bioconvert.readthedocs.io/en/master/"
"references.html#{} for details ".format(
str(class_converter).split("'")[1]))
if args.raise_exception:
return
sys.exit(0)
# Input and output filename
infile = args.input_file
if args.output_file is None and infile:
outext = ConvMeta.split_converter_to_extensions(args.command)
outfile = infile.rsplit(".", 1)[0] + "." + outext[1].lower()
else:
outfile = args.output_file
# Call a generic wrapper of all available conversion
conv = Bioconvert(
infile,
outfile,
in_fmt=in_fmt,
out_fmt=out_fmt,
force=args.force,
)
# # Users may provide information about the input file.
# # Indeed, the input may be a FastQ file but with an extension
# # that is not standard. For instance fq instead of fastq
# # If so, we can use the --input-format fastq to overwrite the
# # provided filename extension
# no need to do this
# if args.input_format:
# inext = args.input_format
# if not conv.inext.startswith("."):
# conv.inext = "." + inext
if not conv.in_fmt:
raise RuntimeError("convert infer the format from the extension name."
" So add extension to the input file name or use"
" --input-format option.")
if not conv.out_fmt:
raise RuntimeError("convert infer the format from the extension name."
" So add extension to the output file name or use"
" --output-format option.")
bioconvert.logger.info("Converting from %s to %s" %
(conv.in_fmt, conv.out_fmt))
# params = {"threads": args.threads}
if args.benchmark:
conv.boxplot_benchmark(N=args.benchmark_N)
import pylab
try:
pylab.savefig("benchmark_{}.png".format(conv.name))
except:
pylab.savefig("benchmark_{}.png".format(conv.converter.name))
else:
# params["method"] = args.method
conv(**vars(args))