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 main(args=None):
# used later on
registry = Registry()
if args is None:
args = sys.argv[1:]
# convenient variable to check implicit/explicit mode and
# get information about the arguments.
ph = ParserHelper(args)
if not len(sys.argv) == 1:
if ph.mode == "implicit":
# Check that the input file exists
# Fixes https://github.com/bioconvert/bioconvert/issues/204
if os.path.exists(args[0]) is False:
_log.error("First input file {} does not exist".format(
args[0]))
sys.exit(1)
# list of filenames from which we get the extensions
filenames = ph.get_filelist()
exts = [
utils.get_extension(x, remove_compression=True)
for x in filenames
]
# We need to get the corresponding converter if any.
# We assume that the input formats are ordered alphabetically
# (bioconvert API).
# For instance fasta,qual to fastq can be
# found but qual,fasta to fastq cannot. Indeed, in more complex
# cases such as a,b -> c,d we cannot know whether there are 1 or 3
# inputs. This would require extra code here below
try:
L = len(exts)
converter = []
# if input is a,b,c,d we want to try a->(b,c,d) and
# (a,b)->(c,d) and (a,b,c)-> c so L-1 case
for i in range(1, L):
in_ext = tuple(exts[0:i])
out_ext = tuple(exts[i:])
try:
converter.extend(registry.get_ext((in_ext, out_ext)))
except KeyError:
pass
except KeyError:
converter = []
# For 1-to-1, if the extensions are identical but different
# compression, this means we just want to decompress and
# re-compress in another format.
if not converter and (exts[0] == exts[1]):
exts_with_comp = [
utils.get_extension(x, remove_compression=False)
for x in filenames
]
in_ext, out_ext = exts_with_comp[0], exts_with_comp[1]
comps = ['gz', 'dsrc', 'bz2']
if in_ext in comps and out_ext in comps:
converter.extend(
registry.get_ext(((in_ext, ), (out_ext, ))))
# if no converter is found, print information
if not converter:
msg = '\nBioconvert does not support conversion {} -> {}. \n\n'
msg = msg.format(in_ext, out_ext)
# maybe it is an indirect conversion ? let us look at the
# digraph
try:
_path = registry._path_dict_ext[in_ext][out_ext]
#Here, we have a transitive list of tuples to go from A to C
# example from fq to clustal returns:
# [('fq',), ('fa',), ('clustal',)]
# If we naively build the converter from those names
# (fq2clustal), this is a non official converter name. The
# official one is fastq2clustal, so we need some hack here:
in_name, int_name, out_name = _path
a = registry._ext_registry[
in_name, int_name][0].__name__.split("2")[0]
b = registry._ext_registry[
int_name, out_name][0].__name__.split("2")[1]
convname = "2".join([a, b]).lower()
msg += "\n".join(
textwrap.wrap(
"Note, however, that an indirect conversion through"
" an intermediate format is possible for your input and "
" output format. To do so, you need to use the -a option "
" and be explicit about the type of conversion. To get "
" the list of possible direct and indirect conversion, "
" please use:\n\n"))
msg += "\n\n bioconvert --help -a\n\n"
msg += "For help and with your input/output most probably"
msg += "the command should be: \n\n bioconvert {} {} -a\n\n ".format(
convname, " ".join(ph.get_filelist()))
except KeyError:
pass # not converter found in the path
error(msg)
# if the ext_pair matches a single converter
elif len(converter) == 1:
args.insert(0, converter[0].__name__.lower())
# if the ext_pair matches multiple converters
else:
_log.error("Ambiguous extension.\n"
"You must specify the right conversion Please "
"choose a conversion from: \n\n"
"{}".format("\n".join(
[c.__name__.lower() for c in converter])))
sys.exit(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
# if there is the ability to convert from A to B to C, we must set
# the option -a (--allow_indirect_conversion)
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
# Now, the instanciation of the main bioconvert user interface
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
If you use known extensions, the converter may be omitted::
bioconvert test.fastq 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. Would you wish to help, please join our open
source collaborative project at https://github/bioconvert/bioconvert
""")
subparsers = arg_parser.add_subparsers(
help='sub-command help',
dest='converter',
)
max_converter_width = 2 + max(
[len(in_fmt) for in_fmt, _, _, _ in registry.iter_converters()])
def sorting_tuple_string(item):
if type(item) is tuple:
return item[0][0]
if type(item) is str:
return item[0]
# show all possible conversion including indirect conversion
for in_fmt, out_fmt, converter, path in \
sorted(registry.iter_converters(allow_indirect_conversion), key=sorting_tuple_string):
in_fmt = ConvBase.lower_tuple(in_fmt)
in_fmt = ["_".join(in_fmt)]
out_fmt = ConvBase.lower_tuple(out_fmt)
out_fmt = ["_".join(out_fmt)]
sub_parser_name = "{}2{}".format("_".join(in_fmt), "_".join(out_fmt))
if converter:
link_char = '-'
if len(converter.available_methods) < 1:
help_details = " (no available methods please see the doc" \
" for install the necessary libraries) "
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 = '{}to{}> {}{}'.format(
("_".join(in_fmt) + ' ').ljust(max_converter_width, link_char),
link_char,
("_".join(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_IO_arguments():
a.add_to_sub_parser(sub_parser)
for a in ConvBase.get_common_arguments():
a.add_to_sub_parser(sub_parser)
# arguments when no explicit conversion provided.
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(
"-l",
"--level",
default=bioconvert.logger.level,
help="Set the outpout verbosity. Same as --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)")
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 converter
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):
in_fmt = ConvBase.lower_tuple(in_fmt)
in_fmt = ["_".join(in_fmt)]
out_fmt = ConvBase.lower_tuple(out_fmt)
out_fmt = ["_".join(out_fmt)]
conversion_name = "{}2{}".format("_".join(in_fmt),
"_".join(out_fmt))
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.converter is None:
msg = "No converter specified. "
msg += "You can list all converters by using:\n\n\tbioconvert --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_format(args.converter) not in registry:
arg_parser.error('The conversion {} is not available directly, '
'you have to accept that we chain converter to do'
' so (--allow-indirect-conversion or -a)'.format(
args.converter))
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 ?
if args.batch:
filenames = glob.glob(args.input_file)
else:
filenames = [args.input_file]
N = len(filenames)
for i, filename in enumerate(filenames):
if N > 1:
_log.info("Converting {} ({}/{})".format(filename, i + 1, N))
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)