def parse_arguments():
parser = argparse.ArgumentParser(
prog='CAT bin',
description='Run Bin Annotation Tool (BAT) on a single bin.',
usage='CAT bin -b -d -t [options] [-h / --help]',
add_help=False)
required = parser.add_argument_group('Required arguments')
shared.add_argument(required, 'bin_fasta', True)
shared.add_argument(required, 'database_folder', True)
shared.add_argument(required, 'taxonomy_folder', True)
optional = parser.add_argument_group('Optional arguments')
shared.add_argument(optional, 'r', False, default=decimal.Decimal(5))
shared.add_argument(optional, 'f', False, default=decimal.Decimal(0.3))
shared.add_argument(optional, 'out_prefix', False, default='./out.BAT')
shared.add_argument(optional, 'proteins_fasta', False)
shared.add_argument(optional, 'alignment_file', False)
shared.add_argument(optional,
'path_to_prodigal',
False,
default='prodigal')
shared.add_argument(optional, 'path_to_diamond', False, default='diamond')
shared.add_argument(optional, 'no_stars', False)
shared.add_argument(optional, 'force', False)
shared.add_argument(optional, 'quiet', False)
shared.add_argument(optional, 'verbose', False)
shared.add_argument(optional, 'no_log', False)
shared.add_argument(optional, 'help', False)
shared.add_argument(optional, 'IkwId', False)
specific = parser.add_argument_group('DIAMOND specific optional arguments')
shared.add_all_diamond_arguments(specific)
(args, extra_args) = parser.parse_known_args()
extra_args = [
arg for (i, arg) in enumerate(extra_args) if (i, arg) != (0, 'bin')
]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Check experimental features.
if not args.IkwId:
if args.top < 50:
sys.exit('error: --top can only be set lower than 50 in '
'combination with the --I_know_what_Im_doing flag. See '
'README.md as to why this is the case.')
# Add extra arguments.
shared.expand_arguments(args)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='CAT add_names',
description='Add taxonomic names to CAT or BAT output files.',
usage='CAT add_names -i -o -t [options] [-h / --help]',
add_help=False)
required = parser.add_argument_group('Required arguments')
shared.add_argument(
required,
'input_file',
True,
help_=('Path to input file. Can be classification or ORF2LCA '
'output file from CAT or BAT.'))
shared.add_argument(required, 'output_file', True)
shared.add_argument(required, 'taxonomy_folder', True)
optional = parser.add_argument_group('Optional arguments')
shared.add_argument(optional, 'only_official', False)
shared.add_argument(optional, 'exclude_scores', False)
shared.add_argument(optional, 'force', False)
shared.add_argument(optional, 'quiet', False)
shared.add_argument(optional, 'help', False)
(args, extra_args) = parser.parse_known_args()
extra_args = [
arg for (i, arg) in enumerate(extra_args)
if (i, arg) != (0, 'add_names')
]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Add extra arguments.
shared.expand_arguments(args)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='CAT summarise',
description='Summarise a named CAT or BAT classification file.',
usage='CAT summarise -i -o (-c) [options] [-h / --help]',
add_help=False)
required = parser.add_argument_group('Required arguments')
required.add_argument(
'-i',
'--input_file',
dest='input_file',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help=('Path to named CAT contig classification file or BAT bin '
'classification file. Currently only official ranks are '
'supported, and only classification files containing a single '
'classification per contig / bin.'))
required.add_argument('-o',
'--output_file',
dest='output_file',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help='Path to output file.')
optional = parser.add_argument_group('Optional arguments')
optional.add_argument(
'-c',
'--contigs_fasta',
dest='contigs_fasta',
metavar='',
required=False,
type=str,
action=shared.PathAction,
help=('Path to contigs fasta file. This is required if you want '
'to summarise a contig classification file.'))
optional.add_argument('--force',
dest='force',
required=False,
action='store_true',
help='Force overwrite existing files.')
optional.add_argument('-q',
'--quiet',
dest='quiet',
required=False,
action='store_true',
help='Suppress verbosity.')
optional.add_argument('-h',
'--help',
action='help',
help='Show this help message and exit.')
(args, extra_args) = parser.parse_known_args()
extra_args = [
arg for (i, arg) in enumerate(extra_args)
if (i, arg) != (0, 'summarise')
]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Add extra arguments.
shared.expand_arguments(args)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='CAT add_names',
description='Add taxonomic names to CAT or BAT output files.',
usage='CAT add_names -i -o -t [options] [-h / --help]',
add_help=False)
required = parser.add_argument_group('Required arguments')
required.add_argument(
'-i',
'--input_file',
dest='input_file',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help=('Path to input file. Can be either classification output '
'file or ORF2LCA output file.'))
required.add_argument('-o',
'--output_file',
dest='output_file',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help='Path to output file.')
required.add_argument('-t',
'--taxonomy_folder',
dest='taxonomy_folder',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help='Path to folder that contains taxonomy files.')
optional = parser.add_argument_group('Optional arguments')
optional.add_argument(
'--only_official',
dest='only_official',
required=False,
action='store_true',
help=('Only output official rank names (i.e., superkingdom, '
'phylum, class, order, family, genus, species).'))
optional.add_argument(
'--exclude_scores',
dest='exclude_scores',
required=False,
action='store_true',
help=('Do not include bit-score support scores in the lineage of '
'a classification output file.'))
optional.add_argument('--force',
dest='force',
required=False,
action='store_true',
help='Force overwrite existing files.')
optional.add_argument('-q',
'--quiet',
dest='quiet',
required=False,
action='store_true',
help='Suppress verbosity.')
optional.add_argument('-h',
'--help',
action='help',
help='Show this help message and exit.')
(args, extra_args) = parser.parse_known_args()
extra_args = [
arg for (i, arg) in enumerate(extra_args)
if (i, arg) != (0, 'add_names')
]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Add extra arguments.
shared.expand_arguments(args)
return args
def parse_arguments():
parser = argparse.ArgumentParser(
prog='CAT bins',
description='Run Bin Annotation Tool (BAT) on a set of bins.',
usage='CAT bins -b -d -t [options] [-h / --help]',
add_help=False)
required = parser.add_argument_group('Required arguments')
shared.add_argument(required, 'bin_folder', True)
shared.add_argument(required, 'database_folder', True)
shared.add_argument(required, 'taxonomy_folder', True)
optional = parser.add_argument_group('Optional arguments')
shared.add_argument(optional, 'bin_suffix', False, default='.fna')
shared.add_argument(optional, 'r', False, default=decimal.Decimal(5))
shared.add_argument(optional, 'f', False, default=decimal.Decimal(0.3))
shared.add_argument(optional, 'out_prefix', False, default='./out.BAT')
shared.add_argument(optional, 'proteins_fasta', False,
help_=(
'Path to concatenated predicted proteins fasta file '
'generated during an earlier run of BAT on the same bins. If '
'supplied, BAT will skip the protein prediction step.'))
shared.add_argument(optional, 'alignment_file', False,
help_=(
'Path to alignment table generated during an earlier run of '
'BAT on the same bins. If supplied, BAT will skip the '
'alignment step and directly classify the bins. A '
'concatenated predicted proteins fasta file should also be '
'supplied with argument [-p / --proteins].'))
shared.add_argument(optional, 'path_to_prodigal', False,
default='prodigal')
shared.add_argument(optional, 'path_to_diamond', False, default='diamond')
shared.add_argument(optional, 'no_stars', False)
shared.add_argument(optional, 'force', False)
shared.add_argument(optional, 'quiet', False)
shared.add_argument(optional, 'verbose', False)
shared.add_argument(optional, 'no_log', False)
shared.add_argument(optional, 'help', False)
shared.add_argument(optional, 'IkwId', False)
specific = parser.add_argument_group('DIAMOND specific optional arguments')
shared.add_all_diamond_arguments(specific)
(args, extra_args) = parser.parse_known_args()
extra_args = [arg for (i, arg) in enumerate(extra_args) if
(i, arg) != (0, 'bins')]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Check experimental features.
if not args.IkwId:
if args.top < 50:
sys.exit('error: --top can only be set lower than 50 in '
'combination with the --I_know_what_Im_doing flag. See '
'README.md as to why this is the case.')
# Add extra arguments.
shared.expand_arguments(args)
return args
def parse_arguments():
date = datetime.datetime.now().strftime('%Y-%m-%d')
parser = argparse.ArgumentParser(
prog='CAT prepare',
description='Download and construct CAT/BAT database files.',
usage=('CAT prepare (--fresh | --existing) '
'[options] [-h / --help]'),
add_help=False)
required_choice = parser.add_argument_group('Required choice')
group = required_choice.add_mutually_exclusive_group(required=True)
group.add_argument('--fresh',
dest='fresh',
action='store_true',
help='Start with a fresh database.')
group.add_argument(
'--existing',
dest='fresh',
action='store_false',
help=('Start with an existing database. CAT will search the '
'supplied database and taxonomy folders and only construct '
'files that do not exist yet.'))
optional = parser.add_argument_group('Optional arguments')
shared.add_argument(
optional,
'database_folder',
False,
default='./CAT_database.{0}'.format(date),
help_=('Name of folder to which database files will be written '
'(default: CAT_database.{date})'))
shared.add_argument(
optional,
'taxonomy_folder',
False,
default='./CAT_taxonomy.{0}'.format(date),
help_=('Name of folder to which taxonomy files will be downloaded '
'(default: CAT_taxonomy.{date})'))
shared.add_argument(optional, 'path_to_diamond', False, default='diamond')
shared.add_argument(optional, 'quiet', False)
shared.add_argument(optional, 'verbose', False)
shared.add_argument(optional, 'no_log', False)
shared.add_argument(optional, 'help', False)
specific = parser.add_argument_group('DIAMOND specific optional arguments')
shared.add_argument(specific,
'nproc',
False,
default=multiprocessing.cpu_count())
(args, extra_args) = parser.parse_known_args()
extra_args = [
arg for (i, arg) in enumerate(extra_args) if (i, arg) != (0, 'prepare')
]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Add extra arguments.
setattr(args, 'date', date)
setattr(args, 'min_mem', 200)
shared.expand_arguments(args)
return (args)
def parse_arguments():
date = datetime.datetime.now().strftime('%Y-%m-%d')
parser = argparse.ArgumentParser(
prog='CAT prepare',
description='Download and construct CAT/BAT database files.',
usage=('CAT prepare (--fresh | --existing) '
'[options] [-h / --help]'),
add_help=False)
required_choice = parser.add_argument_group('Required choice')
group = required_choice.add_mutually_exclusive_group(required=True)
group.add_argument('--fresh',
dest='fresh',
action='store_true',
help='Start with a fresh database.')
group.add_argument(
'--existing',
dest='fresh',
action='store_false',
help=('Start with an existing database. CAT will search the '
'supplied database and taxonomy folders and only construct '
'files that do not exist yet.'))
optional = parser.add_argument_group('Optional arguments')
optional.add_argument(
'-d',
'--database_folder',
dest='database_folder',
metavar='',
required=False,
type=str,
action=shared.PathAction,
default='./{0}_CAT_database'.format(date),
help=('Name of folder to which database files will be written '
'(default: {date}_CAT_database).'))
optional.add_argument(
'-t',
'--taxonomy_folder',
dest='taxonomy_folder',
metavar='',
required=False,
type=str,
action=shared.PathAction,
default='./{0}_taxonomy'.format(date),
help=('Name of folder to which taxonomy files will be downloaded '
'(default: {date}_taxonomy).'))
optional.add_argument(
'--path_to_diamond',
dest='path_to_diamond',
metavar='',
required=False,
type=str,
action=shared.PathAction,
default='diamond',
help=('Path to DIAMOND binaries. Supply if CAT prepare can not '
'find DIAMOND.'))
optional.add_argument('-q',
'--quiet',
dest='quiet',
required=False,
action='store_true',
help='Suppress verbosity.')
optional.add_argument('--verbose',
dest='verbose',
required=False,
action='store_true',
help='Increase verbostity.')
optional.add_argument('--no_log',
dest='no_log',
required=False,
action='store_true',
help='Suppress log file.')
optional.add_argument('-h',
'--help',
action='help',
help='Show this help message and exit.')
specific = parser.add_argument_group('DIAMOND specific optional arguments')
specific.add_argument('-n',
'--nproc',
dest='nproc',
metavar='',
required=False,
type=int,
default=multiprocessing.cpu_count(),
help=('Number of cores to deploy by DIAMOND makedb '
'(default: maximum).'))
(args, extra_args) = parser.parse_known_args()
extra_args = [
arg for (i, arg) in enumerate(extra_args) if (i, arg) != (0, 'prepare')
]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Add extra arguments.
setattr(args, 'date', date)
setattr(args, 'min_mem', 200)
shared.expand_arguments(args)
return (args)
def parse_arguments():
parser = argparse.ArgumentParser(
prog='CAT bins',
description='Run Bin Annotation Tool (BAT) on a set of bins.',
usage='CAT bins -b -d -t [options] [-h / --help]',
add_help=False)
required = parser.add_argument_group('Required arguments')
required.add_argument(
'-b',
'--bin_folder',
dest='bin_folder',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help='Path to directory containing bins.')
required.add_argument(
'-d',
'--database_folder',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help='Path to folder that contains database files.')
required.add_argument(
'-t',
'--taxonomy_folder',
dest='taxonomy_folder',
metavar='',
required=True,
type=str,
action=shared.PathAction,
help='Path to folder that contains taxonomy files.')
optional = parser.add_argument_group('Optional arguments')
optional.add_argument(
'-s',
'--bin_suffix',
dest='bin_suffix',
metavar='',
required=False,
type=str,
default='.fna',
help='Suffix of bins in bin folder (default: .fna).')
optional.add_argument(
'-r',
'--range',
dest='r',
metavar='',
required=False,
type=float,
choices = [i for i in range(50)],
action=shared.DecimalAction,
default=decimal.Decimal(5),
help='r parameter [0-49] (default: 5).')
optional.add_argument(
'-f',
'--fraction',
dest='f',
metavar='',
required=False,
type=float,
choices = [i / 100 for i in range(0, 100)],
action=shared.DecimalAction,
default=decimal.Decimal(0.3),
help='f parameter [0-0.99] (default: 0.3).')
optional.add_argument(
'-o',
'--out_prefix',
dest='out_prefix',
metavar='',
required=False,
type=str,
action=shared.PathAction,
default='./out.BAT',
help='Prefix for output files (default: out.BAT).')
optional.add_argument(
'-p',
'--proteins_fasta',
dest='proteins_fasta',
metavar='',
required=False,
type=str,
action=shared.PathAction,
help=('Path to concatenated predicted proteins fasta file '
'generated during an earlier run of BAT. If supplied, BAT '
'will skip the protein prediction step.'))
optional.add_argument(
'-a',
'--diamond_alignment',
dest='alignment_file',
metavar='',
required=False,
type=str,
action=shared.PathAction,
help=('Path to alignment table generated during an earlier run of '
'BAT. If supplied, BAT will skip the alignment step and '
'directly classify the bins. A concatenated predicted '
'proteins fasta file should also be supplied with argument '
'[-p / --proteins].'))
optional.add_argument(
'--path_to_prodigal',
dest='path_to_prodigal',
metavar='',
required=False,
type=str,
action=shared.PathAction,
default='prodigal',
help=('Path to Prodigal binaries. Supply if BAT can not find '
'Prodigal.'))
optional.add_argument(
'--path_to_diamond',
dest='path_to_diamond',
metavar='',
required=False,
type=str,
action=shared.PathAction,
default='diamond',
help=('Path to DIAMOND binaries. Supply if BAT can not find '
'DIAMOND.'))
optional.add_argument(
'--no_stars',
dest='no_stars',
required=False,
action='store_true',
help='Suppress marking of suggestive taxonomic assignments.')
optional.add_argument(
'--force',
dest='force',
required=False,
action='store_true',
help='Force overwrite existing files.')
optional.add_argument(
'-q',
'--quiet',
dest='quiet',
required=False,
action='store_true',
help='Suppress verbosity.')
optional.add_argument(
'--verbose',
dest='verbose',
required=False,
action='store_true',
help='Increase verbosity.')
optional.add_argument(
'--no_log',
dest='no_log',
required=False,
action='store_true',
help='Suppress log file.')
optional.add_argument(
'-h',
'--help',
action='help',
help='Show this help message and exit.')
optional.add_argument(
'--I_know_what_Im_doing',
dest='IkwId',
required=False,
action='store_true',
help='Flag for experimental features.')
specific = parser.add_argument_group('DIAMOND specific optional arguments')
specific.add_argument(
'-n',
'--nproc',
dest='nproc',
metavar='',
required=False,
type=int,
default=multiprocessing.cpu_count(),
help='Number of cores to deploy by DIAMOND (default: maximum).')
specific.add_argument(
'--sensitive',
dest='sensitive',
required=False,
action='store_true',
help='Run DIAMOND in sensitive mode (default: not enabled).')
specific.add_argument(
'--block_size',
dest='block_size',
metavar='',
required=False,
type=float,
default=2.0,
help=('DIAMOND block-size parameter (default: 2.0). Lower numbers '
'will decrease memory and temporary disk space usage.'))
specific.add_argument(
'--index_chunks',
dest='index_chunks',
metavar='',
required=False,
type=int,
default=4,
help=('DIAMOND index-chunks parameter (default: 4). Set to 1 on '
'high memory machines. The parameter has no effect on '
'temporary disk space usage.'))
specific.add_argument(
'--tmpdir',
dest='tmpdir',
metavar='',
required=False,
type=str,
action=shared.PathAction,
help=('Directory for temporary DIAMOND files (default: directory '
'to which output files are written).'))
specific.add_argument(
'--compress',
dest='compress',
required=False,
action='store_true',
help='Compress DIAMOND alignment file.')
specific.add_argument(
'--top',
dest='top',
metavar='',
required=False,
type=float,
choices = [i for i in range(51)],
default=50,
help=('DIAMOND top parameter [0-50] (default: 50). Governs hits '
'within range of best hit that are written to the alignment '
'file. This is not the [-r / --range] parameter! Can only be '
'set with the [--I_know_what_Im_doing] flag, see README.md.'))
(args, extra_args) = parser.parse_known_args()
extra_args = [arg for (i, arg) in enumerate(extra_args) if
(i, arg) != (0, 'bins')]
if len(extra_args) > 0:
sys.exit('error: too much arguments supplied:\n{0}'.format(
'\n'.join(extra_args)))
# Check experimental features.
if not args.IkwId:
if args.top < 50:
sys.exit('error: --top can only be set lower than 50 in '
'combination with the --I_know_what_Im_doing flag. See '
'README.md as to why this is the case.')
# Add extra arguments.
shared.expand_arguments(args)
return args