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def print_help():
print(f'''
{colour(f'...::: GTDB to NCBI Majority Vote v{__version__} :::...', ['bright'])}
{colour('All arguments are required from:', ['underscore'])}
{colour('--gtdbtk_output_dir', ['bright'])}
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_prefix', ['bright'])}
The prefix of the GTDB-Tk output files specified in --gtdbtk_output_dir.
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_prefix', ['bright'])}
The prefix of the GTDB-Tk output files specified in --gtdbtk_output_dir.
def print_help():
print(f'''
{colour(f'...::: GTDB to NCBI Majority Vote v{__version__} :::...', ['bright'])}
{colour('All arguments are required from:', ['underscore'])}
{colour('--gtdbtk_output_dir', ['bright'])}
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_prefix', ['bright'])}
The prefix of the GTDB-Tk output files specified in --gtdbtk_output_dir.
def print_help():
print(f'''
{colour(f'...::: GTDB to NCBI Majority Vote v{__version__} :::...', ['bright'])}
{colour('All arguments are required from:', ['underscore'])}
{colour('--gtdbtk_output_dir', ['bright'])}
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_output_dir', ['bright'])}
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_prefix', ['bright'])}
The prefix of the GTDB-Tk output files specified in --gtdbtk_output_dir.
def _check_package_compatibility(self):
"""Check that GTDB-Tk is using the most up-to-date reference package."""
pkg_ver = float(Config.VERSION_DATA.replace('r', ''))
min_ver = float(Config.MIN_REF_DATA_VERSION.replace('r', ''))
self.logger.info('Using GTDB-Tk reference data version {}: {}'
.format(Config.VERSION_DATA, Config.GENERIC_PATH))
if pkg_ver < min_ver:
self.logger.warning(colour('You are not using the reference data '
'intended for this release: {}'
.format(Config.MIN_REF_DATA_VERSION),
['bright'], fg='yellow'))
def print_help():
print(f'''
{colour(f'...::: GTDB to NCBI Majority Vote v{__version__} :::...', ['bright'])}
{colour('All arguments are required from:', ['underscore'])}
{colour('--gtdbtk_output_dir', ['bright'])}
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_prefix', ['bright'])}
def print_help():
print(f'''
{colour(f'...::: GTDB to NCBI Majority Vote v{__version__} :::...', ['bright'])}
{colour('All arguments are required from:', ['underscore'])}
{colour('--gtdbtk_output_dir', ['bright'])}
The output directory produced by the GTDB-Tk classify workflow.
{colour('--output_file', ['bright'])}
The output file to write the translated taxonomy.
{colour('At least one argument is required from:', ['underscore'])}
{colour('--ar122_metadata_file', ['bright'])}
The archaeal GTDB metadata file (if processing archaeal genomes).
{colour('--bac120_metadata_file', ['bright'])}
The bacterial GTDB metadata file (if processing bacterial genomes).
NOTE: Metadata files are available for download from the GTDB repository
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ar122_metadata.tsv
https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_metadata.tsv
{colour('Optional arguments:', ['underscore'])}
{colour('--gtdbtk_prefix', ['bright'])}
The prefix of the GTDB-Tk output files specified in --gtdbtk_output_dir.