panorama.utility package

Subpackages

• panorama.utility.translate package
  • Submodules
  • panorama.utility.translate.macsymodel_translator module
    • create_macsyfinder_hmm_list()
    • find_cluster_canonical()
    • find_type_subtype_canonical()
    • get_models_path()
    • parse_macsyfinder_hmm()
    • process_attributes()
    • process_exchangeable()
    • search_canonical_macsyfinder()
    • translate_functional_unit()
    • translate_gene()
    • translate_macsyfinder()
    • translate_macsyfinder_model()
  • panorama.utility.translate.padloc_translator module
    • _add_families_to_functional_unit()
    • parse_meta_padloc()
    • search_canonical_padloc()
    • translate_model_padloc()
    • translate_padloc()
  • panorama.utility.translate.translate module
    • HMMProcessingError
    • ModelTranslationError
    • launch_translate()
    • read_xml()
    • read_yaml()
    • write_model()
  • Module contents
    • ModelTranslationError
    • launch_translate()
    • read_xml()
    • read_yaml()

Submodules

panorama.utility.genInput module

panorama.utility.genInput.create_hmm_list_file(hmm_path: List[Path], output: Path, metadata_df: DataFrame = None, hmm_coverage: float = None, target_coverage: float = None, binary_hmm: bool = False, recursive: bool = False, force: bool = False, disable_bar: bool = False) → None

Creates a TSV file containing information about the given HMM files.

Parameters:

• hmm_path (List[Path]) – The paths to the HMM files.

• output (Path) – The path to the output directory.

• metadata_df (pd.DataFrame, optional) – The metadata dataframe. Defaults to None.

• hmm_coverage – Set a global value of HMM coverage threshold for all HMM. Defaults to None

• target_coverage – Set a global value of the target coverage threshold for all targets. Defaults to None

• binary_hmm – Rewrite the HMM in binary mode. Defaults False

• recursive (bool, optional) – Whether to search for HMM files recursively in the given directory. Defaults to False.

• force – Flag to erase and overwrite files in the output directory

• disable_bar (bool, optional) – Whether to disable the progress bar. Defaults to False.

Raises:

• FileNotFoundError – If any of the given paths are not found.

• Exception – If an unexpected error occurs.

Returns:

None

panorama.utility.genInput.generate_unique_accession(existing_accessions: Set[str]) → str

Generate a unique PANORAMA accession ID.

Parameters:

existing_accessions (Set) – Set of existing accession IDs to avoid duplicates

Returns:

str – Unique accession ID

panorama.utility.genInput.parse_hmm_info(hmm: HMM, panorama_acc: Set[str], metadata: DataFrame = None) → Dict[str, str | int]

Parse the hmm information and set the new value if needed

Parameters:

• hmm – hmm filled with information

• panorama_acc – Set of new accession number already given to not have duplicate

• metadata – metadata dataframe to fill information

Returns:

Dictionary with the parsed information

panorama.utility.genInput.process_hmm_accession(hmm: HMM, panorama_acc: Set[str], hmm_dict: Dict[str, str | int | float]) → Dict[str, str | int | float]

Process or generate HMM accession ID.

Parameters:

• hmm (HMM) – HMM object

• panorama_acc (Set) – Set of existing accession IDs

• hmm_dict (Dict) – HMM dictionary to update

Returns:

Dict – Updated HMM dictionary

panorama.utility.genInput.process_hmm_name(hmm: HMM, hmm_file: Path, hmm_dict: Dict[str, str | int | float]) → Dict[str, str | int | float]

Process HMM name from the HMM object and file path.

Parameters:

• hmm (HMM) – HMM object

• hmm_file (Path) – Path to HMM file

• hmm_dict (Dict) – HMM dictionary to update

Returns:

Dict – Updated HMM dictionary

Raises:

IOError – If HMM name cannot be determined

panorama.utility.genInput.read_hmm(hmm_path: Path) → List[HMM]

Read a HMM file to get a HMM object from pyHMMer.

Parameters:

hmm_path – Path to the HMM file.

Returns:

HMM object

Raises:

• Exception – if opening the HMM file failed

• IOError – if there is a problem in HMM reading

panorama.utility.genInput.read_metadata(metadata: Path) → DataFrame

Read metadata associate with HMM

Parameters:

metadata (Path) – path to the metadata file

Raises:

• FileNotFoundError – If the metadata path is not found.

• IOError – If the metadata path is not a file

• ValueError – If the number of fields is unexpected

• NameError – If the column names used in metadata are not allowed

Returns:

str – metadata dataframe with hmm information

panorama.utility.genInput.write_hmm(hmm: HMM, output: Path, binary: bool = False, name: bool = False) → Path

Write a HMM in text or binary

Parameters:

• hmm – hmm to write

• output – Path to the output directory

• binary – Flag to write the HMM in binary mode

• name – Flag to une the name of the HMM as file name rather than the accession number

Returns:

Path of the HMM file

panorama.utility.utility module

This module provides some utilities function

panorama.utility.utility.check_models(models_list: Path, disable_bar: bool = False) → Models

Checks all JSON files listed in models_list to ensure that they are valid models.

Parameters:

• models_list (Path) – paths to the models_list.tsv.

• disable_bar (bool, optional) – Whether to disable the progress bar. Defaults to False.

Returns

Models: A Models object to get all models

Raises:

Exception – If a model is not readable.

panorama.utility.utility.check_parameters(args: Namespace) → None

Checks the provided arguments to ensure that they are valid.

Parameters:

args – The parsed arguments.

Raises:

argparse.ArgumentError – If any required arguments are missing or invalid.

panorama.utility.utility.create_models_list(models_path: List[Path], output: Path, recursive: bool = False, disable_bar: bool = False) → None

Create a file that listing models and path to them. Also, models are checked

Parameters:

• models_path (List[Path]) – List of paths to models

• output (Path) – Directory to write models’ list file

• recursive (bool, optional) – Flag to read models directory recursively (default: False)

• disable_bar (bool, optional) – Flag to disable progress bar (default: False)

panorama.utility.utility.launch(args: Namespace)

Launches the utilities function for pangenomes.

Parameters:

args – The parsed arguments.

Returns:

None

panorama.utility.utility.parser_utils(parser: ArgumentParser)

Parser for the specific arguments of the utils command.

Parameters:

parser (argparse.ArgumentParser) – The parser for the utils command.

Returns:

None

panorama.utility.utility.subparser(sub_parser: _SubParsersAction) → ArgumentParser

Subparser to launch PANORAMA in the command line.

Parameters:

sub_parser (argparse._SubParsersAction) – The subparser for the utils command.

Returns:

argparse.ArgumentParser – The parser for the utils command.

Module contents