DENOFO Utils

The DENOFO Utils module provides utility functions for working with the DENOFO annotation format and other related tasks distributed over three submodules:

Constants

class denofo.utils.constants.GoQBack

Class to return if the user wants to go back to the previous question.

Helpers

denofo.utils.helpers.add_extension(file_path: Path, extension: str = 'dngf') → Path

Add an extension to a file path if it does not already have one.

Parameters:

  • file_path (Path) – The file path.

  • extension (str) – The extension to add.

Returns:

The file path with the extension added.

Return type:

Path

denofo.utils.helpers.compare_two_models(dngf1: BaseModel, dngf2: BaseModel, mode: str = 'differences') → list[tuple]

Compare two BaseModel objects.

Parameters:

  • dngf1 (BaseModel) – The first BaseModel object.

  • dngf2 (BaseModel) – The second BaseModel object.

  • mode (str) – The mode of comparison. Options: ‘differences’ (default) or ‘similarities’.

  • name1 (str) – The name of the first BaseModel object in output.

  • name2 (str) – The name of the second BaseModel object in output.

Returns:

The comparison result.

Return type:

list[tuple[str]]

denofo.utils.helpers.diff_two_lists(list1: list, list2: list, model_name: str, field_name: str, mode: str = 'differences') → list

Compare two lists.

Parameters:

  • list1 (list) – The first list.

  • list2 (list) – The second list.

Returns:

The comparison result.

Return type:

list

denofo.utils.helpers.different_answers(answer: any, prev_answer: any) → bool

Check if new answer differs from previously given answer.

Parameters:

  • answer (any) – The answer.

  • prev_answer (any) – The previous answer.

Returns:

True if the answers are different, False otherwise.

Return type:

bool

denofo.utils.helpers.get_model_from_qstack_dict(qstack_dict: dict, model: BaseModel) → BaseModel

Get a BaseModel object from a qstack dictionary (which can contain field names and values from other models as well).

Parameters:

  • qstack_dict (dict) – The qstack dictionary. keys = model field names, values = model field values.

  • model (BaseModel) – The BaseModel object.

Returns:

The BaseModel object with respective field values.

Return type:

BaseModel

denofo.utils.helpers.get_model_from_short_repr(short_repr: str, model: BaseModel) → BaseModel

Get a BaseModel object from a short representation string.

Parameters:

  • short_repr (str) – The short representation string.

  • model (BaseModel) – The BaseModel object.

Returns:

The BaseModel object.

Return type:

BaseModel

denofo.utils.helpers.get_short_repr(orig_model: BaseModel) → str

Get a short representation string of a BaseModel object.

Parameters:

orig_model (BaseModel) – The BaseModel object.

Returns:

The short representation of the BaseModel object.

Return type:

str

denofo.utils.helpers.infer_format_from_extension(file_path: Path) → str

Infer the format of a file based on its extension.

Parameters:

file_path (Path) – The file path.

Returns:

The inferred format.

Return type:

str

NCBI Taxonomy Database Check

exception denofo.utils.ncbiTaxDBcheck.NCBITAXDBWarning

Warning raised when NCBI Taxonomy Database is newly built or updated

denofo.utils.ncbiTaxDBcheck.check_NCBI_taxDB() → NCBITaxa

Check if NCBI Taxonomy Database exists and is valid or build it if not

Returns:

NCBI Taxonomy Database object

Return type:

NCBITaxa

denofo.utils.ncbiTaxDBcheck.update_NCBI_taxDB()

Update NCBI Taxonomy Database