source

Represents a collection of data about a Source feature that is commonly used to maintain and update SEA-PHAGES phage genomics data.

class pdm_utils.classes.source.Source

Bases: object

check_attribute(attribute, check_set, expect=False, eval_id=None, success='correct', fail='error', eval_def=None)

Check that the attribute value is valid.

Parameters

  • attribute (str) – Name of the Source feature object attribute to evaluate.

  • check_set (set) – Set of reference ids.

  • expect (bool) – Indicates whether the attribute value is expected to be present in the check set.

  • eval_id (str) – Unique identifier for the evaluation.

  • success (str) – Default status if the outcome is a success.

  • fail (str) – Default status if the outcome is not a success.

  • eval_def (str) – Description of the evaluation.

parse_host()

Retrieve the host_genus name from the ‘host’ field.

parse_lab_host()

Retrieve the host_genus name from the ‘lab_host’ field.

parse_organism()

Retrieve the phage and host_genus names from the ‘organism’ field.

set_eval(eval_id, definition, result, status)

Constructs and adds an Evaluation object to the evaluations list.

Parameters

  • eval_id (str) – Unique identifier for the evaluation.

  • definition (str) – Description of the evaluation.

  • result (str) – Description of the outcome of the evaluation.

  • status (str) – Outcome of the evaluation.