pandaspgs.trait.Trait

An object that stores data of type Trait. To understand the significance of each column of the DataFrame. Please visit "EFOTrait_Ontology" in PGS Catalog Documentation for details.

Attributes:
  • raw_data –

    list. Convert from obtained JSON data

  • traits –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • trait_categories –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • trait_synonyms –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • trait_mapped_terms –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • associated_pgs_ids –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • child_associated_pgs_ids –

    DataFrame. It only exists if the parameter mode of constructor is Fat.

  • mode –

    Fat or Thin. Specifies the mode of the returned object.

 
from pandaspgs.get_trait import get_traits

ch = get_traits(trait_id='EFO_0004214')
ch
ch.raw_data
ch.mode
ch.traits
ch.trait_categories
ch.trait_synonyms
ch.trait_mapped_terms
ch.associated_pgs_ids
ch.child_associated_pgs_ids

Subset object s by either identifier or position

all_df = get_traits()
all_df[0].traits
all_df[0:3].traits
all_df['EFO_0004214'].traits
all_df[('EFO_0004214','HP_0002027','HP_0011458')].traits

Objects can be manipulated like sets in the mathematical sense.

one = get_scores(trait_id='EFO_0004214')
two = get_scores(trait_id='HP_0002027')
three = get_scores(trait_id='HP_0011458')
one_and_two = one+two
two_and_three = two+three
only_one = one_and_two - two_and_three
only_two = one_and_two & two_and_three
one_and_two_and_three = one_and_two | two_and_three
one_and_three = one_and_two ^ two_and_three

__init__ 

__init__(data: list = [], mode: str = 'Fat')
Parameters:
  • data (list, default: [] ) –

    Raw JSON data.

  • mode (str, default: 'Fat' ) –

    Fat or Thin. Specifies the mode of the object.