epistasis.mapping module¶
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class
epistasis.mapping.
EpistasisMap
(sites, order=1, values=None, model_type='global')¶ Bases:
object
DataFrame for epistatic interactions.
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get_orders
(*orders)¶ Get epistasis of a given order.
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index
¶ Get the interaction index in interaction matrix.
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map
(attr1, attr2)¶ Dictionary that maps attr1 to attr2.
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model_type
¶ Type of epistasis model used to get coefficients.
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n
¶ Return the number of Interactions.
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order
¶ Get order of epistasis in system.
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classmethod
read_dataframe
(df, model_type='global')¶ Create an epistasis model from dataframe
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sites
¶ Get the interaction sites, which describe the position of interacting mutations in the genotypes. (type==list of lists, see self._build_interaction_sites)
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to_csv
(filename)¶ Write data to a csv file.
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to_dict
()¶ Get data as dictionary.
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to_excel
(filename)¶ Write data to excel file.
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values
¶ Get the values of the interaction in the system
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class
epistasis.mapping.
Orders
(epistasismap, orders)¶ Bases:
map
An object that provides API for easily calling epistasis of a given order in an epistasis map.
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__call__
()¶ return a dictionary
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df
¶ Dataframe for orders object.
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index
¶ Get indices of epistasis from this order.
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sites
¶ Get epistatic sites
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values
¶ Get values of epistasis for this order.
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epistasis.mapping.
assert_epistasis
(method)¶ Assert that an epistasis map has been attached to the object.
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epistasis.mapping.
genotype_coeffs
(genotype, order=None)¶ List the possible epistatic coefficients (as label form) for a binary genotype up to a given order.
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epistasis.mapping.
key_to_site
(key)¶ Convert an interaction key to label.
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epistasis.mapping.
mutations_to_sites
(order, mutations, start_order=0)¶ Build interaction sites up to nth order given a mutation alphabet.
Parameters: - order (int) – order of interactions
- mutations (dict) – mutations = { site_number : [“mutation-1”, “mutation-2”] }. If the site alphabet is note included, the model will assume binary between wildtype and derived.
Example
mutations = { 0: ["A", "V"], 1: ["A", "V"], ... }
Returns: sites – list of all interaction sites for system with sequences of a given length and epistasis with given order. Return type: list
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epistasis.mapping.
site_to_key
(site, state='')¶ Convert site to key. state is added to end of key.