pypath.core.enz_sub.EnzymeSubstrateAggregator

class pypath.core.enz_sub.EnzymeSubstrateAggregator(input_param=None, exclude=None, ncbi_tax_id=9606, map_by_orthology_from=None, trace=False, orthology_only_swissprot=True, ptm_orthology_strict=False, nonhuman_direct_lookup=True, inputargs=None, pickle_file=None)

Bases: Logger

__init__(input_param=None, exclude=None, ncbi_tax_id=9606, map_by_orthology_from=None, trace=False, orthology_only_swissprot=True, ptm_orthology_strict=False, nonhuman_direct_lookup=True, inputargs=None, pickle_file=None)

Docs not written yet.

Methods

__init__([input_param, exclude, ...])	Docs not written yet.
assign_to_network(pa)	Assigns enzyme-substrate interactions to the edges of a network in a py:class:pypath.legacy.main.PyPath instance.
build()
build_list()	Builds a full list of enzyme-substrate interactions from all the requested sources.
export_table(fname)
get_enzyme_substrate(enzyme, substrate)
load_from_pickle([pickle_file])
main()
make_df([tax_id, resources_only_primary])
reload()
save_to_pickle(pickle_file)
set_inputs()
summaries_tab([outfile, return_table])
uniq_enz_sub(enz_sub)
unique()	Merges the redundant elements of the interaction list.
update_ptm_lookup_dict()
update_summaries([collect_args])

Attributes

resources
resources_sorted

assign_to_network(pa)

Assigns enzyme-substrate interactions to the edges of a network in a py:class:pypath.legacy.main.PyPath instance.

build_list()

Builds a full list of enzyme-substrate interactions from all the requested sources. This list might contain redundant elements which later will be merged by unique. This ‘full list’ is organised into a dict by pairs of proteins in order to make it more efficient to compile a unique set for each pair.

unique()

Merges the redundant elements of the interaction list. Elements are redundant if they agree in all their attributes except the sources, references and isoforms.