pypath.core.enz_sub.EnzymeSubstrateProcessor

class pypath.core.enz_sub.EnzymeSubstrateProcessor(input_param=None, input_method=None, ncbi_tax_id=None, trace=False, id_type_enzyme=None, id_type_substrate=None, name=None, allow_mixed_organisms=None, organisms_supported=False, **kwargs)

Bases: Proteomes, SequenceContainer

__init__(input_param=None, input_method=None, ncbi_tax_id=None, trace=False, id_type_enzyme=None, id_type_substrate=None, name=None, allow_mixed_organisms=None, organisms_supported=False, **kwargs)

Processes enzyme-substrate interaction data from various databases. Provides generators to iterate over these interactions. For organisms other than human obtains the organism specific interactions from databases.

Parameters:

• input_method (str) – Either a method name in the inputs module or a database name e.g. PhosphoSite or a callable which returns data in list of dicts format.

• ncbi_tax_id (int) – NCBI Taxonomy ID used at the database lookups.

• trace (bool) – Keep data about ambiguous ID mappings and PTM data in mismatch with UniProt sequences.

• pypath.mapping.Mapper – A Mapper instance. If None a new instance will be created.

• id_type_enzyme (str) – The ID type of the enzyme in the database.

• id_type_substrate (str) – The ID type of the substrate in the database.

• nonhuman_direct_lookup (bool) – Use direct lookup at non-human target species.

• **kwargs –

  Args to be forwarded to the input method.

Methods

__init__([input_param, input_method, ...])	Processes enzyme-substrate interaction data from various databases.
get_seq(protein[, taxon])
get_taxon(protein[, only_swissprot])
get_taxon_trembl(protein)
has_protein(protein)
input_is(i[, op])
is_swissprot(protein)
load_data()	Loads the data by the defined input method.
load_enz_sub()
load_proteome(taxon[, only_swissprot])
load_seq(taxon)
load_taxonomy()
reload()
reset_ptmprocessor([seq, ncbi_tax_id])
set_inputargs(**inputargs)	Sets the arguments to be provided for the input method.
set_method()	Selects the input method.
set_taxon(ncbi_tax_id)
setup()

load_data()

Loads the data by the defined input method.

set_inputargs(**inputargs)

Sets the arguments to be provided for the input method.

set_method()

Selects the input method.