pypath.utils.pyreact.PyReact

class pypath.utils.pyreact.PyReact(ncbi_tax_id=9606, default_id_types={}, modifications=True, seq=None, silent=False, max_complex_combinations=100, max_reaction_combinations=100)

Bases: Logger

__init__(ncbi_tax_id=9606, default_id_types={}, modifications=True, seq=None, silent=False, max_complex_combinations=100, max_reaction_combinations=100)

Make this instance a logger.

Parameters:

• name – The label of this instance that will be prepended to all messages it sends to the logger.

• module – Send the messages by the logger of this module.

Methods

__init__([ncbi_tax_id, default_id_types, ...])	Make this instance a logger.
add_dataset(parser[, id_types, process_id])
add_pfamily(proteins, pfid)
basic_stats([exclude_empty])
co_control([by_source])
complex_get_mods(source, complex_elem)
complex_get_refs(source, cplex_elem)
expand()
expand_by_source()
gen_cvariations()	Because one key from the BioPax file might represent more complexes, complexvariations are created to give a way to represent sets of combinations.
in_same_component([by_source])	For all complexes connects all members of the complex with each other.
interacts_with([by_source])
iterate_reactions()
load_acsn()
load_all()
load_kegg()
load_netpath()
load_panther()
load_pid()
load_reactome()
load_sequences()
load_wikipathways()
merge()
merge_cassemblies()
merge_catalyses()
merge_complexes([this_round])	Merges complexes from the active BioPaxReader object.
merge_controls()
merge_cvariations()	This processes those complexes which are in fact a set of complex variations.
merge_modifications()
merge_pfamilies()
merge_proteins()
merge_reactions()
merge_refs()
netpath_names()
preprocess_seqmodvoc()
protein_get_mods(source, protein_elem)
protein_get_refs(source, protein_elem)
reaction_mod_diff(source, reaction[, by_rid])
reaction_side_get_mods(source, rside[, by_rid])
reload()
remove_defaults()
resource_graph_edges(etyp)
set_corrections()
simpson_stats()
state_change([by_source])

gen_cvariations()

Because one key from the BioPax file might represent more complexes, complexvariations are created to give a way to represent sets of combinations. These are created for all complexes, even with only one unambiguous constitution. The keys are the constitutions of all the combinations listed in alphabetic order, separated by |. For example, A,B,C|A,B,D|A,B,E.

in_same_component(by_source=False)

For all complexes connects all members of the complex with each other.

merge_complexes(this_round=None)

Merges complexes from the active BioPaxReader object. Protein families and subcomplexes are expanded, and all combinations are created as separate complexes. The complexes from the same ID are added to sets in the rcomplexes dict.

merge_cvariations()

This processes those complexes which are in fact a set of complex variations. As simple complexes also are always extended to complex variations because they might have not only simple proteins but protein families as members, here we only add new records to the attributes of already existing complexes. After merge_complexes will be called again, to process those simple complexes which have any of the complex variations processed here among their subcomplexes.