# -*- coding: utf-8 -*-
"""This module helps handle node data dictionaries."""
from typing import List
from .constants import (
CONCEPT, FRAGMENT, FRAGMENT_DESCRIPTION, FRAGMENT_START, FRAGMENT_STOP, FUNCTION, FUSION, FUSION_MISSING,
FUSION_REFERENCE, FUSION_START, FUSION_STOP, GMOD, HGVS, IDENTIFIER, KIND, MEMBERS, MODIFIER, NAME, NAMESPACE,
PARTNER_3P, PARTNER_5P, PMOD, PMOD_CODE, PMOD_POSITION, PRODUCTS, RANGE_3P, RANGE_5P, REACTANTS, REACTION, TARGET,
VARIANTS, XREFS,
)
from .dsl import (
BaseAbundance, BaseEntity, CentralDogma, EnumeratedFusionRange, FUNC_TO_DSL, FUNC_TO_FUSION_DSL, FUNC_TO_LIST_DSL,
Fragment, FusionBase, FusionRangeBase, GeneModification, Hgvs, ListAbundance, MissingFusionRange,
ProteinModification, Reaction, Variant,
)
__all__ = [
'parse_result_to_dsl',
]
[docs]def parse_result_to_dsl(tokens) -> BaseEntity:
"""Convert a ParseResult to a PyBEL DSL object.
:type tokens: dict or pyparsing.ParseResults
"""
if MODIFIER in tokens:
return parse_result_to_dsl(tokens[TARGET])
elif REACTION == tokens[FUNCTION]:
return _reaction_po_to_dict(tokens)
elif VARIANTS in tokens:
return _variant_po_to_dict(tokens)
elif MEMBERS in tokens:
return _list_po_to_dict(tokens)
elif FUSION in tokens:
return _fusion_to_dsl(tokens)
return _simple_po_to_dict(tokens)
def _fusion_to_dsl(tokens) -> FusionBase:
"""Convert a PyParsing data dictionary to a PyBEL fusion data dictionary.
:param tokens: A PyParsing data dictionary representing a fusion
:type tokens: ParseResult
"""
func = tokens[FUNCTION]
fusion_dsl = FUNC_TO_FUSION_DSL[func]
member_dsl = FUNC_TO_DSL[func]
partner_5p = tokens[FUSION][PARTNER_5P]
partner_5p_concept = (
partner_5p[CONCEPT]
if CONCEPT in tokens[FUSION][PARTNER_5P] else
partner_5p
)
partner_5p_node = member_dsl(
namespace=partner_5p_concept[NAMESPACE],
name=partner_5p_concept[NAME],
identifier=partner_5p_concept.get(IDENTIFIER),
xrefs=partner_5p.get(XREFS),
)
partner_3p = tokens[FUSION][PARTNER_3P]
partner_3p_concept = (
partner_3p[CONCEPT]
if CONCEPT in tokens[FUSION][PARTNER_3P] else
partner_3p
)
partner_3p_node = member_dsl(
namespace=partner_3p_concept[NAMESPACE],
name=partner_3p_concept[NAME],
identifier=partner_3p_concept.get(IDENTIFIER),
xrefs=partner_3p.get(XREFS),
)
range_5p = _fusion_range_to_dsl(tokens[FUSION][RANGE_5P])
range_3p = _fusion_range_to_dsl(tokens[FUSION][RANGE_3P])
return fusion_dsl(
partner_5p=partner_5p_node,
partner_3p=partner_3p_node,
range_5p=range_5p,
range_3p=range_3p,
)
def _fusion_range_to_dsl(tokens) -> FusionRangeBase:
"""Convert a PyParsing data dictionary into a PyBEL.
:type tokens: ParseResult
"""
if FUSION_MISSING in tokens:
return MissingFusionRange()
return EnumeratedFusionRange(
reference=tokens[FUSION_REFERENCE],
start=tokens[FUSION_START],
stop=tokens[FUSION_STOP],
)
def _simple_po_to_dict(tokens) -> BaseAbundance:
"""Convert a simple named entity to a DSL object.
:type tokens: ParseResult
"""
dsl = FUNC_TO_DSL.get(tokens[FUNCTION])
if dsl is None:
raise ValueError('invalid tokens: {}'.format(tokens))
concept = tokens[CONCEPT]
return dsl(
namespace=concept[NAMESPACE],
name=concept.get(NAME),
identifier=concept.get(IDENTIFIER),
xrefs=tokens.get(XREFS),
)
def _variant_po_to_dict(tokens) -> CentralDogma:
"""Convert a PyParsing data dictionary to a central dogma abundance (i.e., Protein, RNA, miRNA, Gene).
:type tokens: ParseResult
"""
dsl = FUNC_TO_DSL.get(tokens[FUNCTION])
if dsl is None:
raise ValueError('invalid tokens: {}'.format(tokens))
concept = tokens[CONCEPT]
return dsl(
namespace=concept[NAMESPACE],
name=concept[NAME],
identifier=concept.get(IDENTIFIER),
xrefs=tokens.get(XREFS),
variants=[
_variant_to_dsl_helper(variant_tokens)
for variant_tokens in tokens[VARIANTS]
],
)
def _variant_to_dsl_helper(tokens) -> Variant:
"""Convert variant tokens to DSL objects.
:type tokens: ParseResult
"""
kind = tokens[KIND]
if kind == HGVS:
return Hgvs(tokens[HGVS])
if kind == GMOD:
concept = tokens[CONCEPT]
return GeneModification(
name=concept[NAME],
namespace=concept[NAMESPACE],
identifier=concept.get(IDENTIFIER),
xrefs=tokens.get(XREFS),
)
if kind == PMOD:
concept = tokens[CONCEPT]
return ProteinModification(
name=concept[NAME],
namespace=concept[NAMESPACE],
identifier=concept.get(IDENTIFIER),
xrefs=tokens.get(XREFS),
code=tokens.get(PMOD_CODE),
position=tokens.get(PMOD_POSITION),
)
if kind == FRAGMENT:
start, stop = tokens.get(FRAGMENT_START), tokens.get(FRAGMENT_STOP)
return Fragment(
start=start,
stop=stop,
description=tokens.get(FRAGMENT_DESCRIPTION),
)
raise ValueError('invalid fragment kind: {}'.format(kind))
def _reaction_po_to_dict(tokens) -> Reaction:
"""Convert a reaction parse object to a DSL.
:type tokens: ParseResult
"""
return Reaction(
reactants=_parse_tokens_list(tokens[REACTANTS]),
products=_parse_tokens_list(tokens[PRODUCTS]),
)
def _list_po_to_dict(tokens) -> ListAbundance:
"""Convert a list parse object to a node.
:type tokens: ParseResult
"""
func = tokens[FUNCTION]
dsl = FUNC_TO_LIST_DSL[func]
members = _parse_tokens_list(tokens[MEMBERS])
return dsl(members)
def _parse_tokens_list(tokens) -> List[BaseEntity]:
"""Convert a PyParsing result to a reaction.
:type tokens: ParseResult
"""
return [
parse_result_to_dsl(token)
for token in tokens
]