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""" |
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Run searches and write files. |
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3
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""" |
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4
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5
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from __future__ import annotations |
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6
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7
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import abc |
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from pathlib import Path |
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from typing import Generic, Mapping, Optional, Sequence, Set, Type, TypeVar, Union |
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11
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import typer |
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from typer.models import OptionInfo |
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13
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14
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from mandos import logger |
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from mandos.entries import EntryMeta |
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from mandos.entries._entry_args import EntryArgs |
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from mandos.entries.api_singletons import Apis |
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from mandos.entries.common_args import CommonArgs |
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from mandos.entries.searcher import Searcher |
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from mandos.model import InjectionError, ReflectionUtils |
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from mandos.model.apis.chembl_api import ChemblApi |
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from mandos.model.apis.chembl_support import DataValidityComment |
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from mandos.model.apis.chembl_support.chembl_targets import TargetType |
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from mandos.model.apis.pubchem_support.pubchem_models import ( |
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ClinicalTrialsGovUtils, |
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CoOccurrenceType, |
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DrugbankTargetType, |
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) |
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from mandos.model.searches import Search |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.model.taxonomy import Taxonomy |
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from mandos.model.taxonomy_caches import TaxonomyFactories |
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from mandos.search.chembl.atc_search import AtcSearch |
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from mandos.search.chembl.binding_search import BindingSearch |
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from mandos.search.chembl.go_search import GoSearch, GoType |
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from mandos.search.chembl.indication_search import IndicationSearch |
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from mandos.search.chembl.mechanism_search import MechanismSearch |
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from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch |
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39
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from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search |
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40
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from mandos.search.pubchem.bioactivity_search import BioactivitySearch |
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from mandos.search.pubchem.computed_property_search import ComputedPropertySearch |
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from mandos.search.pubchem.cooccurrence_search import ( |
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ChemicalCoOccurrenceSearch, |
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CoOccurrenceSearch, |
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DiseaseCoOccurrenceSearch, |
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GeneCoOccurrenceSearch, |
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) |
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from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch |
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from mandos.search.pubchem.dgidb_search import DgiSearch |
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from mandos.search.pubchem.disease_search import DiseaseSearch |
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from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch |
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from mandos.search.pubchem.drugbank_interaction_search import ( |
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DrugbankGeneralFunctionSearch, |
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DrugbankTargetSearch, |
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55
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) |
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56
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57
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S = TypeVar("S", bound=Search, covariant=True) |
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58
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U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch) |
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59
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60
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61
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class Utils: |
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62
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""" """ |
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63
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64
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@staticmethod |
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def split(st: str) -> Set[str]: |
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66
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return {s.strip() for s in st.split(",")} |
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68
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@staticmethod |
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def get_taxa(taxa: str) -> Sequence[Taxonomy]: |
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70
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return [ |
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71
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TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path).load( |
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str(taxon).strip() |
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) |
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for taxon in taxa.split(",") |
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] |
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77
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@staticmethod |
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def get_trial_statuses(st: str) -> Set[str]: |
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return ClinicalTrialsGovUtils.resolve_statuses(st) |
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81
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@staticmethod |
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def get_target_types(st: str) -> Set[str]: |
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83
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return {s.name for s in TargetType.resolve(st)} |
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85
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@staticmethod |
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def get_flags(st: str) -> Set[str]: |
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87
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return {s.name for s in DataValidityComment.resolve(st)} |
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89
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90
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class Entry(Generic[S], metaclass=abc.ABCMeta): |
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91
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@classmethod |
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def cmd(cls) -> str: |
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93
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key = cls._get_default_key() |
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94
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if isinstance(key, typer.models.OptionInfo): |
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key = key.default |
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if key is None or not isinstance(key, str): |
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raise AssertionError(f"Key for {cls.__name__} is {key}") |
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return key |
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100
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@classmethod |
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def describe(cls) -> str: |
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102
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lines = [line.strip() for line in cls.run.__doc__.splitlines() if line.strip() != ""] |
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return lines[0] |
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105
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@classmethod |
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def run(cls, path: Path, **params) -> None: |
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107
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raise NotImplementedError() |
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108
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109
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@classmethod |
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110
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def get_search_type(cls) -> Type[S]: |
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111
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# noinspection PyTypeChecker |
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112
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return ReflectionUtils.get_generic_arg(cls, Search) |
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113
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114
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# noinspection PyUnusedLocal |
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@classmethod |
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def test(cls, path: Path, **params) -> None: |
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cls.run(path, **{**params, **dict(check=True)}) |
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119
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@classmethod |
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def _run( |
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cls, |
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122
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built: S, |
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123
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path: Path, |
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124
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to: Optional[Path], |
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125
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check: bool, |
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log: Optional[Path], |
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127
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quiet: bool, |
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128
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verbose: bool, |
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no_setup: bool, |
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130
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): |
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if not no_setup: |
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level = EntryMeta.set_logging(verbose, quiet, log) |
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logger.notice(f"Ready. Set log level to {level}") |
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searcher = cls._get_searcher(built, path, to) |
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logger.notice(f"Searching {built.key} [{built.search_class}] on {path}") |
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out = searcher.output_paths[built.key] |
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if not check: |
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searcher.search() |
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logger.notice(f"Done! Wrote to {out}") |
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return searcher |
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141
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142
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@classmethod |
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143
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def _get_searcher( |
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144
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cls, |
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145
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built: S, |
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146
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path: Path, |
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147
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to: Optional[Path], |
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148
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): |
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149
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return Searcher([built], [to], path) |
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150
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151
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@classmethod |
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152
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def default_param_values(cls) -> Mapping[str, Union[str, float, int, Path]]: |
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153
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return { |
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154
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param: (value.default if isinstance(value, OptionInfo) else value) |
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155
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for param, value in ReflectionUtils.default_arg_values(cls.run).items() |
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156
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if param not in {"key", "path"} |
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} |
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158
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159
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@classmethod |
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160
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def _get_default_key(cls) -> str: |
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161
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vals = ReflectionUtils.default_arg_values(cls.run) |
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162
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try: |
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163
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return vals["key"] |
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164
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except KeyError: |
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165
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logger.error(f"key not in {vals.keys()} for {cls.__name__}") |
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166
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raise |
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167
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168
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169
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class EntryChemblBinding(Entry[BindingSearch]): |
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170
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@classmethod |
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171
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def run( |
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172
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cls, |
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173
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path: Path = CommonArgs.compounds, |
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174
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key: str = EntryArgs.key("chembl:binding"), |
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175
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to: Optional[Path] = CommonArgs.to_single, |
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176
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taxa: str = CommonArgs.taxa, |
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177
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traversal: str = EntryArgs.traversal_strategy, |
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178
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target_types: str = EntryArgs.target_types, |
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179
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confidence: int = EntryArgs.min_confidence, |
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180
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binding: float = EntryArgs.binds_cutoff, |
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181
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nonbinding: float = EntryArgs.does_not_bind_cutoff, |
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182
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relations: str = EntryArgs.relations, |
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183
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min_pchembl: float = EntryArgs.min_pchembl, |
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184
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banned_flags: str = EntryArgs.banned_flags, |
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185
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as_of: Optional[str] = CommonArgs.as_of, |
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186
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check: bool = EntryArgs.check, |
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187
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log: Optional[Path] = CommonArgs.log_path, |
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188
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quiet: bool = CommonArgs.quiet, |
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189
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verbose: bool = CommonArgs.verbose, |
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190
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no_setup: bool = CommonArgs.no_setup, |
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191
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) -> Searcher: |
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192
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""" |
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193
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Binding data from ChEMBL. |
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194
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These are 'activity' annotations of the type 'B' that have a pCHEMBL value. |
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195
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There is extended documentation on this search; see: |
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196
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197
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https://mandos-chem.readthedocs.io/en/latest/binding.html |
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198
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199
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OBJECT: ChEMBL preferred target name |
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200
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201
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PREDICATE: Either "binds", "does not bind", or "binding <relation> at" |
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202
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203
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OTHER COLUMNS: |
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204
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205
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- taxon_id: From UniProt |
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206
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207
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- taxon_name: From Uniprot (scientific name) |
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208
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209
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- pchembl: Negative base-10 log of activity value (see docs on ChEMBL) |
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210
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211
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- standard_relation: One of '<', '<=', '=', '>=', '>', '~'. Consider using <, <=, and = to indicate hits. |
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212
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213
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- std_type: e.g. EC50, Kd |
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214
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""" |
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215
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built = BindingSearch( |
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216
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key=key, |
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217
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api=Apis.Chembl, |
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218
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taxa=Utils.get_taxa(taxa), |
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219
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traversal=traversal, |
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220
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target_types=Utils.get_target_types(target_types), |
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221
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min_conf_score=confidence, |
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222
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allowed_relations=Utils.split(relations), |
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223
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min_pchembl=min_pchembl, |
|
224
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banned_flags=Utils.get_flags(banned_flags), |
|
225
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binds_cutoff=binding, |
|
226
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does_not_bind_cutoff=nonbinding, |
|
227
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) |
|
228
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
229
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230
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|
231
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class EntryChemblMechanism(Entry[MechanismSearch]): |
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|
232
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@classmethod |
|
233
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def run( |
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|
234
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cls, |
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235
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path: Path = CommonArgs.compounds, |
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|
236
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key: str = EntryArgs.key("chembl:mechanism"), |
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237
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to: Optional[Path] = CommonArgs.to_single, |
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238
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taxa: Optional[str] = CommonArgs.taxa, |
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|
239
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traversal: str = EntryArgs.traversal_strategy, |
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|
240
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|
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target_types: str = EntryArgs.target_types, |
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241
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min_confidence: Optional[int] = EntryArgs.min_confidence, |
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242
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as_of: Optional[str] = CommonArgs.as_of, |
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|
243
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check: bool = EntryArgs.check, |
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244
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log: Optional[Path] = CommonArgs.log_path, |
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|
245
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quiet: bool = CommonArgs.quiet, |
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|
246
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verbose: bool = CommonArgs.verbose, |
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|
|
247
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|
|
no_setup: bool = CommonArgs.no_setup, |
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|
|
|
|
248
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|
|
) -> Searcher: |
|
249
|
|
|
""" |
|
250
|
|
|
Mechanism of action (MoA) data from ChEMBL. |
|
251
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|
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|
|
252
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|
|
OBJECT: ChEMBL preferred target name |
|
253
|
|
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|
254
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|
|
PREDICATE: Target action; e.g. "agonist of" or "positive allosteric modulator of" |
|
255
|
|
|
|
|
256
|
|
|
OTHER COLUMNS: |
|
257
|
|
|
|
|
258
|
|
|
- direct_interaction: true or false |
|
259
|
|
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|
|
260
|
|
|
- description: From ChEMBL |
|
261
|
|
|
|
|
262
|
|
|
- exact_target_id: the specifically annotated target, before traversal |
|
263
|
|
|
""" |
|
264
|
|
|
built = MechanismSearch( |
|
265
|
|
|
key=key, |
|
266
|
|
|
api=Apis.Chembl, |
|
267
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taxa=Utils.get_taxa(taxa), |
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268
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traversal_strategy=traversal, |
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269
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allowed_target_types=Utils.get_target_types(target_types), |
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270
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min_confidence_score=min_confidence, |
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271
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) |
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272
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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273
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274
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275
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class EntryChemblTrials(Entry[IndicationSearch]): |
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276
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@classmethod |
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277
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def run( |
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278
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cls, |
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279
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path: Path = CommonArgs.compounds, |
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280
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key: str = EntryArgs.key("chembl:trial"), |
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281
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to: Optional[Path] = CommonArgs.to_single, |
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282
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min_phase: Optional[int] = EntryArgs.chembl_trial, |
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283
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as_of: Optional[str] = CommonArgs.as_of, |
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284
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check: bool = EntryArgs.check, |
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285
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log: Optional[Path] = CommonArgs.log_path, |
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286
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quiet: bool = CommonArgs.quiet, |
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287
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verbose: bool = CommonArgs.verbose, |
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288
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no_setup: bool = CommonArgs.no_setup, |
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289
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) -> Searcher: |
|
290
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""" |
|
291
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Diseases from clinical trials listed in ChEMBL. |
|
292
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293
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OBJECT: MeSH code |
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294
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295
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PREDICATE: "phase <level> trial" |
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296
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""" |
|
297
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built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase) |
|
298
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
299
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300
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301
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class EntryChemblAtc(Entry[AtcSearch]): |
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302
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@classmethod |
|
303
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def run( |
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304
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cls, |
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305
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path: Path = CommonArgs.compounds, |
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306
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key: str = EntryArgs.key("chembl:atc"), |
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|
307
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to: Optional[Path] = CommonArgs.to_single, |
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|
308
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|
|
levels: str = EntryArgs.atc_level, |
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|
309
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|
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as_of: Optional[str] = CommonArgs.as_of, |
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|
310
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|
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check: bool = EntryArgs.check, |
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311
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|
|
log: Optional[Path] = CommonArgs.log_path, |
|
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|
312
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|
|
quiet: bool = CommonArgs.quiet, |
|
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|
313
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|
|
verbose: bool = CommonArgs.verbose, |
|
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|
314
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
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|
315
|
|
|
) -> Searcher: |
|
316
|
|
|
""" |
|
317
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|
|
ATC codes from ChEMBL. |
|
318
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|
|
|
|
319
|
|
|
OBJECT: ATC Code |
|
320
|
|
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|
321
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|
|
PREDICATE: "ATC L<leveL> code" |
|
322
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|
|
""" |
|
323
|
|
|
built = AtcSearch( |
|
324
|
|
|
key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")} |
|
325
|
|
|
) |
|
326
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
327
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|
|
|
|
328
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|
329
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|
|
class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta): |
|
330
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|
|
@classmethod |
|
331
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|
|
def go_type(cls) -> GoType: |
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|
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|
332
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|
|
raise NotImplementedError() |
|
333
|
|
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|
334
|
|
|
@classmethod |
|
335
|
|
|
def cmd(cls) -> str: |
|
|
|
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|
|
336
|
|
|
me = str(cls.go_type().name) |
|
|
|
|
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|
337
|
|
|
return f"chembl:go.{me.lower()}" |
|
338
|
|
|
|
|
339
|
|
|
@classmethod |
|
340
|
|
|
def run( |
|
|
|
|
|
|
341
|
|
|
cls, |
|
|
|
|
|
|
342
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
343
|
|
|
key: str = EntryArgs.key("<see above>"), |
|
|
|
|
|
|
344
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
345
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|
|
taxa: Optional[str] = CommonArgs.taxa, |
|
|
|
|
|
|
346
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|
|
traversal_strategy: str = EntryArgs.traversal_strategy, |
|
|
|
|
|
|
347
|
|
|
target_types: str = EntryArgs.target_types, |
|
|
|
|
|
|
348
|
|
|
confidence: Optional[int] = EntryArgs.min_confidence, |
|
|
|
|
|
|
349
|
|
|
relations: str = EntryArgs.relations, |
|
|
|
|
|
|
350
|
|
|
min_pchembl: float = EntryArgs.min_pchembl, |
|
|
|
|
|
|
351
|
|
|
banned_flags: Optional[str] = EntryArgs.banned_flags, |
|
|
|
|
|
|
352
|
|
|
binding_search: Optional[str] = EntryArgs.binding_search_name, |
|
|
|
|
|
|
353
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
354
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
355
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
356
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
357
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
358
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
359
|
|
|
) -> Searcher: |
|
360
|
|
|
""" |
|
361
|
|
|
GO terms associated with ChEMBL binding targets. |
|
362
|
|
|
|
|
363
|
|
|
OBJECT: GO Term name |
|
364
|
|
|
|
|
365
|
|
|
PREDICATE: "associated with ""Function"|"Process"|"Component"" term" |
|
366
|
|
|
|
|
367
|
|
|
OTHER COLUMNS: |
|
368
|
|
|
See the docs for ``mandos chembl:binding`` |
|
369
|
|
|
|
|
370
|
|
|
Note: |
|
371
|
|
|
|
|
372
|
|
|
By default, the key is the "chembl:go.function", "chembl:go.process", or "chembl:go.component". |
|
|
|
|
|
|
373
|
|
|
|
|
374
|
|
|
""" |
|
375
|
|
|
if key is None or key == "<see above>": |
|
376
|
|
|
key = cls.cmd() |
|
377
|
|
|
api = ChemblApi.wrap(Apis.Chembl) |
|
378
|
|
|
if binding_search is None: |
|
379
|
|
|
binding_clazz = BindingSearch |
|
380
|
|
|
else: |
|
381
|
|
|
binding_clazz = ReflectionUtils.injection(binding_search, BindingSearch) |
|
382
|
|
|
logger.info(f"NOTICE: Passing parameters to {binding_clazz.__qualname__}") |
|
383
|
|
|
try: |
|
384
|
|
|
binding_search = binding_clazz( |
|
385
|
|
|
key=key, |
|
386
|
|
|
api=Apis.Chembl, |
|
387
|
|
|
taxa=Utils.get_taxa(taxa), |
|
388
|
|
|
traversal=traversal_strategy, |
|
389
|
|
|
target_types=Utils.get_target_types(target_types), |
|
390
|
|
|
min_conf_score=confidence, |
|
391
|
|
|
allowed_relations=Utils.split(relations), |
|
392
|
|
|
min_pchembl=min_pchembl, |
|
393
|
|
|
banned_flags=Utils.get_flags(banned_flags), |
|
394
|
|
|
) |
|
395
|
|
|
except (TypeError, ValueError): |
|
396
|
|
|
raise InjectionError(f"Failed to build {binding_clazz.__qualname__}") |
|
397
|
|
|
built = GoSearch(key, api, cls.go_type(), binding_search) |
|
398
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
399
|
|
|
|
|
400
|
|
|
|
|
401
|
|
|
class EntryGoFunction(_EntryChemblGo): |
|
|
|
|
|
|
402
|
|
|
@classmethod |
|
403
|
|
|
def go_type(cls) -> GoType: |
|
404
|
|
|
return GoType.function |
|
405
|
|
|
|
|
406
|
|
|
|
|
407
|
|
|
class EntryGoProcess(_EntryChemblGo): |
|
|
|
|
|
|
408
|
|
|
@classmethod |
|
409
|
|
|
def go_type(cls) -> GoType: |
|
410
|
|
|
return GoType.process |
|
411
|
|
|
|
|
412
|
|
|
|
|
413
|
|
|
class EntryGoComponent(_EntryChemblGo): |
|
|
|
|
|
|
414
|
|
|
@classmethod |
|
415
|
|
|
def go_type(cls) -> GoType: |
|
416
|
|
|
return GoType.component |
|
417
|
|
|
|
|
418
|
|
|
|
|
419
|
|
|
class EntryPubchemDisease(Entry[DiseaseSearch]): |
|
|
|
|
|
|
420
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
421
|
|
|
def run( |
|
|
|
|
|
|
422
|
|
|
cls, |
|
|
|
|
|
|
423
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
424
|
|
|
key: str = EntryArgs.key("disease.ctd:mesh"), |
|
|
|
|
|
|
425
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
426
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
427
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
428
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
429
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
430
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
431
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
432
|
|
|
) -> Searcher: |
|
433
|
|
|
""" |
|
434
|
|
|
Diseases in the CTD. |
|
435
|
|
|
|
|
436
|
|
|
Comparative Toxicogenomics Database. |
|
437
|
|
|
|
|
438
|
|
|
OBJECT: MeSH code of disease |
|
439
|
|
|
|
|
440
|
|
|
PREDICATE: "marker/mechanism evidence for" or "disease evidence for" |
|
441
|
|
|
""" |
|
442
|
|
|
built = DiseaseSearch(key, Apis.Pubchem) |
|
443
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
444
|
|
|
|
|
445
|
|
|
|
|
446
|
|
|
class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
|
447
|
|
|
@classmethod |
|
448
|
|
|
def cmd(cls) -> str: |
|
|
|
|
|
|
449
|
|
|
me = str(cls.get_cooccurrence_type().name) |
|
|
|
|
|
|
450
|
|
|
return f"lit.pubchem:{me.lower()}" |
|
451
|
|
|
|
|
452
|
|
|
@classmethod |
|
453
|
|
|
def get_cooccurrence_type(cls) -> CoOccurrenceType: |
|
|
|
|
|
|
454
|
|
|
s: CoOccurrenceSearch = cls.get_search_type() |
|
|
|
|
|
|
455
|
|
|
return s.cooccurrence_type() |
|
456
|
|
|
|
|
457
|
|
|
@classmethod |
|
458
|
|
|
def run( |
|
|
|
|
|
|
459
|
|
|
cls, |
|
|
|
|
|
|
460
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
461
|
|
|
key: str = EntryArgs.key("<see above>"), |
|
|
|
|
|
|
462
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
463
|
|
|
min_score: float = EntryArgs.min_cooccurrence_score, |
|
|
|
|
|
|
464
|
|
|
min_articles: int = EntryArgs.min_cooccurring_articles, |
|
|
|
|
|
|
465
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
466
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
467
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
468
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
469
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
470
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
471
|
|
|
) -> Searcher: |
|
472
|
|
|
""" |
|
473
|
|
|
Co-occurrences from PubMed articles. |
|
474
|
|
|
There is extended documentation on this search. |
|
475
|
|
|
Also refer to https://pubchemdocs.ncbi.nlm.nih.gov/knowledge-panels |
|
476
|
|
|
|
|
477
|
|
|
OBJECT: Name of gene/chemical/disease |
|
478
|
|
|
|
|
479
|
|
|
PREDICATE: "co-occurs with <gene/chemical/disease>" |
|
480
|
|
|
|
|
481
|
|
|
OTHER COLUMNS: |
|
482
|
|
|
|
|
483
|
|
|
- score: enrichment score; see PubChem docs |
|
484
|
|
|
|
|
485
|
|
|
- intersect_count: Number of articles co-occurring |
|
486
|
|
|
|
|
487
|
|
|
- query_count: Total number of articles for query compound |
|
488
|
|
|
|
|
489
|
|
|
- neighbor_count: Total number of articles for target (co-occurring) compound |
|
490
|
|
|
""" |
|
491
|
|
|
if key is None or key == "<see above>": |
|
492
|
|
|
key = cls.cmd() |
|
493
|
|
|
clazz = cls.get_search_type() |
|
494
|
|
|
built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles) |
|
495
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
496
|
|
|
|
|
497
|
|
|
|
|
498
|
|
|
class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]): |
|
|
|
|
|
|
499
|
|
|
""" """ |
|
500
|
|
|
|
|
501
|
|
|
|
|
502
|
|
|
class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]): |
|
|
|
|
|
|
503
|
|
|
""" """ |
|
504
|
|
|
|
|
505
|
|
|
|
|
506
|
|
|
class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]): |
|
|
|
|
|
|
507
|
|
|
""" """ |
|
508
|
|
|
|
|
509
|
|
|
|
|
510
|
|
|
class EntryPubchemDgi(Entry[DgiSearch]): |
|
|
|
|
|
|
511
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
512
|
|
|
def run( |
|
|
|
|
|
|
513
|
|
|
cls, |
|
|
|
|
|
|
514
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
515
|
|
|
key: str = EntryArgs.key("inter.dgidb:gene"), |
|
|
|
|
|
|
516
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
517
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
518
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
519
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
520
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
521
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
522
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
523
|
|
|
) -> Searcher: |
|
524
|
|
|
""" |
|
525
|
|
|
Drug/gene interactions in the DGIDB. |
|
526
|
|
|
|
|
527
|
|
|
Drug Gene Interaction Database. |
|
528
|
|
|
Also see ``disease.dgidb:int``. |
|
529
|
|
|
|
|
530
|
|
|
OBJECT: Name of the gene |
|
531
|
|
|
|
|
532
|
|
|
PREDICATE: "interacts with gene" |
|
533
|
|
|
""" |
|
534
|
|
|
built = DgiSearch(key, Apis.Pubchem) |
|
535
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
536
|
|
|
|
|
537
|
|
|
|
|
538
|
|
|
class EntryPubchemCgi(Entry[CtdGeneSearch]): |
|
|
|
|
|
|
539
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
540
|
|
|
def run( |
|
|
|
|
|
|
541
|
|
|
cls, |
|
|
|
|
|
|
542
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
543
|
|
|
key: str = EntryArgs.key("inter.ctd:gene"), |
|
|
|
|
|
|
544
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
545
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
546
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
547
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
548
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
549
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
550
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
551
|
|
|
) -> Searcher: |
|
552
|
|
|
""" |
|
553
|
|
|
Compound/gene interactions in the DGIDB. |
|
554
|
|
|
|
|
555
|
|
|
Drug Gene Interaction Database. |
|
556
|
|
|
Also see ``interact.dgidb:int``. |
|
557
|
|
|
|
|
558
|
|
|
OBJECT: Name of the gene |
|
559
|
|
|
|
|
560
|
|
|
PREDICATE: "compound/gene interaction" |
|
561
|
|
|
|
|
562
|
|
|
""" |
|
563
|
|
|
built = CtdGeneSearch(key, Apis.Pubchem) |
|
564
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
565
|
|
|
|
|
566
|
|
|
|
|
567
|
|
View Code Duplication |
class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
568
|
|
|
@classmethod |
|
569
|
|
|
def run( |
|
|
|
|
|
|
570
|
|
|
cls, |
|
|
|
|
|
|
571
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
572
|
|
|
key: str = EntryArgs.key("inter.drugbank:target"), |
|
|
|
|
|
|
573
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
574
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
575
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
576
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
577
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
578
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
579
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
580
|
|
|
) -> Searcher: |
|
581
|
|
|
""" |
|
582
|
|
|
Protein targets from DrugBank. |
|
583
|
|
|
|
|
584
|
|
|
OBJECT: Target name (e.g. "Solute carrier family 22 member 11") from DrugBank |
|
585
|
|
|
|
|
586
|
|
|
PREDICATE: Action (e.g. "binder", "downregulator", or "agonist") |
|
587
|
|
|
""" |
|
588
|
|
|
built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
|
589
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
590
|
|
|
|
|
591
|
|
|
|
|
592
|
|
View Code Duplication |
class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
|
|
|
|
|
593
|
|
|
@classmethod |
|
594
|
|
|
def run( |
|
|
|
|
|
|
595
|
|
|
cls, |
|
|
|
|
|
|
596
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
597
|
|
|
key: str = EntryArgs.key("inter.drugbank:target-fn"), |
|
|
|
|
|
|
598
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
599
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
600
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
601
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
602
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
603
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
604
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
605
|
|
|
) -> Searcher: |
|
606
|
|
|
""" |
|
607
|
|
|
General functions from DrugBank targets. |
|
608
|
|
|
|
|
609
|
|
|
OBJECT: Name of the general function (e.g. "Toxic substance binding") |
|
610
|
|
|
|
|
611
|
|
|
PREDICATE: against on target (e.g. "binder", "downregulator", or "agonist"). |
|
612
|
|
|
""" |
|
613
|
|
|
built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
|
614
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
615
|
|
|
|
|
616
|
|
|
|
|
617
|
|
View Code Duplication |
class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
618
|
|
|
@classmethod |
|
619
|
|
|
def run( |
|
|
|
|
|
|
620
|
|
|
cls, |
|
|
|
|
|
|
621
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
622
|
|
|
key: str = EntryArgs.key("inter.drugbank:pk"), |
|
|
|
|
|
|
623
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
624
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
625
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
626
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
627
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
628
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
629
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
630
|
|
|
) -> Searcher: |
|
631
|
|
|
""" |
|
632
|
|
|
PK-related proteins from DrugBank. |
|
633
|
|
|
|
|
634
|
|
|
OBJECT: Transporter name (e.g. "Solute carrier family 22 member 11") from DrugBank |
|
635
|
|
|
|
|
636
|
|
|
PREDICATE: "transported by", "carried by", or "metabolized by" |
|
637
|
|
|
""" |
|
638
|
|
|
target_types = { |
|
639
|
|
|
DrugbankTargetType.transporter, |
|
640
|
|
|
DrugbankTargetType.carrier, |
|
641
|
|
|
DrugbankTargetType.enzyme, |
|
642
|
|
|
} |
|
643
|
|
|
built = DrugbankTargetSearch(key, Apis.Pubchem, target_types) |
|
644
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
645
|
|
|
|
|
646
|
|
|
|
|
647
|
|
View Code Duplication |
class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
|
|
|
|
|
648
|
|
|
@classmethod |
|
649
|
|
|
def run( |
|
|
|
|
|
|
650
|
|
|
cls, |
|
|
|
|
|
|
651
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
652
|
|
|
key: str = EntryArgs.key("inter.drugbank:pk-fn"), |
|
|
|
|
|
|
653
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
654
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
655
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
656
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
657
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
658
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
659
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
660
|
|
|
) -> Searcher: |
|
661
|
|
|
""" |
|
662
|
|
|
DrugBank PK-related protein functions. |
|
663
|
|
|
|
|
664
|
|
|
OBJECT: Name of the general function (e.g. "Toxic substance binding") |
|
665
|
|
|
|
|
666
|
|
|
PREDICATE: "transported by", "carried by", or "metabolized by" |
|
667
|
|
|
""" |
|
668
|
|
|
target_types = { |
|
669
|
|
|
DrugbankTargetType.transporter, |
|
670
|
|
|
DrugbankTargetType.carrier, |
|
671
|
|
|
DrugbankTargetType.enzyme, |
|
672
|
|
|
} |
|
673
|
|
|
built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types) |
|
674
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
675
|
|
|
|
|
676
|
|
|
|
|
677
|
|
|
class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
|
|
|
|
|
|
678
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
679
|
|
|
def run( |
|
|
|
|
|
|
680
|
|
|
cls, |
|
|
|
|
|
|
681
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
682
|
|
|
key: str = EntryArgs.key("inter.drugbank:ddi"), |
|
|
|
|
|
|
683
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
684
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
685
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
686
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
687
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
688
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
689
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
690
|
|
|
) -> Searcher: |
|
691
|
|
|
""" |
|
692
|
|
|
Drug/drug interactions listed by DrugBank. |
|
693
|
|
|
|
|
694
|
|
|
The 'description' column includes useful information about the interaction, |
|
695
|
|
|
such as diseases and whether a risk is increased or decreased. |
|
696
|
|
|
|
|
697
|
|
|
OBJECT: name of the drug (e.g. "ibuprofen") |
|
698
|
|
|
|
|
699
|
|
|
PREDICATE: "ddi" |
|
700
|
|
|
""" |
|
701
|
|
|
built = DrugbankDdiSearch(key, Apis.Pubchem) |
|
702
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
703
|
|
|
|
|
704
|
|
|
|
|
705
|
|
|
class EntryPubchemAssay(Entry[BioactivitySearch]): |
|
|
|
|
|
|
706
|
|
|
@classmethod |
|
707
|
|
|
def run( |
|
|
|
|
|
|
708
|
|
|
cls, |
|
|
|
|
|
|
709
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
710
|
|
|
key: str = EntryArgs.key("assay.pubchem:activity"), |
|
|
|
|
|
|
711
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
712
|
|
|
name_must_match: bool = EntryArgs.name_must_match, |
|
|
|
|
|
|
713
|
|
|
ban_sources: Optional[str] = None, |
|
|
|
|
|
|
714
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
715
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
716
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
717
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
718
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
719
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
720
|
|
|
) -> Searcher: |
|
721
|
|
|
""" |
|
722
|
|
|
PubChem bioactivity results. |
|
723
|
|
|
|
|
724
|
|
|
Note: The species name, if present, is taken from the target name. |
|
725
|
|
|
The taxon ID is what was curated in PubChem. |
|
726
|
|
|
|
|
727
|
|
|
OBJECT: Name of the target without species suffix (e.g. "Slc6a3 - solute carrier family 6 member 3") |
|
|
|
|
|
|
728
|
|
|
|
|
729
|
|
|
PREDICATE: "active"|"inactive"|"inconclusive"|"undetermined" |
|
730
|
|
|
|
|
731
|
|
|
SOURCE: "PubChem: <referrer> "(""confirmatory"|"literature"|"other"")" |
|
732
|
|
|
""" |
|
733
|
|
|
built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=name_must_match) |
|
734
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
735
|
|
|
|
|
736
|
|
|
|
|
737
|
|
|
class EntryDeaSchedule(Entry[BioactivitySearch]): |
|
|
|
|
|
|
738
|
|
|
@classmethod |
|
739
|
|
|
def run( |
|
|
|
|
|
|
740
|
|
|
cls, |
|
|
|
|
|
|
741
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
742
|
|
|
key: str = EntryArgs.key("drug.dea:schedule"), |
|
|
|
|
|
|
743
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
744
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
745
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
746
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
747
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
748
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
749
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
750
|
|
|
) -> Searcher: |
|
751
|
|
|
""" |
|
752
|
|
|
DEA schedules (PENDING). |
|
753
|
|
|
|
|
754
|
|
|
OBJECT: (1 to 4, or "unscheduled") |
|
755
|
|
|
|
|
756
|
|
|
PREDICATE: "has DEA schedule" |
|
757
|
|
|
""" |
|
758
|
|
|
pass |
|
|
|
|
|
|
759
|
|
|
|
|
760
|
|
|
|
|
761
|
|
|
class EntryDeaClass(Entry[BioactivitySearch]): |
|
|
|
|
|
|
762
|
|
|
@classmethod |
|
763
|
|
|
def run( |
|
|
|
|
|
|
764
|
|
|
cls, |
|
|
|
|
|
|
765
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
766
|
|
|
key: str = EntryArgs.key("drug.dea:class"), |
|
|
|
|
|
|
767
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
768
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
769
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
770
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
771
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
772
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
773
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
774
|
|
|
) -> Searcher: |
|
775
|
|
|
""" |
|
776
|
|
|
DEA classes (PENDING). |
|
777
|
|
|
|
|
778
|
|
|
OBJECT: e.g. "hallucinogen" |
|
779
|
|
|
|
|
780
|
|
|
PREDICATE: "is in DEA class" |
|
781
|
|
|
""" |
|
782
|
|
|
pass |
|
|
|
|
|
|
783
|
|
|
|
|
784
|
|
|
|
|
785
|
|
|
class EntryChemidPlusAcute(Entry[AcuteEffectSearch]): |
|
|
|
|
|
|
786
|
|
|
@classmethod |
|
787
|
|
|
def run( |
|
|
|
|
|
|
788
|
|
|
cls, |
|
|
|
|
|
|
789
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
790
|
|
|
key: str = EntryArgs.key("tox.chemidplus:acute"), |
|
|
|
|
|
|
791
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
792
|
|
|
level: int = EntryArgs.acute_effect_level, |
|
|
|
|
|
|
793
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
794
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
795
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
796
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
797
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
798
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
799
|
|
|
) -> Searcher: |
|
800
|
|
|
""" |
|
801
|
|
|
Acute effect codes from ChemIDPlus. |
|
802
|
|
|
|
|
803
|
|
|
OBJECT: E.g. "behavioral: excitement" |
|
804
|
|
|
|
|
805
|
|
|
PREDICATE: "causes acute effect" |
|
806
|
|
|
|
|
807
|
|
|
OTHER COLUMNS: |
|
808
|
|
|
|
|
809
|
|
|
- organism: e.g. 'women', 'infant', 'men', 'human', 'dog', 'domestic animals - sheep and goats' |
|
|
|
|
|
|
810
|
|
|
- human: true or false |
|
811
|
|
|
- test_type: e.g. 'TDLo' |
|
812
|
|
|
- route: e.g. 'skin' |
|
813
|
|
|
- mg_per_kg: e.g. 17.5 |
|
814
|
|
|
""" |
|
815
|
|
|
built = AcuteEffectSearch( |
|
816
|
|
|
key, |
|
817
|
|
|
Apis.Pubchem, |
|
818
|
|
|
top_level=level == 1, |
|
819
|
|
|
) |
|
820
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
821
|
|
|
|
|
822
|
|
|
|
|
823
|
|
|
class EntryChemidPlusLd50(Entry[Ld50Search]): |
|
|
|
|
|
|
824
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
825
|
|
|
def run( |
|
|
|
|
|
|
826
|
|
|
cls, |
|
|
|
|
|
|
827
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
828
|
|
|
key: str = EntryArgs.key("tox.chemidplus:ld50"), |
|
|
|
|
|
|
829
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
830
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
831
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
832
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
833
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
834
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
835
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
836
|
|
|
) -> Searcher: |
|
837
|
|
|
""" |
|
838
|
|
|
LD50 acute effects from ChemIDPlus. |
|
839
|
|
|
|
|
840
|
|
|
OBJECT: A dose in mg/kg (e.g. 3100) |
|
841
|
|
|
|
|
842
|
|
|
PREDICATE: "LD50 :: <route>" (e.g. "LD50 :: intravenous) |
|
843
|
|
|
|
|
844
|
|
|
OTHER COLUMNS: |
|
845
|
|
|
|
|
846
|
|
|
- organism: e.g. 'women', 'infant', 'men', 'human', 'dog', 'domestic animals - sheep and goats' |
|
|
|
|
|
|
847
|
|
|
- human: true or false |
|
848
|
|
|
""" |
|
849
|
|
|
built = Ld50Search(key, Apis.Pubchem) |
|
850
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
851
|
|
|
|
|
852
|
|
|
|
|
853
|
|
|
class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
|
|
|
|
|
|
854
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
855
|
|
|
def run( |
|
|
|
|
|
|
856
|
|
|
cls, |
|
|
|
|
|
|
857
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
858
|
|
|
key: str = EntryArgs.key("g2p:interactions"), |
|
|
|
|
|
|
859
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
860
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
861
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
862
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
863
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
864
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
865
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
866
|
|
|
) -> Searcher: |
|
867
|
|
|
""" |
|
868
|
|
|
Target interactions with affinities from Guide to Pharmacology. |
|
869
|
|
|
|
|
870
|
|
|
OBJECT: A molecular target |
|
871
|
|
|
|
|
872
|
|
|
PREDICATE: "agonism at", etc. |
|
873
|
|
|
|
|
874
|
|
|
OTHER COLUMNS: |
|
875
|
|
|
|
|
876
|
|
|
- affinity: log affinity value |
|
877
|
|
|
- measurement: e.g. pIC50 |
|
878
|
|
|
- primary: whether it is the primary target of the drug |
|
879
|
|
|
- selective: whether it is selective for that target |
|
880
|
|
|
- endogenous: whether the interaction is endogenous |
|
881
|
|
|
- organism: e.g. 'human', 'pig' |
|
882
|
|
|
""" |
|
883
|
|
|
built = G2pInteractionSearch(key, Apis.G2p) |
|
884
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
885
|
|
|
|
|
886
|
|
|
|
|
887
|
|
|
class EntryHmdbTissue(Entry[BioactivitySearch]): |
|
|
|
|
|
|
888
|
|
|
@classmethod |
|
889
|
|
|
def run( |
|
|
|
|
|
|
890
|
|
|
cls, |
|
|
|
|
|
|
891
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
892
|
|
|
key: str = EntryArgs.key("hmdb:tissue"), |
|
|
|
|
|
|
893
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
894
|
|
|
min_nanomolar: Optional[float] = None, |
|
|
|
|
|
|
895
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
896
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
897
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
898
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
899
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
900
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
901
|
|
|
) -> Searcher: |
|
902
|
|
|
""" |
|
903
|
|
|
Tissue concentrations from HMDB (PENDING). |
|
904
|
|
|
|
|
905
|
|
|
OBJECT: |
|
906
|
|
|
|
|
907
|
|
|
PREDICATE: "tissue" |
|
908
|
|
|
""" |
|
909
|
|
|
pass |
|
|
|
|
|
|
910
|
|
|
|
|
911
|
|
|
|
|
912
|
|
|
class EntryHmdbComputed(Entry[BioactivitySearch]): |
|
|
|
|
|
|
913
|
|
|
@classmethod |
|
914
|
|
|
def run( |
|
|
|
|
|
|
915
|
|
|
cls, |
|
|
|
|
|
|
916
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
917
|
|
|
key: str = EntryArgs.key("hmdb:computed"), |
|
|
|
|
|
|
918
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
919
|
|
|
min_nanomolar: Optional[float] = None, |
|
|
|
|
|
|
920
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
921
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
922
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
923
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
924
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
925
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
926
|
|
|
) -> Searcher: |
|
927
|
|
|
""" |
|
928
|
|
|
Computed properties from HMDB (PENDING). |
|
929
|
|
|
|
|
930
|
|
|
Keys include pKa, logP, logS, etc. |
|
931
|
|
|
|
|
932
|
|
|
OBJECT: A number; booleans are converted to 0/1 |
|
933
|
|
|
|
|
934
|
|
|
PREDICATE: The name of the property |
|
935
|
|
|
""" |
|
936
|
|
|
pass |
|
|
|
|
|
|
937
|
|
|
|
|
938
|
|
|
|
|
939
|
|
|
class EntryPubchemReact(Entry[BioactivitySearch]): |
|
|
|
|
|
|
940
|
|
|
@classmethod |
|
941
|
|
|
def run( |
|
|
|
|
|
|
942
|
|
|
cls, |
|
|
|
|
|
|
943
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
944
|
|
|
key: str = EntryArgs.key("inter.pubchem:react"), |
|
|
|
|
|
|
945
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
946
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
947
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
948
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
949
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
950
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
951
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
952
|
|
|
) -> Searcher: |
|
953
|
|
|
""" |
|
954
|
|
|
Metabolic reactions (PENDING). |
|
955
|
|
|
|
|
956
|
|
|
OBJECT: Equation |
|
957
|
|
|
|
|
958
|
|
|
PREDICATE: "<pathway>" |
|
959
|
|
|
""" |
|
960
|
|
|
pass |
|
|
|
|
|
|
961
|
|
|
|
|
962
|
|
|
|
|
963
|
|
|
class EntryPubchemComputed(Entry[ComputedPropertySearch]): |
|
|
|
|
|
|
964
|
|
|
@classmethod |
|
965
|
|
|
def run( |
|
|
|
|
|
|
966
|
|
|
cls, |
|
|
|
|
|
|
967
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
968
|
|
|
key: str = EntryArgs.key("chem.pubchem:computed"), |
|
|
|
|
|
|
969
|
|
|
keys: str = EntryArgs.pubchem_computed_keys, |
|
|
|
|
|
|
970
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
971
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
972
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
973
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
974
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
975
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
976
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
977
|
|
|
) -> Searcher: |
|
978
|
|
|
""" |
|
979
|
|
|
Computed properties from PubChem. |
|
980
|
|
|
|
|
981
|
|
|
OBJECT: Number |
|
982
|
|
|
|
|
983
|
|
|
PREDICATE: e.g. "complexity" |
|
984
|
|
|
""" |
|
985
|
|
|
# replace acronyms, etc. |
|
986
|
|
|
# ComputedPropertySearch standardizes punctuation and casing |
|
987
|
|
|
known = { |
|
988
|
|
|
k: v |
|
989
|
|
|
for k, v in { |
|
990
|
|
|
**EntryArgs.KNOWN_USEFUL_KEYS, |
|
991
|
|
|
**EntryArgs.KNOWN_USELESS_KEYS, |
|
992
|
|
|
}.items() |
|
993
|
|
|
if v is not None |
|
994
|
|
|
} |
|
995
|
|
|
keys = {known.get(s.strip(), s) for s in keys.split(",")} |
|
996
|
|
|
built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys) |
|
997
|
|
|
return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
|
998
|
|
|
|
|
999
|
|
|
|
|
1000
|
|
|
class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
1001
|
|
|
@classmethod |
|
1002
|
|
|
def run( |
|
|
|
|
|
|
1003
|
|
|
cls, |
|
|
|
|
|
|
1004
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
1005
|
|
|
key: str = EntryArgs.key("drugbank.admet:properties"), |
|
|
|
|
|
|
1006
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
1007
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1008
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1009
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
1010
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
1011
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
1012
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1013
|
|
|
) -> Searcher: |
|
1014
|
|
|
""" |
|
1015
|
|
|
Enzyme predictions from DrugBank (PENDING). |
|
1016
|
|
|
|
|
1017
|
|
|
OBJECT: Enzyme name |
|
1018
|
|
|
|
|
1019
|
|
|
PREDICATE: Action |
|
1020
|
|
|
""" |
|
1021
|
|
|
|
|
1022
|
|
|
|
|
1023
|
|
|
class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
1024
|
|
|
@classmethod |
|
1025
|
|
|
def run( |
|
|
|
|
|
|
1026
|
|
|
cls, |
|
|
|
|
|
|
1027
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
1028
|
|
|
key: str = EntryArgs.key("drugbank.admet:metabolites"), |
|
|
|
|
|
|
1029
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
1030
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1031
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1032
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
1033
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
1034
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
1035
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1036
|
|
|
) -> Searcher: |
|
1037
|
|
|
""" |
|
1038
|
|
|
Metabolites from DrugBank (PENDING). |
|
1039
|
|
|
|
|
1040
|
|
|
OBJECT: Compound name (e.g. "norcocaine"). |
|
1041
|
|
|
|
|
1042
|
|
|
PREDICATE: "metabolized to" |
|
1043
|
|
|
""" |
|
1044
|
|
|
|
|
1045
|
|
|
|
|
1046
|
|
|
class EntryDrugbankDosage(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
1047
|
|
|
@classmethod |
|
1048
|
|
|
def run( |
|
|
|
|
|
|
1049
|
|
|
cls, |
|
|
|
|
|
|
1050
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
1051
|
|
|
key: str = EntryArgs.key("drugbank.admet:dosage"), |
|
|
|
|
|
|
1052
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
1053
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1054
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1055
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
1056
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
1057
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
1058
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1059
|
|
|
) -> Searcher: |
|
1060
|
|
|
""" |
|
1061
|
|
|
Dosage from DrugBank (PENDING). |
|
1062
|
|
|
|
|
1063
|
|
|
OBJECT: concentration in mg/mL |
|
1064
|
|
|
|
|
1065
|
|
|
PREDICATE: "dosage :: <route>" |
|
1066
|
|
|
|
|
1067
|
|
|
OTHER COLUMNS: |
|
1068
|
|
|
|
|
1069
|
|
|
- form (e.g. liquid) |
|
1070
|
|
|
""" |
|
1071
|
|
|
|
|
1072
|
|
|
|
|
1073
|
|
|
class EntryMetaRandom(Entry[BioactivitySearch]): |
|
|
|
|
|
|
1074
|
|
|
@classmethod |
|
1075
|
|
|
def run( |
|
|
|
|
|
|
1076
|
|
|
cls, |
|
|
|
|
|
|
1077
|
|
|
path: Path = CommonArgs.compounds, |
|
|
|
|
|
|
1078
|
|
|
key: str = EntryArgs.key("meta:random"), |
|
|
|
|
|
|
1079
|
|
|
to: Optional[Path] = CommonArgs.to_single, |
|
|
|
|
|
|
1080
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1081
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1082
|
|
|
log: Optional[Path] = CommonArgs.log_path, |
|
|
|
|
|
|
1083
|
|
|
quiet: bool = CommonArgs.quiet, |
|
|
|
|
|
|
1084
|
|
|
verbose: bool = CommonArgs.verbose, |
|
|
|
|
|
|
1085
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1086
|
|
|
) -> Searcher: |
|
1087
|
|
|
""" |
|
1088
|
|
|
Random class assignment (PENDING). |
|
1089
|
|
|
|
|
1090
|
|
|
OBJECT: 1 thru n-compounds |
|
1091
|
|
|
|
|
1092
|
|
|
PREDICATE: "random" |
|
1093
|
|
|
""" |
|
1094
|
|
|
pass |
|
|
|
|
|
|
1095
|
|
|
|
|
1096
|
|
|
|
|
1097
|
|
|
Entries = [ |
|
1098
|
|
|
EntryChemblBinding, |
|
1099
|
|
|
EntryChemblMechanism, |
|
1100
|
|
|
EntryChemblAtc, |
|
1101
|
|
|
EntryChemblTrials, |
|
1102
|
|
|
EntryGoFunction, |
|
1103
|
|
|
EntryGoProcess, |
|
1104
|
|
|
EntryGoComponent, |
|
1105
|
|
|
EntryPubchemComputed, |
|
1106
|
|
|
EntryPubchemDisease, |
|
1107
|
|
|
EntryPubchemGeneCoOccurrence, |
|
1108
|
|
|
EntryPubchemDiseaseCoOccurrence, |
|
1109
|
|
|
EntryPubchemChemicalCoOccurrence, |
|
1110
|
|
|
EntryPubchemDgi, |
|
1111
|
|
|
EntryPubchemCgi, |
|
1112
|
|
|
EntryDrugbankTarget, |
|
1113
|
|
|
EntryGeneralFunction, |
|
1114
|
|
|
EntryDrugbankTransporter, |
|
1115
|
|
|
EntryTransporterGeneralFunction, |
|
1116
|
|
|
EntryDrugbankDdi, |
|
1117
|
|
|
EntryPubchemAssay, |
|
1118
|
|
|
EntryDeaSchedule, |
|
1119
|
|
|
EntryDeaClass, |
|
1120
|
|
|
EntryChemidPlusAcute, |
|
1121
|
|
|
EntryChemidPlusLd50, |
|
1122
|
|
|
EntryHmdbTissue, |
|
1123
|
|
|
EntryPubchemReact, |
|
1124
|
|
|
EntryMetaRandom, |
|
1125
|
|
|
] |
|
1126
|
|
|
|
dmyersturnbull /
mandos
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