pyobo 0.12.7__py3-none-any.whl → 0.12.9__py3-none-any.whl

pyobo/sources/chembl/chembl_target.py

@@ -138,7 +138,7 @@ def iter_terms(version: str) -> Iterable[Term]:
 def get_chembl_protein_equivalences(version: str | None = None) -> dict[str, list[str]]:
     """Get ChEMBL protein equivalences."""
     if version is None:
-        version = chembl_downloader.latest()
+        version = chembl_downloader.latest(full=False)
     url = f"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_{version}/chembl_uniprot_mapping.txt"
     df = ensure_df(
         PREFIX,

pyobo/sources/expasy.py

@@ -160,7 +160,8 @@ def normalize_expasy_id(expasy_id: str) -> str:
     """Return a standardized ExPASy identifier string.
 
     :param expasy_id: A possibly non-normalized ExPASy identifier
-    :return: A normalized string.
+
+    :returns: A normalized string.
     """
     return expasy_id.replace(" ", "")
 
@@ -211,6 +212,7 @@ def get_database(lines: Iterable[str]) -> Mapping[str, dict[str, Any]]:
     """Parse the ExPASy database file and returns a list of enzyme entry dictionaries.
 
     :param lines: An iterator over the ExPASy database file or file-like
+
     :returns: A mapping from EC code to data
     """
     rv = {}
@@ -285,6 +287,7 @@ def _parse_transfer(value: str) -> list[str]:
     """Parse transferred entry string.
 
     :param value: A string for a transferred entry
+
     :returns: A list of EC codes that it got transferred to
 
     >>> _parse_transfer("Transferred entry: 1.1.1.198, 1.1.1.227 and 1.1.1.228.")

pyobo/sources/go.py

@@ -13,7 +13,8 @@ def is_biological_process(identifier: str) -> bool:
     """Return if the given GO identifier is a biological process.
 
     :param identifier: A local unique identifier from GO
-    :return: If the identifier is a biological process
+
+    :returns: If the identifier is a biological process
 
     >>> is_biological_process("0006915")
     True
@@ -27,7 +28,8 @@ def is_molecular_function(identifier: str) -> bool:
     """Return if the given GO identifier is a molecular function.
 
     :param identifier: A local unique identifier from GO
-    :return: If the identifier is a molecular function
+
+    :returns: If the identifier is a molecular function
 
     >>> is_molecular_function("0006915")
     False
@@ -39,7 +41,8 @@ def is_cellular_component(identifier: str) -> bool:
     """Return if the given GO identifier is a cellular component.
 
     :param identifier: A local unique identifier from GO
-    :return: If the identifier is a cellular component
+
+    :returns: If the identifier is a cellular component
 
     >>> is_cellular_component("0006915")
     False

pyobo/sources/gtdb.py

@@ -117,6 +117,7 @@ def _parse_name(part: str) -> tuple[str, str] | None:
     """Parse a GTDB taxonomy identifier.
 
     :param part: The string
+
     :returns: A tuple with the level and name, if parsable
 
     >>> _parse_name("f__Sulfolobaceae")

pyobo/sources/iana_media_type.py

@@ -1,6 +1,8 @@
 """An ontology representation of IANA media types (i.e. MIME types).
 
-.. seealso:: https://www.iana.org/assignments/media-types/media-types.xhtml
+.. seealso::
+
+    https://www.iana.org/assignments/media-types/media-types.xhtml
 """
 
 from collections.abc import Iterable

pyobo/sources/iconclass.py

@@ -0,0 +1,55 @@
+"""Get ICONCLASS as OBO."""
+
+from collections.abc import Iterable
+from urllib.parse import quote
+
+import pandas as pd
+
+from pyobo.struct import Obo, Term
+from pyobo.utils.path import ensure_df
+
+__all__ = [
+    "IconclassGetter",
+]
+
+PREFIX = "iconclass"
+BASE_URL = "https://github.com/iconclass/data/raw/refs/heads/main/txt/en/txt_en_{}.txt"
+URLS = [
+    BASE_URL.format("0_1"),
+    BASE_URL.format("2_3"),
+    BASE_URL.format("4"),
+    BASE_URL.format("5_6_7_8"),
+    BASE_URL.format("9"),
+    BASE_URL.format("keys"),
+    # shakespeare
+]
+
+
+def get_df() -> pd.DataFrame:
+    """Get an ICONCLASS terms dataframe."""
+    df = pd.concat(
+        ensure_df(prefix=PREFIX, url=url, sep="|", names=["luid", "name"]) for url in URLS
+    )
+    return df
+
+
+def iter_terms() -> Iterable[Term]:
+    """Iterate over terms in ICONCLASS."""
+    for luid, name in get_df().values:
+        yv = Term.from_triple(prefix=PREFIX, identifier=quote(luid), name=name)
+        yield yv
+
+
+class IconclassGetter(Obo):
+    """An ontology representation of ICONCLASS."""
+
+    ontology = PREFIX
+    dynamic_version = True
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iter_terms()
+
+
+if __name__ == "__main__":
+    IconclassGetter.cli()

pyobo/struct/functional/macros.py

@@ -1,7 +1,7 @@
 """Macros over functional OWL.
 
-This module contains classes that are extensions
-to functional OWL that reflect common usage.
+This module contains classes that are extensions to functional OWL that reflect common
+usage.
 """
 
 import typing as t
@@ -57,8 +57,7 @@ class Macro(f.Box):
 class RelationshipMacro(Macro):
     """A macro for an object-to-object relationship.
 
-    Assert that the RAET1E gene from HGNC (16793) is
-    only in the human taxon (9606)
+    Assert that the RAET1E gene from HGNC (16793) is only in the human taxon (9606)
 
     >>> RelationshipMacro("hgnc:16793", "RO:0002160", "NCBITaxon:9606").to_funowl()
     'SubClassOf(hgnc:16793 ObjectSomeValuesFrom(RO:0002160 NCBITaxon:9606))'
@@ -226,8 +225,8 @@ class SynonymMacro(Macro):
     >>> SynonymMacro("hgnc:16793", "ULBP4").to_funowl()
     'AnnotationAssertion(oboInOwl:hasRelatedSynonym hgnc:16793 "ULBP4")'
 
-    You can make the predicate more explicit either with OBO-style
-    scoping (``EXACT``, ``BROAD``, ``NARROW``, ``RELATED``) or a CURIE/:class:`curies.Reference`/URIRef
+    You can make the predicate more explicit either with OBO-style scoping (``EXACT``,
+    ``BROAD``, ``NARROW``, ``RELATED``) or a CURIE/:class:`curies.Reference`/URIRef
 
     >>> SynonymMacro("hgnc:16793", "ULBP4", "EXACT").to_funowl()
     'AnnotationAssertion(oboInOwl:hasExactSynonym hgnc:16793 "ULBP4")'
@@ -337,14 +336,15 @@ class HoldsOverChain(Macro):
 class TransitiveOver(HoldsOverChain):
     """A macro for the OBO-style "transitive over" annotation.
 
-    For example, ``BFO:0000066`` (occurs in) is transitive over
-    ``BFO:0000050`` (part of). This means that if X occurs in Y,
-    and Y is a part of Z, then X occurs in Z.
+    For example, ``BFO:0000066`` (occurs in) is transitive over ``BFO:0000050`` (part
+    of). This means that if X occurs in Y, and Y is a part of Z, then X occurs in Z.
 
     >>> TransitiveOver("BFO:0000066", "BFO:0000050").to_funowl()
     'SubObjectPropertyOf(ObjectPropertyChain(BFO:0000066 BFO:0000050) BFO:0000066)'
 
-    .. note:: This is a special case of :class:`HoldsOverChain`
+    .. note::
+
+        This is a special case of :class:`HoldsOverChain`
     """
 
     def __init__(self, predicate: f.IdentifierBoxOrHint, target: f.IdentifierBoxOrHint):
@@ -355,8 +355,8 @@ class TransitiveOver(HoldsOverChain):
 class DataPropertyMaxCardinality(Macro):
     r"""A macro over :class:`DataMaxCardinality` that adds an axiom.
 
-    For example, each person can be annotated with a maximum of one age.
-    This can be represented as:
+    For example, each person can be annotated with a maximum of one age. This can be
+    represented as:
 
     >>> DataPropertyMaxCardinality(1, "a:hasAge").to_funowl()
     'SubClassOf(owl:Thing DataMaxCardinality(1 a:hasAge))'

pyobo/struct/reference.py

@@ -142,9 +142,11 @@ def get_preferred_curie(
 def default_reference(prefix: str, identifier: str, name: str | None = None) -> Reference:
     """Create a CURIE for an "unqualified" reference.
 
-    :param prefix: The prefix of the ontology in which the "unqualified" reference is made
+    :param prefix: The prefix of the ontology in which the "unqualified" reference is
+        made
     :param identifier: The "unqualified" reference. For example, if you just write
         "located_in" somewhere there is supposed to be a CURIE
+
     :returns: A CURIE for the "unqualified" reference based on the OBO semantic space
 
     >>> default_reference("chebi", "conjugate_base_of")

pyobo/struct/struct.py

@@ -383,7 +383,8 @@ class Term(Stanza):
     def get_species(self, prefix: str = NCBITAXON_PREFIX) -> Reference | None:
         """Get the species if it exists.
 
-        :param prefix: The prefix to use in case the term has several species annotations.
+        :param prefix: The prefix to use in case the term has several species
+            annotations.
         """
         for species in self.get_relationships(v.from_species):
             if species.prefix == prefix:
@@ -1651,7 +1652,9 @@ class Obo:
     ) -> Mapping[str, str]:
         """Get a mapping from a term's identifier to the property.
 
-        .. warning:: Assumes there's only one version of the property for each term.
+        .. warning::
+
+            Assumes there's only one version of the property for each term.
         """
         return {
             term.identifier: value
@@ -1692,8 +1695,8 @@ class Obo:
     ) -> Iterable[tuple[Stanza, TypeDef, Reference]]:
         """Iterate over tuples of terms, relations, and their targets.
 
-        This only outputs stuff from the `relationship:` tag, not
-        all possible triples. For that, see :func:`iterate_edges`.
+        This only outputs stuff from the `relationship:` tag, not all possible triples.
+        For that, see :func:`iterate_edges`.
         """
         _warned: set[ReferenceTuple] = set()
         typedefs = self._index_typedefs()
@@ -1804,9 +1807,11 @@ class Obo:
     ) -> Mapping[str, str]:
         """Get a mapping from the term's identifier to the target's identifier.
 
-        .. warning:: Assumes there's only one version of the property for each term.
+        .. warning::
+
+            Assumes there's only one version of the property for each term.
 
-         Example usage: get homology between HGNC and MGI:
+        Example usage: get homology between HGNC and MGI:
 
         >>> from pyobo.sources.hgnc import HGNCGetter
         >>> obo = HGNCGetter()
@@ -2031,7 +2036,8 @@ class Obo:
 class TypeDef(Stanza):
     """A type definition in OBO.
 
-    See the subsection of https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html#S.2.2.
+    See the subsection of
+    https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html#S.2.2.
     """
 
     reference: Annotated[Reference, 1]
@@ -2126,14 +2132,16 @@ class TypeDef(Stanza):
     ) -> Iterable[str]:
         """Iterate over the lines to write in an OBO file.
 
-        :param ontology_prefix:
-            The prefix of the ontology into which the type definition is being written.
-            This is used for compressing builtin identifiers
-        :yield:
-            The lines to write to an OBO file
+        :param ontology_prefix: The prefix of the ontology into which the type
+            definition is being written. This is used for compressing builtin
+            identifiers
+
+        :yield: The lines to write to an OBO file
 
-        `S.3.5.5 <https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html#S.3.5.5>`_
-        of the OBO Flat File Specification v1.4 says tags should appear in the following order:
+        `S.3.5.5
+        <https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html#S.3.5.5>`_ of
+        the OBO Flat File Specification v1.4 says tags should appear in the following
+        order:
 
         1. id
         2. is_anonymous