Calculate ortholog relationships in Reactome

scripts/generate_reactome_orthologs.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+
+"""Generate orthologous relations between Reactome pathways."""
+
+from collections import defaultdict
+from typing import Iterable, List, Mapping
+
+from biomappings.orthologs import iterate_orthologs
+from biomappings.resources import MappingTuple, append_true_mapping_tuples
+
+
+def _get_species_to_identifiers(names: Mapping[str, str]) -> Mapping[str, List[str]]:
+    species_to_identifiers = defaultdict(list)
+    for identifier in names:
+        species_to_identifiers[identifier.split("-")[-1]].append(identifier)
+    return species_to_identifiers
+
+
+def iterate_orthologous_lexical_matches() -> Iterable[MappingTuple]:
+    """Generate orthologous relations between Reactome pathways."""
+    yield from iterate_orthologs("reactome", _get_species_to_identifiers)
+
+
+if __name__ == "__main__":
+    append_true_mapping_tuples(iterate_orthologous_lexical_matches())

src/biomappings/orthologs.py

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+# -*- coding: utf-8 -*-
+
+"""Utilities for generating ortholog predictions."""
+
+import itertools as itt
+import logging
+from typing import Callable, Iterable, List, Mapping
+
+import pyobo
+from tqdm import tqdm
+
+from .resources import MappingTuple
+from .utils import get_script_url
+
+__all__ = [
+    "iterate_orthologs",
+]
+
+logger = logging.getLogger(__name__)
+
+
+def iterate_orthologs(
+    prefix: str,
+    f: Callable[[Mapping[str, str]], Mapping[str, List[str]]],
+) -> Iterable[MappingTuple]:
+    """Iterate over orthologs based on identifier matching."""
+    provenance = get_script_url(__file__)
+    names = pyobo.get_id_name_mapping(prefix)
+    parent_identifier_to_species_identifier = f(names)
+    count = 0
+    for identifiers in tqdm(parent_identifier_to_species_identifier.values()):
+        for source_id, target_id in itt.product(identifiers, repeat=2):
+            if source_id >= target_id:
+                continue
+            count += 1
+            yield MappingTuple(
+                prefix,
+                source_id,
+                names[source_id],
+                "RO:HOM0000017",
+                prefix,
+                target_id,
+                names[target_id],
+                "calculated",
+                provenance,
+            )
+    logger.info(f"[{prefix}] Identified {count} orthologs")