New source: BiGG Models Metabolite Database

src/pyobo/sources/bigg.py

@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for bigg."""
+import click
+import bioversions
+from typing import Iterable
+from more_click import verbose_option
+from pyobo.path_utils import ensure_df, ensure_tar_df
+from pyobo.struct import Obo, Reference, Synonym, SynonymTypeDef, Term, from_species, TypeDef
+
+HEADER = ['bigg_id', 'universal_bigg_id', 'name', 'model_list', 'database_links',
+          'old_bigg_ids']
+PREFIX = 'bigg'
+
+URL = 'http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt'
+
+alias_type = SynonymTypeDef(id="alias", name="alias")
+has_role = TypeDef(reference=Reference(prefix="bigg", identifier="has_role"))
+
+
+def get_obo(force: bool = False) -> Obo:
+    """Get bigg as OBO."""
+    version = bioversions.get_version("bigg")
+    #version = '1.2'
+    return Obo(
+        ontology=PREFIX,
+        name="bigg models metabolites database",
+        iter_terms=get_terms,
+        iter_terms_kwargs=dict(force=False),
+        typedefs=[has_role],
+        synonym_typedefs=[alias_type],
+        auto_generated_by=f"bio2obo:{PREFIX}",
+        data_version=version,
+    )
+
+
+def get_terms(force: bool = False) -> Iterable[Term]:
+    bigg_df = ensure_df(
+        prefix=PREFIX,
+        url=URL,
+        sep="\t",
+        skiprows=18,
+        header=None,
+        names=HEADER,
+        )
+
+    for r, c in bigg_df.iterrows():
+        bigg_id = c[0]
+        name = c[2]
+        synonyms = []
+        term = Term(
+            reference=Reference(prefix=PREFIX, identifier=bigg_id, name=name),
+            definition=[],
+            synonyms=synonyms,
+        )
+        yield term
+
+
+@click.command()
+@verbose_option
+def _main():
+    obo = get_obo(force=True)
+    obo.write_default(force=True, write_obo=True)
+
+
+if __name__ == "__main__":
+    #get_obo(force=True).write_default(write_obo=True, write_obograph=True, force=True)
+    _main()