New source: BiGG Models Metabolite Database #124
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cthoyt
reviewed
Nov 10, 2021
cthoyt
reviewed
Nov 10, 2021
cthoyt
reviewed
Nov 10, 2021
…eded from ensure_df()
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Hi Charlie, I just added new changes. Please review them in your free time. Thanks! |
cthoyt
reviewed
Nov 12, 2021
| version=version, | ||
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| for v in bigg_df.values: |
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v is a bad variable name. Better is to use tuple unpacking
Suggested change
| for v in bigg_df.values: | |
| for bigg_id, name in bigg_df.values: |
cthoyt
requested changes
Nov 12, 2021
src/pyobo/sources/bigg.py
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| skiprows=18, | ||
| header=None, | ||
| names=HEADER, | ||
| usecols=['bigg_id', 'name'], |
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what about the other columns? database_links has lots of information worth parsing out, for example. old_bigg_ids can be put in the alternative identifier field in the pyobo.Term
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| def get_terms(force: bool = False, version: Optional[str] = None) -> Iterable[Term]: |
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check CI - this needs a docstring
cthoyt
reviewed
Nov 12, 2021
| @@ -0,0 +1,63 @@ | |||
| # -*- coding: utf-8 -*- | |||
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| """Converter for bigg.""" | |||
cthoyt
requested changes
Nov 12, 2021
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| def get_obo(force: bool = False) -> Obo: | ||
| """Get bigg as OBO.""" |
| def get_obo(force: bool = False) -> Obo: | ||
| """Get bigg as OBO.""" | ||
| version = bioversions.get_version("bigg") | ||
| # version = '1.2' |
| # version = '1.2' | ||
| return Obo( | ||
| ontology=PREFIX, | ||
| name="bigg models metabolites database", |
| name="bigg models metabolites database", | ||
| iter_terms=get_terms, | ||
| iter_terms_kwargs=dict(force=force, version=version), | ||
| typedefs=[has_role], |
src/pyobo/sources/bigg.py
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| for v in bigg_df.values: | ||
| bigg_id = v[0] | ||
| name = v[1] | ||
| synonyms = [] |
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@cthoyt This is still a work in progress PR.
get_obofunction. Could you please test it on your end and see where I am going wrong?Thanks!