How to use the protmapper.uniprot_client.get_mnemonic function in protmapper

To help you get started, we’ve selected a few protmapper examples, based on popular ways it is used in public projects.

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github pybel / pybel / src / pybel / grounding.py View on Github external
concept[NAMESPACE] = _mapped[NAMESPACE]
        concept[IDENTIFIER] = _mapped[IDENTIFIER]
        concept[NAME] = _mapped[NAME]
        return True
    elif prefix == 'bel':
        logger.warning('could not figure out how to map bel ! %s', name)
        return False

    if prefix == 'uniprot':
        # assume identifier given as name
        identifier = get_id_from_mnemonic(name)
        if identifier is not None:
            concept[IDENTIFIER] = identifier
            return True

        mnemomic = get_mnemonic(name, web_fallback=True)
        if mnemomic is not None:
            concept[IDENTIFIER] = name
            concept[NAME] = mnemomic
            return True

        logger.warning('could not interpret uniprot name: %s', name)
        return False

    try:
        id_name_mapping = get_name_id_mapping(prefix)
    except (NoOboFoundry, MissingOboBuild) as e:
        logger.warning('could not get namespace %s - %s', prefix, e)
        return False

    if id_name_mapping is None:
        logger.warning('unhandled namespace in %s ! %s', prefix, name)
github pybel / pybel / src / pybel / grounding.py View on Github external
def _handle_identifier_not_name(*, concept, prefix, identifier) -> bool:
    # Some namespaces are just too much of a problem at the moment to look up
    if prefix in SKIP:
        return False

    if prefix in NO_NAMES:
        concept[NAME] = concept[IDENTIFIER]
        return True

    if prefix == 'uniprot':
        concept[NAME] = get_mnemonic(identifier)
        return True

    try:
        id_name_mapping = get_id_name_mapping(prefix)
    except (NoOboFoundry, MissingOboBuild):
        return False

    if id_name_mapping is None:
        logger.warning('could not get names for prefix %s', prefix)
        return False
    name = id_name_mapping.get(identifier)
    if name is None:
        logger.warning('could not get name for %s:%s', prefix, identifier)
        return False
    concept[NAME] = name

protmapper

Map protein sites to human reference sequence.

BSD-2-Clause
Latest version published 2 months ago

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