How to use the protmapper.api.default_site_map function in protmapper

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github sorgerlab / indra / indra / preassembler / sitemapper.py View on Github external
return None
        # If no site information for this residue, skip
        if mod_condition.position is None or mod_condition.residue is None:
            return None
        # Otherwise, try to map it and return the mapped site
        mapped_site = \
            self.map_to_human_ref(up_id, 'uniprot',
                mod_condition.residue,
                mod_condition.position,
                do_methionine_offset=self.do_methionine_offset,
                do_orthology_mapping=self.do_orthology_mapping,
                do_isoform_mapping=self.do_isoform_mapping)
        return mapped_site


default_mapper = SiteMapper(default_site_map)


# TODO: determine if this should be done in the protmapper or if this is the
# preferred place
@lru_cache(maxsize=10000)
def _get_uniprot_id(agent):
    """Return the UniProt ID for an agent, looking up in HGNC if necessary.

    If the UniProt ID is a list then return the first ID by default.
    """
    up_id = agent.db_refs.get('UP')
    hgnc_id = agent.db_refs.get('HGNC')
    if up_id is None:
        if hgnc_id is None:
            # If both UniProt and HGNC refs are missing we can't
            # sequence check and so don't report a failure.

protmapper

Map protein sites to human reference sequence.

BSD-2-Clause
Latest version published 4 months ago

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