How to use the protmapper.uniprot_client function in protmapper

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github sorgerlab / indra / indra / sources / hprd / processor.py View on Github external
assert hgnc_name is not None
        # See if we can get a Uniprot ID from the HGNC symbol--if there is
        # a RefSeq ID we wil also try to use it to get an isoform specific
        # UP ID, but we will have this one to fall back on. But if we can't
        # get one here, then we skip the Statement
        up_id_from_hgnc = hgnc_client.get_uniprot_id(hgnc_id)
        if not up_id_from_hgnc:
            self.no_up_for_hgnc.append((egid, hgnc_name, hgnc_id))
            return None
        # If we have provided the RefSeq ID, it's because we need to make
        # sure that we are getting the right isoform-specific ID (for sequence
        # positions of PTMs). Here we try to get the Uniprot ID from the
        # Refseq->UP mappings in the protmapper.uniprot_client.
        if refseq_id is not None:
            # Get the Uniprot IDs from the uniprot client
            up_ids = uniprot_client.get_ids_from_refseq(refseq_id,
                                                        reviewed_only=True)
            # Nothing for this RefSeq ID (quite likely because the RefSeq ID
            # is obsolete; take the UP ID from HGNC
            if len(up_ids) == 0:
                self.no_up_for_refseq.append(refseq_id)
                up_id = up_id_from_hgnc
            # More than one reviewed entry--no thanks, we'll take the one from
            # HGNC instead
            elif len(up_ids) > 1:
                self.many_ups_for_refseq.append(refseq_id)
                up_id = up_id_from_hgnc
            # We got a unique, reviewed UP entry for the RefSeq ID
            else:
                up_id = up_ids[0]
                # If it's the canonical isoform, strip off the '-1'
                if up_id.endswith('-1'):

protmapper

Map protein sites to human reference sequence.

BSD-2-Clause
Latest version published 11 months ago

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