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

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github sorgerlab / indra / indra / preassembler / sitemapper.py View on Github external
mm_ws = '\n' + (' ' * 17)
            mm_str = mm_ws.join([str(mm) for mm in self.mapped_mods])

        summary = textwrap.dedent("""
            MappedStatement:
                original_stmt: {0}
                mapped_mods: {1}
                mapped_stmt: {2}
            """)
        return summary.format(self.original_stmt, mm_str, self.mapped_stmt)

    def __repr__(self):
        return str(self)


class SiteMapper(ProtMapper):
    """
    Use site information to fix modification sites in Statements.

    This is a wrapper around the protmapper package's ProtMapper class and adds
    all the additional functionality to handle INDRA Statements and Agents.

    Parameters
    ----------
    site_map : dict (as returned by :py:func:`load_site_map`)
        A dict mapping tuples of the form `(gene, orig_res, orig_pos)` to a
        tuple of the form `(correct_res, correct_pos, comment)`, where `gene`
        is the string name of the gene (canonicalized to HGNC); `orig_res` and
        `orig_pos` are the residue and position to be mapped; `correct_res` and
        `correct_pos` are the corrected residue and position, and `comment` is
        a string describing the reason for the mapping (species error, isoform
        error, wrong residue name, etc.).

protmapper

Map protein sites to human reference sequence.

BSD-2-Clause
Latest version published 3 months ago

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