Source code for lineage.individual

"""Class for representing individuals within the `lineage` framework."""

import inspect

from snps import SNPs
from snps.utils import clean_str




class Individual(SNPs):
    """Object used to represent and interact with an individual.

    The ``Individual`` object maintains information about an individual. The object provides
    methods for loading an individual's genetic data (SNPs) and normalizing it for use with the
    `lineage` framework.

    ``Individual`` inherits from ``snps.SNPs``. See here for details about the ``SNPs`` object:
    https://snps.readthedocs.io/en/latest/snps.html
    """



    def __init__(self, name, raw_data=(), **kwargs):
        """Initialize an ``Individual`` object.

        Parameters
        ----------
        name : str
            name of the individual
        raw_data : str, bytes, ``SNPs`` (or list or tuple thereof)
            path(s) to file(s), bytes, or ``SNPs`` object(s) with raw genotype data
        **kwargs
            parameters to ``snps.SNPs`` and/or ``snps.SNPs.merge``
        """
        self._name = name

        init_args = self._get_defined_kwargs(SNPs, kwargs)
        merge_args = self._get_defined_kwargs(SNPs.merge, kwargs)

        super().__init__(**init_args)

        # load raw data by merging `SNPs` objects into this object
        if not isinstance(raw_data, list) and not isinstance(raw_data, tuple):
            s = (
                SNPs(raw_data, **init_args)
                if not isinstance(raw_data, SNPs)
                else raw_data
            )
            self.merge([s], **merge_args)
        else:
            for file in raw_data:
                s = file
                if not isinstance(file, SNPs):
                    s = SNPs(file, **init_args)

                self.merge([s], **merge_args)


    def _get_defined_kwargs(self, callable, kwargs):
        sig = inspect.signature(callable)
        return {k: kwargs[k] for k in kwargs if k in sig.parameters}

    def __repr__(self):
        return "Individual({!r})".format(self._name)

    @property
    def name(self):
        """Get this ``Individual``'s name.

        Returns
        -------
        str
        """
        return self._name



    def get_var_name(self):
        return clean_str(self.name)