annotate Population.py @ 4:7a94f11fe71f

change output.extra_files_path to output.files_path

#!/usr/bin/env python

from OrderedDict import OrderedDict

class Individual(object):
    __slots__ = ['_column', '_name', '_alias']

    def __init__(self, column, name, alias=None):
        self._column = column
        self._name = name
        self._alias = alias

    @property
    def column(self):
        return self._column

    @property
    def name(self):
        return self._name if self._alias is None else self._alias

    @property
    def alias(self):
        return self._alias

    @alias.setter
    def alias(self, alias):
        self._alias = alias

    @property
    def real_name(self):
        return self._name

    def __eq__(self, other):
        return self._column == other._column and self._name == other._name

    def __ne__(self, other):
        return not self.__eq__(other)

    def __repr__(self):
        return 'Individual: column={0} name={1} alias={2}'.format(self._column, self._name, self._alias)


class Population(object):
    def __init__(self, name=None):
        self._columns = OrderedDict()
        self._name = name

    @property
    def name(self):
        return self._name

    @name.setter
    def name(self, name):
        self._name = name

    def add_individual(self, individual, alias=None):
        if individual.column not in self._columns:
            self._columns[individual.column] = individual
        elif self._columns[individual.column] == individual:
            # should should this be an error?
            # should we replace the alias using this entry?
            pass
        else:
            raise 'Duplicate column: {0}'.format(individual)

    def is_superset(self, other):
        for column, other_individual in other._columns.items():
            our_individual = self._columns.get(column)
            if our_individual is None or our_individual != other_individual:
                return False
        return True

    def is_disjoint(self, other):
        for column, our_individual in self._columns.items():
            other_individual = other._columns.get(column)
            if other_individual is not None and other_individual == our_individual:
                return False
        return True

    def column_list(self):
        return self._columns.keys()

    def individual_with_column(self, column):
        if column in self._columns:
            return self._columns[column]
        return None

    def tag_list(self, delimiter=':'):
        entries = []
        for column, individual in self._columns.items():
            entry = '{0}{1}{2}'.format(column, delimiter, individual.name)
            entries.append(entry)
        return entries

    def to_string(self, delimiter=':', separator=' ', replace_names_with=None):
        entries = []
        for column, individual in self._columns.items():
            value = individual.name
            if replace_names_with is not None:
                value = replace_names_with
            entry = '{0}{1}{2}'.format(column, delimiter, value)
            entries.append(entry)
        return separator.join(entries)

    def __str__(self):
        return self.to_string()

    def from_population_file(self, filename):
        with open(filename) as fh:
            for line in fh:
                line = line.rstrip('\r\n')
                column, name, alias = line.split('\t')
                alias = alias.strip()
                individual = Individual(column, name)
                if alias:
                    individual.alias = alias
                self.add_individual(individual)

    def from_tag_list(self, tag_list):
        for tag in tag_list:
            column, name = tag.split(':')
            individual = Individual(column, name)
            self.add_individual(individual)

    def individual_names(self):
        for column, individual in self._columns.items():
            yield individual.name