comparison Population.py @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

26:91e835060ad2

#!/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 '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

            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 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

27:8997f2ca8c7a

#!/usr/bin/env python

import OrderedDict
import base64
import json
import zlib

import sys

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

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

    @property
    def column(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.OrderedDict()
        self._name = name

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

            return self._columns[column]
        return None

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

    def to_string(self, delimiter=':', separator=' ', replace_names_with=None):
        entries = []

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

    def from_wrapped_dict(self, wrapped_dict):
        unwraped_dict = self.unwrap_dict(wrapped_dict)
        for name, column in unwraped_dict.iteritems():
            individual = Individual(column, name)
            self.add_individual(individual)

    def unwrap_dict(self, wrapped_dict):
        decoded_value = self.decode_value(wrapped_dict)
        decompressed_value = self.decompress_value(decoded_value)
        def _decode_list(data):
            rv = []
            for item in data:
                if isinstance(item, unicode):
                    item = item.encode('utf-8')
                elif isinstance(item, list):
                    item = _decode_list(item)
                elif isinstance(item, dict):
                    item = _decode_dict(item)
                rv.append(item)
            return rv
        def _decode_dict(data):
            rv = {}
            for key, value in data.iteritems():
                if isinstance(key, unicode):
                    key = key.encode('utf-8')
                if isinstance(value, unicode):
                    value = value.encode('utf-8')
                elif isinstance(value, list):
                    value = _decode_list(value)
                elif isinstance(value, dict):
                    value = _decode_dict(value)
                rv[key] = value
            return rv
        unwrapped_dict = json.loads(decompressed_value, object_hook=_decode_dict)
        return unwrapped_dict

    def decode_value(self, value):
        try:
            return base64.b64decode(value)
        except TypeError, message:
            print >> sys.stderr, 'base64.b64decode: {0}: {1}'.format(message, value)
            sys.exit(1)

    def decompress_value(self, value):
        try:
            return zlib.decompress(value)
        except zlib.error, message:
            print >> sys.stderr, 'zlib.decompress: {0}'.format(message)
            sys.exit(1)

    def individual_names(self):
        for column, individual in self._columns.items():
            first_token = individual.name.split()[0]
            yield first_token