Package Bio :: Package PopGen :: Package GenePop :: Class Record
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Class Record

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object --+
         |
        Record

Holds information from a GenePop record.

Members:

In most genepop files, the population name is not trustable. It is strongly recommended that populations are referred by index.

populations has one element per population. Each element is itself a list of individuals, each individual is a pair composed by individual name and a list of alleles (2 per marker or 1 for haploids): Example:

[
    [
        ('Ind1', [(1,2),    (3,3), (200,201)],
        ('Ind2', [(2,None), (3,3), (None,None)],
    ],
    [
        ('Other1', [(1,1),  (4,3), (200,200)],
    ]
]
Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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__str__(self)
Returns (reconstructs) a GenePop textual representation.
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split_in_pops(self, pop_names)
Splits a GP record in a dictionary with 1 pop per entry.
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split_in_loci(self, gp)
Splits a GP record in a dictionary with 1 locus per entry.
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remove_population(self, pos)
Removes a population (by position).
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remove_locus_by_position(self, pos)
Removes a locus by position.
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remove_locus_by_name(self, name)
Removes a locus by name.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

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Returns (reconstructs) a GenePop textual representation.
Overrides: object.__str__

split_in_pops(self, pop_names)

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Splits a GP record in a dictionary with 1 pop per entry.

Given a record with n pops and m loci returns a dictionary of records (key pop_name) where each item is a record with a single pop and m loci.

Parameters: pop_names - Population names

split_in_loci(self, gp)

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Splits a GP record in a dictionary with 1 locus per entry.

Given a record with n pops and m loci returns a dictionary of records (key locus name) where each item is a record with a single locus and n pops.