Class FileRecord
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Holds information from a GenePop record.
Members:
marker_len The marker length (2 or 3 digit code per allele).
comment_line Comment line.
loci_list List of loci names.
Functions:
get_individual Returns the next individual of the current population.
skip_population Skips the current population.
skip_population skips the individuals of the current population, returns
True if there are more populations.
get_individual returns an individual of the current population (or None
if the list ended).
Each individual is a pair composed by individual
name and a list of alleles (2 per marker or 1 for haploid data).
Examples
('Ind1', [(1,2), (3,3), (200,201)]
('Ind2', [(2,None), (3,3), (None,None)]
('Other1', [(1,1), (4,3), (200,200)]
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start_read(self)
Starts parsing a file containing a GenePop file. |
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__str__(self)
(Informal representation operator)
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Returns (reconstructs) a GenePop textual representation.
This might take a lot of memory. Marker length will be 3.
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Skips the Header. To be done after a re-open.
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Seeks a certain position in the file.
pop - pop position (0 is first) indiv - individual in pop
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Skips the current population. Returns true if there is another
pop.
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Gets the next individual.
Returns individual information if there are more individuals in the
current population. Returns True if there are no more individuals in the
current population, but there are more populations. Next read will be of
the following pop. Returns False if at end of file.
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Removes a population (by position).
pos - position fname - file to be created with population removed
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Removes a locus by position.
pos - position fname - file to be created with locus removed
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remove_loci_by_position(self,
positions,
fname)
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Removes a set of loci by position.
positions - positions fname - file to be created with locus
removed
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Removes a locus by name.
name - name fname - file to be created with locus removed
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Removes a loci list (by name).
names - names fname - file to be created with loci removed
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