Class FileRecord
source code
object --+
|
FileRecord
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)]
|
|
__init__(self,
fname)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
source code
|
|
|
|
|
|
|
start_read(self)
Starts parsing a file containing a GenePop file. |
source code
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Inherited from object:
__delattr__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__
|
|
Inherited from object:
__class__
|
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
- Overrides:
object.__init__
- (inherited documentation)
|
__str__(self)
(Informal representation operator)
| source code
|
Returns (reconstructs) a GenePop textual representation.
This might take a lot of memory.
Marker length will be 3.
- Overrides:
object.__str__
|
Skips the Header. To be done after a re-open.
|
Seeks a certain position in the file.
pop - pop position (0 is first)
indiv - individual in pop
|
Skips the current population. Returns true if there is another pop.
|
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.
|
Removes a population (by position).
pos - position
fname - file to be created with population removed
|
Removes a locus by position.
pos - position
fname - file to be created with locus removed
|
remove_loci_by_position(self,
positions,
fname)
| source code
|
Removes a set of loci by position.
positions - positions
fname - file to be created with locus removed
|
Removes a locus by name.
name - name
fname - file to be created with locus removed
|
Removes a loci list (by name).
names - names
fname - file to be created with loci removed
|