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# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""This module provides code to work with FDist (DEPRECATED).
See http://www.rubic.rdg.ac.uk/~mab/software.html (old) and
http://www.maths.bris.ac.uk/~mamab/ (new) for downloading the
FDist tool by Mark Beaumont.
Classes:
Record Holds FDist data.
Functions:
read Parses a FDist record (file) into a Record object.
"""
import warnings
from Bio import BiopythonDeprecationWarning
warnings.warn("Bio.PopGen.FDist has been deprecated, and we intend to remove"
" it in a future release of Biopython. If you would like to"
" continue using it, please contact the Biopython developers"
" via the mailing list.", BiopythonDeprecationWarning)
def read(handle):
"""Parses FDist data into a Record object.
handle is a file-like object that contains a FDist record.
"""
record = Record()
record.data_org = int(str(next(handle)).rstrip())
record.num_pops = int(str(next(handle)).rstrip())
record.num_loci = int(str(next(handle)).rstrip())
for i in range(record.num_loci):
next(handle)
num_alleles = int(str(next(handle)).rstrip())
pops_data = []
if record.data_org == 0:
for j in range(record.num_pops):
line_comp = str(next(handle)).rstrip().split(' ')
pop_dist = [int(x) for x in line_comp]
pops_data.append(pop_dist)
else:
raise NotImplementedError('1/alleles by rows not implemented')
record.loci_data.append((num_alleles, pops_data))
return record
class Record(object):
"""Holds information from a FDist record.
Members:
- data_org Data organization (0 pops by rows, 1 alleles by rows).
The Record will behave as if data was 0 (converting if needed)
- num_pops Number of populations
- num_loci Number of loci
- loci_data Loci data
loci_data is a list, where each element represents a locus. Each element
is a tuple, the first element is the number of alleles, the second
element a list. Each element of the list is the count of each allele
per population.
"""
def __init__(self):
self.data_org = 0
self.num_pops = 0
self.num_loci = 0
self.loci_data = []
def __str__(self):
rep = ['0\n'] # We only export in 0 format, even if originally was 1
rep.append(str(self.num_pops) + '\n')
rep.append(str(self.num_loci) + '\n')
rep.append('\n')
for locus_data in self.loci_data:
num_alleles, pops_data = locus_data
rep.append(str(num_alleles) + '\n')
for pop_data in pops_data:
for allele_count in pop_data:
rep.append(str(allele_count) + ' ')
rep.append('\n')
rep.append('\n')
return "".join(rep)
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