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# Copyright 2010 by Tiago Antao. 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.
"""
Large file parsing of Genepop files
The standard parser loads the whole file into memory. This parser
provides an iterator over data.
Classes:
LargeRecord Holds GenePop data.
Functions:
read Parses a GenePop record (file) into a Record object.
"""
def get_indiv(line):
indiv_name, marker_line = line.split(',')
markers = marker_line.replace('\t', ' ').split(' ')
markers = [marker for marker in markers if marker != '']
if len(markers[0]) in [2, 4]: # 2 digits per allele
marker_len = 2
else:
marker_len = 3
try:
allele_list = [(int(marker[0:marker_len]),
int(marker[marker_len:]))
for marker in markers]
except ValueError: # Haploid
allele_list = [(int(marker[0:marker_len]),)
for marker in markers]
return indiv_name, allele_list, marker_len
def read(handle):
"""Parses a handle containing a GenePop file.
handle is a file-like object that contains a GenePop record.
"""
record = Record(handle)
record.comment_line = str(handle.readline()).rstrip()
# We can now have one loci per line or all loci in a single line
# separated by either space or comma+space...
# We will remove all commas on loci... that should not be a problem
sample_loci_line = str(handle.readline()).rstrip().replace(',', '')
all_loci = sample_loci_line.split(' ')
record.loci_list.extend(all_loci)
line = handle.readline()
while line != "":
line = line.rstrip()
if line.upper() == "POP":
record.stack.append("POP")
break
record.loci_list.append(line)
line = handle.readline()
next_line = handle.readline().rstrip()
indiv_name, allele_list, record.marker_len = get_indiv(next_line)
record.stack.append(next_line)
return record
class Record(object):
"""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.
data_generator Iterates over population data.
The generator will only work once. If you want to read a handle
twice you have to re-open it!
data_generator can either be () - an empty tuple - marking a new
population or an individual. An individual is something like
('Ind1', [(1,1), (3,None), (200,201)],
In the case above the individual is called Ind1,
has three diploid loci. For the second loci, one of the alleles
is unknown.
"""
def __init__(self, handle):
self.handle = handle
self.marker_len = 0
self.comment_line = ""
self.loci_list = []
self.populations = []
self.stack = []
def data_generator(self):
for handle in [self.stack, self.handle]:
for line in handle:
line = line.rstrip()
if line.upper() == 'POP':
yield ()
else:
indiv_name, allele_list, marker_len = get_indiv(line)
clean_list = []
for locus in allele_list:
mk_real = []
for al in locus:
if al == 0:
mk_real.append(None)
else:
mk_real.append(al)
clean_list.append(tuple(mk_real))
yield indiv_name, clean_list
raise StopIteration()
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