def _convert_genepop_to_fdist_big(gp_rec, report_pops=None):
"""Converts a big GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Big)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
fd_rec.data_org = 1
fd_rec.num_loci = len(gp_rec.loci_list)
num_loci = len(gp_rec.loci_list)
loci = []
for i in range(num_loci):
loci.append(set())
pops = []
work_rec = FileParser.read(gp_rec.fname)
lParser = work_rec.get_individual()
def init_pop():
my_pop = []
for i in range(num_loci):
my_pop.append({})
return my_pop
curr_pop = init_pop()
num_pops = 1
if report_pops:
report_pops(num_pops)
while lParser:
if lParser is not True:
for loci_pos in range(num_loci):
for al in lParser[1][loci_pos]:
if al is not None:
loci[loci_pos].add(al)
curr_pop[loci_pos][al] = curr_pop[loci_pos].get(al,
0) + 1
else:
pops.append(curr_pop)
num_pops += 1
if report_pops:
report_pops(num_pops)
curr_pop = init_pop()
lParser = work_rec.get_individual()
work_rec._handle.close() # TODO - Needs a proper fix
pops.append(curr_pop)
fd_rec.num_pops = num_pops
for loci_pos in range(num_loci):
alleles = sorted(loci[loci_pos])
loci_rec = [len(alleles), []]
for pop in pops:
pop_rec = []
for allele in alleles:
pop_rec.append(pop[loci_pos].get(allele, 0))
loci_rec[1].append(pop_rec)
fd_rec.loci_data.append(tuple(loci_rec))
return fd_rec
def _convert_genepop_to_fdist_big(gp_rec, report_pops = None):
"""Converts a big GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Big)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
fd_rec.data_org = 1
fd_rec.num_loci = len(gp_rec.loci_list)
num_loci = len(gp_rec.loci_list)
loci = []
for i in range(num_loci):
loci.append(set())
pops = []
work_rec = FileParser.read(gp_rec.fname)
lParser = work_rec.get_individual()
def init_pop():
my_pop = []
for i in range(num_loci):
my_pop.append({})
return my_pop
curr_pop = init_pop()
num_pops = 1
if report_pops:
report_pops(num_pops)
while lParser:
if lParser is not True:
for loci_pos in range(num_loci):
for al in lParser[1][loci_pos]:
if al is not None:
loci[loci_pos].add(al)
curr_pop[loci_pos][al]= curr_pop[loci_pos].get(al, 0)+1
else:
pops.append(curr_pop)
num_pops += 1
if report_pops:
report_pops(num_pops)
curr_pop = init_pop()
lParser = work_rec.get_individual()
work_rec._handle.close() # TODO - Needs a proper fix
pops.append(curr_pop)
fd_rec.num_pops = num_pops
for loci_pos in range(num_loci):
alleles = sorted(loci[loci_pos])
loci_rec = [len(alleles), []]
for pop in pops:
pop_rec = []
for allele in alleles:
pop_rec.append(pop[loci_pos].get(allele, 0))
loci_rec[1].append(pop_rec)
fd_rec.loci_data.append(tuple(loci_rec))
return fd_rec
def countPops(rec):
f2 = FileParser.read(rec.fname)
popCnt = 1
while f2.skip_population():
popCnt += 1
return popCnt
def _convert_genepop_to_fdist_big_old(gp_rec, report_loci=None):
"""Converts a big GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Big)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
def countPops(rec):
f2 = FileParser.read(rec.fname)
popCnt = 1
while f2.skip_population():
popCnt += 1
return popCnt
fd_rec.data_org = 0
fd_rec.num_loci = len(gp_rec.loci_list)
work_rec0 = FileParser.read(gp_rec.fname)
fd_rec.num_pops = countPops(work_rec0)
num_loci = len(gp_rec.loci_list)
for lc_i in range(num_loci):
if report_loci:
report_loci(lc_i, num_loci)
work_rec = FileParser.read(gp_rec.fname)
work_rec2 = FileParser.read(gp_rec.fname)
alleles = []
pop_data = []
lParser = work_rec.get_individual()
while lParser:
if lParser is not True:
for al in lParser[1][lc_i]:
if al is not None and al not in alleles:
alleles.append(al)
lParser = work_rec.get_individual()
#here we go again (necessary...)
alleles.sort()
def process_pop(pop_data, alleles, allele_counts):
allele_array = [] # We need the same order as in alleles
for allele in alleles:
allele_array.append(allele_counts.get(allele, 0))
pop_data.append(allele_array)
lParser = work_rec2.get_individual()
allele_counts = {}
for allele in alleles:
allele_counts[allele] = 0
allele_counts[None] = 0
while lParser:
if lParser is True:
process_pop(pop_data, alleles, allele_counts)
allele_counts = {}
for allele in alleles:
allele_counts[allele] = 0
allele_counts[None] = 0
else:
for al in lParser[1][lc_i]:
allele_counts[al] += 1
lParser = work_rec2.get_individual()
process_pop(pop_data, alleles, allele_counts)
fd_rec.loci_data.append((len(alleles), pop_data))
return fd_rec
def countPops(rec):
f2 = FileParser.read(rec.fname)
popCnt = 1
while f2.skip_population():
popCnt += 1
return popCnt
def _convert_genepop_to_fdist_big_old(gp_rec, report_loci = None):
"""Converts a big GenePop record to a FDist one.
Parameters:
gp_rec - Genepop Record (Big)
Returns:
FDist record.
"""
fd_rec = Bio.PopGen.FDist.Record()
def countPops(rec):
f2 = FileParser.read(rec.fname)
popCnt = 1
while f2.skip_population():
popCnt += 1
return popCnt
fd_rec.data_org = 0
fd_rec.num_loci = len(gp_rec.loci_list)
work_rec0 = FileParser.read(gp_rec.fname)
fd_rec.num_pops = countPops(work_rec0)
num_loci = len(gp_rec.loci_list)
for lc_i in range(num_loci):
if report_loci:
report_loci(lc_i, num_loci)
work_rec = FileParser.read(gp_rec.fname)
work_rec2 = FileParser.read(gp_rec.fname)
alleles = []
pop_data = []
lParser = work_rec.get_individual()
while lParser:
if lParser is not True:
for al in lParser[1][lc_i]:
if al is not None and al not in alleles:
alleles.append(al)
lParser = work_rec.get_individual()
#here we go again (necessary...)
alleles.sort()
def process_pop(pop_data, alleles, allele_counts):
allele_array = [] # We need the same order as in alleles
for allele in alleles:
allele_array.append(allele_counts.get(allele, 0))
pop_data.append(allele_array)
lParser = work_rec2.get_individual()
allele_counts = {}
for allele in alleles:
allele_counts[allele] = 0
allele_counts[None]=0
while lParser:
if lParser is True:
process_pop(pop_data, alleles, allele_counts)
allele_counts = {}
for allele in alleles:
allele_counts[allele] = 0
allele_counts[None]=0
else:
for al in lParser[1][lc_i]:
allele_counts[al] += 1
lParser = work_rec2.get_individual()
process_pop(pop_data, alleles, allele_counts)
fd_rec.loci_data.append((len(alleles), pop_data))
return fd_rec