def test_convert(self):
"""Basic conversion test.
"""
for i in range(len(self.handles)):
gp_rec = GenePop.parse(self.handles[i])
fd_rec = convert_genepop_to_fdist(gp_rec)
assert(fd_rec.num_loci == 3)
assert(fd_rec.num_pops == 3)
def test_convert(self):
"""Basic conversion test.
"""
for i in range(len(self.handles)):
gp_rec = GenePop.parse(self.handles[i])
fd_rec = convert_genepop_to_fdist(gp_rec)
assert (fd_rec.num_loci == 3)
assert (fd_rec.num_pops == 3)
def test_wrong_file_parser(self):
"""Testing the ability to deal with wrongly formatted files
"""
f = open(os.path.join("PopGen", "fdist1"))
try:
rec = GenePop.parse(f)
raise Error("Should have raised exception")
except ValueError:
pass
f.close()
def test_wrong_file_parser(self):
"""Testing the ability to deal with wrongly formatted files
"""
f = open(os.path.join("PopGen", "fdist1"))
try:
rec = GenePop.parse(f)
raise Error("Should have raised exception")
except ValueError:
pass
f.close()
def test_record_parser(self):
"""Basic operation of the Record Parser.
"""
for index in range(len(self.handles)):
handle = self.handles[index]
rec = GenePop.parse(handle)
assert isinstance(rec, GenePop.Record)
assert len(rec.loci_list) == self.num_loci[index]
assert rec.marker_len == self.marker_len[index]
assert len(rec.populations) == self.pops_indivs[index][0]
for i in range(self.pops_indivs[index][0]):
assert len(rec.populations[i]) == \
self.pops_indivs[index][1][i]
def test_record_parser(self):
"""Basic operation of the Record Parser.
"""
for index in range(len(self.handles)):
handle = self.handles[index]
rec = GenePop.parse(handle)
assert isinstance(rec, GenePop.Record)
assert len(rec.loci_list) == self.num_loci[index]
assert rec.marker_len == self.marker_len[index]
assert len(rec.populations) == self.pops_indivs[index][0]
for i in range(self.pops_indivs[index][0]):
assert len(rec.populations[i]) == \
self.pops_indivs[index][1][i]
def getRefs(expr, gen, numReps):
refs = []
for rep in range(numReps):
fname = eval(expr)
fi = open(fname)
rec = GenePop.parse(fi)
fi.close()
csld = GenePop.Record()
csld.loci_list = deepcopy(rec.loci_list)
csld.populations=[[]]
for pop in rec.populations:
csld.populations[0].extend(pop)
refs.append(csld)
return refs
def test_utils(self):
"""Basic operation of GenePop Utils.
"""
for index in range(len(self.handles)):
handle = self.handles[index]
rec = GenePop.parse(handle)
initial_pops = len(rec.populations)
initial_loci = len(rec.loci_list)
first_loci = rec.loci_list[0]
rec.remove_population(0)
assert len(rec.populations) == initial_pops - 1
rec.remove_locus_by_name(first_loci)
assert len(rec.loci_list) == initial_loci - 1
assert rec.loci_list[0] != first_loci
rec.remove_locus_by_position(0)
assert len(rec.loci_list) == initial_loci - 2
def test_utils(self):
"""Basic operation of GenePop Utils.
"""
for index in range(len(self.handles)):
handle = self.handles[index]
rec = GenePop.parse(handle)
initial_pops = len(rec.populations)
initial_loci = len(rec.loci_list)
first_loci = rec.loci_list[0]
rec.remove_population(0)
assert len(rec.populations) == initial_pops - 1
rec.remove_locus_by_name(first_loci)
assert len(rec.loci_list) == initial_loci - 1
assert rec.loci_list[0] != first_loci
rec.remove_locus_by_position(0)
assert len(rec.loci_list) == initial_loci - 2
def calcFs(expr, numReps, gpRefs, gen, refGen):
for rep in range(numReps):
fname = eval(expr)
gpRef = gpRefs[rep]
fi = open(fname)
rec = GenePop.parse(fi)
fi.close()
Nes = []
NesP = []
for pop in rec.populations:
F = calcF(gpRef.populations[0], pop, len(gpRef.loci_list))
Mes = calcNe(F, gen-refGen, len(gpRef.populations[0]), len(pop))
Ne = Mes[0]
NeP = Mes[1:]
#print Ne
#print "F", F, 100.0*F/129.0, 100*F/74.0
#Ne = (1.0*(gen-refGen))/ (2*F)
NesP.append(str(min(NeP))+"#"+str(max(NeP)))
Nes.append(Ne)
print gen, rep, "NeF", " ".join(map(lambda x: str(x), Nes))
print gen, rep, "NeFPow", " ".join(map(lambda x: str(x), NesP))
def get_basic_info(self):
f = open(self._fname)
rec = GenePop.parse(f)
f.close()
return rec.pop_list, rec.loci_list