def runtest(infile, L, nboots, snpfreq, submitted):
" print test "
print L
" split each locus "
loci = open(infile).read().strip().split("|")[:-1]
loci[0] = "\n" + loci[0]
" returns a {} of Locus5 objects with data for tiptaxa L "
Ldict = makeSNP(L, snpfreq, loci)
" calculate discordant patterns for each locus "
for loc in Ldict:
if snpfreq:
Ldict[loc] = IUAfreq(Ldict[loc], L)
else:
Ldict[loc] = IUA(Ldict[loc], L)
################################################
" final D12 "
dft_12 = sum([Ldict[l].abbba - Ldict[l].babba for l in Ldict])
dbt_12 = sum([Ldict[l].abbba + Ldict[l].babba for l in Ldict])
if dbt_12 > 0:
D12 = float(dft_12) / dbt_12
else:
D12 = 0.
" final D1 "
dft_1 = sum([Ldict[l].abbaa - Ldict[l].babaa for l in Ldict])
dbt_1 = sum([Ldict[l].abbaa + Ldict[l].babaa for l in Ldict])
if dbt_1 > 0:
D1 = float(dft_1) / dbt_1
else:
D1 = 0.
" final D2 "
dft_2 = sum([Ldict[l].ababa - Ldict[l].baaba for l in Ldict])
dbt_2 = sum([Ldict[l].ababa + Ldict[l].baaba for l in Ldict])
if dbt_2 > 0:
D2 = float(dft_2) / dbt_2
else:
D2 = 0.
" proportion of discordant loci "
try:
pdisc = len([
i for i in Ldict
if any([Ldict[i].D12(), Ldict[i].D1(), Ldict[i].D2()])
]) / float(len(Ldict))
except ValueError:
pdisc = 0.0
#################################################
" do bootstrapping "
BB12 = []
BB1 = []
BB2 = []
for i in xrange(nboots):
which = iter(sample_wr(xrange(len(Ldict)), len(Ldict)))
if snpfreq:
bb12, bb1, bb2 = bootfreq(Ldict, which)
else:
#bb12,bb1,bb2 = bootfixed(Ldict, which)
bb12, bb1, bb2 = bootfreq(Ldict, which)
BB12.append(bb12)
BB1.append(bb1)
BB2.append(bb2)
STD12 = numpy.std(BB12)
STD1 = numpy.std(BB1)
STD2 = numpy.std(BB2)
##################################################
" stats out "
if STD12 > 0:
Z12 = (abs(D12 / STD12))
else:
Z12 = 0.
if STD1 > 0:
Z1 = (abs(D1 / STD1))
else:
Z1 = 0.
if STD2 > 0:
Z2 = (abs(D2 / STD2))
else:
Z2 = 0.
## make loci files here
ABBBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() > 0]
BABBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() < 0]
ABBAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() > 0]
BABAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() < 0]
ABABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() > 0]
BAABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() < 0]
" pickle to prevent multiprocessing from freezing on large returns "
ret = [
L, D12, Z12, D1, Z1, D2, Z2,
len(Ldict),
sum([Ldict[l].abbba for l in Ldict]),
sum([Ldict[l].babba for l in Ldict]),
sum([Ldict[l].abbaa for l in Ldict]),
sum([Ldict[l].babaa for l in Ldict]),
sum([Ldict[l].ababa for l in Ldict]),
sum([Ldict[l].baaba for l in Ldict]), pdisc, submitted, ABBBAloci,
BABBAloci, ABBAAloci, BABAAloci, ABABAloci, BAABAloci, BB12, BB1, BB2
]
pickle.dump(ret, open(".save." + str(submitted), 'wb'))
def runtest(infile, L, nboots, snpfreq, submitted, noterminals):
" print test "
print L
" split each locus "
loci = open(infile).read().strip().split("|")[:-1]
loci[0] = "\n" + loci[0]
" returns a {} of Locusfoil objects with data for tiptaxa L "
Ldict = makeSNP(L, snpfreq, loci, noterminals)
" calculate discordant patterns for each locus "
for loc in Ldict:
if snpfreq:
Ldict[loc] = IUAfreq(Ldict[loc], L)
else:
Ldict[loc] = IUA(Ldict[loc], L)
################################################
" final DFO "
DFO_t = sum([(Ldict[l].babaa + Ldict[l].bbbaa + Ldict[l].ababa + Ldict[l].aaaba) -\
(Ldict[l].baaba + Ldict[l].bbaba + Ldict[l].abbaa + Ldict[l].aabaa) for l in Ldict])
DFO_b = sum([(Ldict[l].babaa + Ldict[l].bbbaa + Ldict[l].ababa + Ldict[l].aaaba) + \
(Ldict[l].baaba + Ldict[l].bbaba + Ldict[l].abbaa + Ldict[l].aabaa) for l in Ldict])
if DFO_b > 0:
DFO = float(DFO_t) / DFO_b
else:
DFO = 0.
" final DIL "
DIL_t = sum([(Ldict[l].abbaa + Ldict[l].bbbaa + Ldict[l].baaba + Ldict[l].aaaba) - \
(Ldict[l].ababa + Ldict[l].bbaba + Ldict[l].babaa + Ldict[l].aabaa) for l in Ldict])
DIL_b = sum([(Ldict[l].abbaa + Ldict[l].bbbaa + Ldict[l].baaba + Ldict[l].aaaba) + \
(Ldict[l].ababa + Ldict[l].bbaba + Ldict[l].babaa + Ldict[l].aabaa) for l in Ldict])
if DIL_b > 0:
DIL = float(DIL_t) / DIL_b
else:
DIL = 0.
" final DFI "
DFI_t = sum([(Ldict[l].babaa + Ldict[l].babba + Ldict[l].ababa + Ldict[l].abaaa) - \
(Ldict[l].abbaa + Ldict[l].abbba + Ldict[l].baaba + Ldict[l].baaaa) for l in Ldict])
DFI_b = sum([(Ldict[l].babaa + Ldict[l].babba + Ldict[l].ababa + Ldict[l].abaaa) + \
(Ldict[l].abbaa + Ldict[l].abbba + Ldict[l].baaba + Ldict[l].baaaa) for l in Ldict])
if DFI_b > 0:
DFI = float(DFI_t) / DFI_b
else:
DFI = 0.
" final DOL "
DOL_t = sum([(Ldict[l].baaba + Ldict[l].babba + Ldict[l].abbaa + Ldict[l].abaaa) - \
(Ldict[l].ababa + Ldict[l].abbba + Ldict[l].babaa + Ldict[l].baaaa) for l in Ldict])
DOL_b = sum([(Ldict[l].baaba + Ldict[l].babba + Ldict[l].abbaa + Ldict[l].abaaa) + \
(Ldict[l].ababa + Ldict[l].abbba + Ldict[l].babaa + Ldict[l].baaaa) for l in Ldict])
if DOL_b > 0:
DOL = float(DOL_t) / DOL_b
else:
DOL = 0.
" proportion of discordant loci "
#try: pdisc = len([i for i in Ldict if any([Ldict[i].D12(),Ldict[i].D1(),Ldict[i].D2()])]) / float(len(Ldict))
#except ValueError:
# pdisc = 0.0
" TODO "
pdisc = 0.0
#################################################
" do bootstrapping "
BBFO = []
BBIL = []
BBFI = []
BBOL = []
for i in xrange(nboots):
which = iter(sample_wr(xrange(len(Ldict)), len(Ldict)))
bbfo, bbil, bbfi, bbol = bootfreq(Ldict, which)
BBFO.append(bbfo)
BBIL.append(bbil)
BBFI.append(bbfi)
BBOL.append(bbol)
STDfo = numpy.std(BBFO)
STDil = numpy.std(BBIL)
STDfi = numpy.std(BBFI)
STDol = numpy.std(BBOL)
##################################################
" stats out "
if STDfo > 0:
ZFO = (abs(DFO / STDfo))
else:
ZFO = 0.
if STDil > 0:
ZIL = (abs(DIL / STDil))
else:
ZIL = 0.
if STDfi > 0:
ZFI = (abs(DFI / STDfi))
else:
ZFI = 0.
if STDol > 0:
ZOL = (abs(DOL / STDol))
else:
ZOL = 0.
## make loci files here
#ABBBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() > 0]
#BABBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() < 0]
#ABBAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() > 0]
#BABAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() < 0]
#ABABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() > 0]
#BAABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() < 0]
return [
L, DFO, ZFO, DIL, ZIL, DFI, ZFI, DOL, ZOL,
len(Ldict),
sum([Ldict[l].babba for l in Ldict]),
sum([Ldict[l].abbba for l in Ldict]),
sum([Ldict[l].babaa for l in Ldict]),
sum([Ldict[l].abbaa for l in Ldict]),
sum([Ldict[l].baaba for l in Ldict]),
sum([Ldict[l].ababa for l in Ldict]),
sum([Ldict[l].bbbaa for l in Ldict]),
sum([Ldict[l].bbaba for l in Ldict]),
sum([Ldict[l].aabaa for l in Ldict]),
sum([Ldict[l].aaaba for l in Ldict]),
sum([Ldict[l].baaaa for l in Ldict]),
sum([Ldict[l].abaaa for l in Ldict]), pdisc, submitted, BBFO, BBIL,
BBFI, BBOL
]
def runtest(infile, L, nboots, snpfreq, submitted):
" print test "
print L
" split each locus "
loci = open(infile).read().strip().split("|")[:-1]
loci[0] = "\n"+loci[0]
" returns a {} of Locus5 objects with data for tiptaxa L "
Ldict = makeSNP(L, snpfreq, loci)
" calculate discordant patterns for each locus "
for loc in Ldict:
if snpfreq:
Ldict[loc] = IUAfreq(Ldict[loc],L)
else:
Ldict[loc] = IUA(Ldict[loc],L)
################################################
" final D12 "
dft_12 = sum([Ldict[l].abbba - Ldict[l].babba for l in Ldict])
dbt_12 = sum([Ldict[l].abbba + Ldict[l].babba for l in Ldict])
if dbt_12 > 0:
D12 = float(dft_12)/dbt_12
else: D12 = 0.
" final D1 "
dft_1 = sum([Ldict[l].abbaa - Ldict[l].babaa for l in Ldict])
dbt_1 = sum([Ldict[l].abbaa + Ldict[l].babaa for l in Ldict])
if dbt_1 > 0:
D1 = float(dft_1)/dbt_1
else: D1 = 0.
" final D2 "
dft_2 = sum([Ldict[l].ababa - Ldict[l].baaba for l in Ldict])
dbt_2 = sum([Ldict[l].ababa + Ldict[l].baaba for l in Ldict])
if dbt_2 > 0:
D2 = float(dft_2)/dbt_2
else: D2 = 0.
" proportion of discordant loci "
try: pdisc = len([i for i in Ldict if any([Ldict[i].D12(),Ldict[i].D1(),Ldict[i].D2()])]) / float(len(Ldict))
except ValueError:
pdisc = 0.0
#################################################
" do bootstrapping "
BB12 = []
BB1 = []
BB2 = []
for i in xrange(nboots):
which = iter(sample_wr(xrange(len(Ldict)), len(Ldict)))
if snpfreq:
bb12,bb1,bb2 = bootfreq(Ldict, which)
else:
#bb12,bb1,bb2 = bootfixed(Ldict, which)
bb12,bb1,bb2 = bootfreq(Ldict, which)
BB12.append(bb12)
BB1.append(bb1)
BB2.append(bb2)
STD12 = numpy.std(BB12)
STD1 = numpy.std(BB1)
STD2 = numpy.std(BB2)
##################################################
" stats out "
if STD12 > 0:
Z12 = (abs(D12/STD12))
else: Z12 = 0.
if STD1 > 0:
Z1 = (abs(D1/STD1))
else: Z1 = 0.
if STD2 > 0:
Z2 = (abs(D2/STD2))
else: Z2 = 0.
## make loci files here
ABBBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() > 0]
BABBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() < 0]
ABBAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() > 0]
BABAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() < 0]
ABABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() > 0]
BAABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() < 0]
" pickle to prevent multiprocessing from freezing on large returns "
ret = [L,
D12,Z12,
D1,Z1,
D2,Z2,
len(Ldict),
sum([Ldict[l].abbba for l in Ldict]),
sum([Ldict[l].babba for l in Ldict]),
sum([Ldict[l].abbaa for l in Ldict]),
sum([Ldict[l].babaa for l in Ldict]),
sum([Ldict[l].ababa for l in Ldict]),
sum([Ldict[l].baaba for l in Ldict]),
pdisc, submitted,
ABBBAloci, BABBAloci,
ABBAAloci, BABAAloci,
ABABAloci, BAABAloci,
BB12, BB1, BB2]
pickle.dump(ret, open(".save."+str(submitted),'wb'))
def runtest(infile, L, nboots, snpfreq, submitted, noterminals):
" print test "
print L
" split each locus "
loci = open(infile).read().strip().split("|")[:-1]
loci[0] = "\n"+loci[0]
" returns a {} of Locusfoil objects with data for tiptaxa L "
Ldict = makeSNP(L, snpfreq, loci, noterminals)
" calculate discordant patterns for each locus "
for loc in Ldict:
if snpfreq:
Ldict[loc] = IUAfreq(Ldict[loc],L)
else:
Ldict[loc] = IUA(Ldict[loc],L)
################################################
" final DFO "
DFO_t = sum([(Ldict[l].babaa + Ldict[l].bbbaa + Ldict[l].ababa + Ldict[l].aaaba) -\
(Ldict[l].baaba + Ldict[l].bbaba + Ldict[l].abbaa + Ldict[l].aabaa) for l in Ldict])
DFO_b = sum([(Ldict[l].babaa + Ldict[l].bbbaa + Ldict[l].ababa + Ldict[l].aaaba) + \
(Ldict[l].baaba + Ldict[l].bbaba + Ldict[l].abbaa + Ldict[l].aabaa) for l in Ldict])
if DFO_b > 0:
DFO = float(DFO_t)/DFO_b
else: DFO = 0.
" final DIL "
DIL_t = sum([(Ldict[l].abbaa + Ldict[l].bbbaa + Ldict[l].baaba + Ldict[l].aaaba) - \
(Ldict[l].ababa + Ldict[l].bbaba + Ldict[l].babaa + Ldict[l].aabaa) for l in Ldict])
DIL_b = sum([(Ldict[l].abbaa + Ldict[l].bbbaa + Ldict[l].baaba + Ldict[l].aaaba) + \
(Ldict[l].ababa + Ldict[l].bbaba + Ldict[l].babaa + Ldict[l].aabaa) for l in Ldict])
if DIL_b > 0:
DIL = float(DIL_t)/DIL_b
else: DIL = 0.
" final DFI "
DFI_t = sum([(Ldict[l].babaa + Ldict[l].babba + Ldict[l].ababa + Ldict[l].abaaa) - \
(Ldict[l].abbaa + Ldict[l].abbba + Ldict[l].baaba + Ldict[l].baaaa) for l in Ldict])
DFI_b = sum([(Ldict[l].babaa + Ldict[l].babba + Ldict[l].ababa + Ldict[l].abaaa) + \
(Ldict[l].abbaa + Ldict[l].abbba + Ldict[l].baaba + Ldict[l].baaaa) for l in Ldict])
if DFI_b > 0:
DFI = float(DFI_t)/DFI_b
else: DFI = 0.
" final DOL "
DOL_t = sum([(Ldict[l].baaba + Ldict[l].babba + Ldict[l].abbaa + Ldict[l].abaaa) - \
(Ldict[l].ababa + Ldict[l].abbba + Ldict[l].babaa + Ldict[l].baaaa) for l in Ldict])
DOL_b = sum([(Ldict[l].baaba + Ldict[l].babba + Ldict[l].abbaa + Ldict[l].abaaa) + \
(Ldict[l].ababa + Ldict[l].abbba + Ldict[l].babaa + Ldict[l].baaaa) for l in Ldict])
if DOL_b > 0:
DOL = float(DOL_t)/DOL_b
else: DOL = 0.
" proportion of discordant loci "
#try: pdisc = len([i for i in Ldict if any([Ldict[i].D12(),Ldict[i].D1(),Ldict[i].D2()])]) / float(len(Ldict))
#except ValueError:
# pdisc = 0.0
" TODO "
pdisc = 0.0
#################################################
" do bootstrapping "
BBFO = []
BBIL = []
BBFI = []
BBOL = []
for i in xrange(nboots):
which = iter(sample_wr(xrange(len(Ldict)), len(Ldict)))
bbfo,bbil,bbfi,bbol = bootfreq(Ldict, which)
BBFO.append(bbfo)
BBIL.append(bbil)
BBFI.append(bbfi)
BBOL.append(bbol)
STDfo = numpy.std(BBFO)
STDil = numpy.std(BBIL)
STDfi = numpy.std(BBFI)
STDol = numpy.std(BBOL)
##################################################
" stats out "
if STDfo > 0:
ZFO = (abs(DFO/STDfo))
else: ZFO = 0.
if STDil > 0:
ZIL = (abs(DIL/STDil))
else: ZIL = 0.
if STDfi > 0:
ZFI = (abs(DFI/STDfi))
else: ZFI = 0.
if STDol > 0:
ZOL = (abs(DOL/STDol))
else: ZOL = 0.
## make loci files here
#ABBBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() > 0]
#BABBAloci = [Ldict[l].number for l in Ldict if Ldict[l].D12() < 0]
#ABBAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() > 0]
#BABAAloci = [Ldict[l].number for l in Ldict if Ldict[l].D1() < 0]
#ABABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() > 0]
#BAABAloci = [Ldict[l].number for l in Ldict if Ldict[l].D2() < 0]
return [L,
DFO,ZFO,
DIL,ZIL,
DFI,ZFI,
DOL,ZOL,
len(Ldict),
sum([Ldict[l].babba for l in Ldict]),
sum([Ldict[l].abbba for l in Ldict]),
sum([Ldict[l].babaa for l in Ldict]),
sum([Ldict[l].abbaa for l in Ldict]),
sum([Ldict[l].baaba for l in Ldict]),
sum([Ldict[l].ababa for l in Ldict]),
sum([Ldict[l].bbbaa for l in Ldict]),
sum([Ldict[l].bbaba for l in Ldict]),
sum([Ldict[l].aabaa for l in Ldict]),
sum([Ldict[l].aaaba for l in Ldict]),
sum([Ldict[l].baaaa for l in Ldict]),
sum([Ldict[l].abaaa for l in Ldict]),
pdisc, submitted,
BBFO, BBIL, BBFI, BBOL]