コード例 #1
0
def get_mean_r2(Ne, S, n_loci, gens, n_subpops, initial_frequencies, m):
    """Returns the mean r2 value for each subpopulation, in list of length n_subpops"""

    # make pairwise migration matrix
    M = get_migration_matrix(m, n_subpops)

    # initialise population
    n_alleles = 2
    pop = sim.Population(size=[Ne] * n_subpops,
                         ploidy=2,
                         loci=[1] * n_loci,
                         alleleNames=[str(i) for i in range(n_alleles)],
                         infoFields='migrate_to')
    sim.initGenotype(pop, freq=[initial_frequencies, 1 - initial_frequencies])
    #sim.initGenotype(pop, freq = [1/n_alleles for i in range(n_alleles)])
    sim.initSex(pop)
    print(M)
    # run burn in generations
    pop.evolve(initOps=[],
               preOps=sim.Migrator(M, mode=sim.BY_PROBABILITY),
               matingScheme=sim.RandomMating(),
               gen=gens)

    # take sample from each subpopulation
    sample_pop = drawRandomSample(pop, sizes=[S] + [0] * (n_subpops - 1))
    #sim.dump(sample_pop)

    # get allele frequencies
    sim.stat(sample_pop, alleleFreq=range(0, n_loci), vars=['alleleFreq_sp'])
    #print(sample_pop.dvars(0).alleleFreq)
    # calculate r2 values
    sim.stat(sample_pop,
             LD=list(itertools.combinations(list(range(n_loci)), r=2)),
             vars=['R2_sp'])
    #print(sample_pop.dvars(0).R2)
    r2s = []

    for sp in [0]:  #range(n_subpops*0):

        allele_freqs = sample_pop.dvars(sp).alleleFreq
        seg_alleles = [
            k for k in range(n_loci)
            if np.abs(.5 - allele_freqs[k][0]) < .5 - 0.05
        ]
        if len(seg_alleles) < 2: raise Exception("<2 segregating alleles")

        r2_sum = 0
        count = 0

        for pairs in itertools.combinations(seg_alleles, r=2):
            r2_sum += sample_pop.dvars(sp).R2[pairs[0]][pairs[1]]
            count += 1

        mean_r2 = r2_sum / count
        r2s.append(mean_r2)

    return r2s
コード例 #2
0
ファイル: Simulation.py プロジェクト: airanmehr/bio
 def simulateSingleLoci(nu0=0.005, T=100, s=0.1, N=1000):
     print '.',
     step = 1
     pop = sim.Population(size=N, ploidy=2, loci=[1],infoFields=['fitness']);sim.initGenotype(pop, prop=[1-nu0,nu0]);simulator = sim.Simulator(pop.clone(), rep=1);
     # sim.stat(pop, alleleFreq=[0]);        print pop.dvars().alleleFreq[0][1]
     global a;a = "0;;{}\n".format(nu0)
     simulator.evolve(initOps=[sim.InitSex()],
                      preOps=sim.MapSelector(loci=0, fitness={(0, 0): 1, (0, 1): 1 + s * 0.5, (1, 1): 1 + s}),
                      matingScheme=sim.RandomMating(), postOps=[sim.Stat(alleleFreq=[0], step=step),
                                                                sim.PyEval("'%d;;' % (gen+1)", reps=0, step=step,
                                                                           output=fff), sim.PyEval(
                 r"'{}\n'.format(map(lambda x: round(x[1],5),alleleFreq.values())[0])", step=step, output=fff)],
                      gen=T)
     return pd.DataFrame(zip(*map(lambda x: x.split(';;'), a.strip().split('\n')))).T.set_index(0)[1].astype(float)
コード例 #3
0
def get_mean_r2(Ne, S, n_loci, gens, repeats, n_subpops, initial_frequencies,
                m):
    M = get_migration_matrix(m, n_subpops)
    pop = sim.Population(size=[Ne] * n_subpops,
                         ploidy=2,
                         loci=[1] * n_loci,
                         infoFields='migrate_to')
    sim.initGenotype(pop, freq=initial_frequencies)
    pop.evolve(
        initOps=[sim.InitSex(),
                 sim.InitGenotype(freq=initial_frequencies)],
        preOps=sim.Migrator(rate=M),
        matingScheme=sim.RandomMating(),
        gen=gens)

    sample_pop = drawRandomSample(pop, sizes=[S] * n_subpops)

    # get allele frequencies
    sim.stat(sample_pop, alleleFreq=range(0, n_loci), vars=['alleleFreq_sp'])
    # calculate r2 values
    sim.stat(sample_pop,
             LD=list(combinations(list(range(n_loci)), r=2)),
             vars=['R2_sp'])

    r2s = []

    for sp in range(n_subpops):

        allele_freqs = sample_pop.dvars(sp).alleleFreq
        seg_alleles = [
            k for k in range(n_loci)
            if np.abs(.5 - allele_freqs[k][0]) < .5 - 0.05
        ]
        if len(seg_alleles) < 2: raise Exception("<2 segregating alleles")

        r2_sum = count = 0

        for pairs in combinations(seg_alleles, r=2):
            r2_sum += sample_pop.dvars(sp).R2[pairs[0]][pairs[1]]
            count += 1

        mean_r2 = r2_sum / count
        r2s.append(mean_r2)

    return r2s
コード例 #4
0
ファイル: allelic.py プロジェクト: SamT123/VectorSim
def get_FCs(Ne, S, n_loci, gens, n_subpops, initial_frequencies, m):
    ''''Runs simulations for allelic fluctuations model with n subpopulations, and returns a list of FC values (one for each subpopulation)'''
    # population to evolve ((from infinite gamete pool))
    popNe = sim.Population(size=[Ne] * n_subpops,
                           ploidy=2,
                           loci=[1] * n_loci,
                           infoFields='migrate_to')
    # initial sample population (from infinite gamete pool)
    popS = sim.Population(size=[S] * n_subpops, ploidy=2, loci=[1] * n_loci)
    sim.initGenotype(popNe, freq=initial_frequencies)
    sim.initGenotype(popS, freq=initial_frequencies)

    # get initial sample allele frequencies
    sim.stat(popS, alleleFreq=range(n_loci), vars=['alleleFreq_sp'])

    M = get_migration_matrix(m, n_subpops)

    popNe.evolve(initOps=[sim.InitSex()],
                 preOps=sim.Migrator(rate=M),
                 matingScheme=sim.RandomMating(),
                 gen=gens)

    sample_pop = drawRandomSample(popNe, sizes=[S] * n_subpops)
    sim.stat(sample_pop, alleleFreq=range(n_loci), vars=['alleleFreq_sp'])
    all_FCs = []

    for sp in range(n_subpops):
        initial_allele_frequencies = popS.dvars(sp).alleleFreq
        final_allele_frequencies = sample_pop.dvars(sp).alleleFreq
        sp_count = 0
        sp_FC = 0
        for locus in range(n_loci):
            init_pair = repair(initial_allele_frequencies[locus])
            end_pair = repair(final_allele_frequencies[locus])
            if init_pair[0]**2 + init_pair[1]**2 != 1:
                sp_FC += fc_variant([init_pair[0], init_pair[1]],
                                    [end_pair[0], end_pair[1]])
                sp_count += 1

        all_FCs.append(sp_FC / sp_count)

    return all_FCs
コード例 #5
0
ファイル: selector_test.py プロジェクト: skumagai/migselsim
 def setUp(self):
     self.fs = 0.9
     self.ms = 0.5
     self.pop = sim.Population(size=[4, 4],
                               loci=[1, 1, 1, 1],
                               chromTypes=[sim.AUTOSOME,
                                           sim.CHROMOSOME_X,
                                           sim.CHROMOSOME_Y,
                                           sim.CUSTOMIZED],
                               infoFields=['fitness'])
     self.pop.setVirtualSplitter(sim.SexSplitter())
     sim.initSex(self.pop, sex=[sim.MALE, sim.FEMALE])
     for i in range(2):
         for j in range(2):
             sim.initGenotype(self.pop,
                              loci=[0], # Autosome
                              prop=[0.5, 0.5],
                              subPops=[(i,j)])
             sim.initGenotype(self.pop,
                              loci=[3], # Mitochondria
                              ploidy=0,
                              prop=[0.5, 0.5],
                              subPops=[(i,j)])
         sim.initGenotype(self.pop,
                          loci=[1], # Chromosome X
                          prop=[0.5, 0.5],
                          subPops=[(i,1)])
         sim.initGenotype(self.pop,
                          loci=[1], # Chromosome X
                          prop=[0.5, 0.5],
                          ploidy=0,
                          subPops=[(i,0)])
         sim.initGenotype(self.pop,
                          loci=[2], # Chromosome Y
                          prop=[0.5, 0.5],
                          ploidy=1,
                          subPops=[(i,0)])
コード例 #6
0
ファイル: viewVars.py プロジェクト: sudorook/simuPOP
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
from simuPOP.utils import viewVars
pop = sim.Population([1000, 2000], loci=3)
sim.initGenotype(pop, freq=[0.2, 0.4, 0.4], loci=0)
sim.initGenotype(pop, freq=[0.2, 0.8], loci=2)
sim.stat(pop, genoFreq=[0, 1, 2], haploFreq=[0, 1, 2],
    alleleFreq=range(3),
    vars=['genoFreq', 'genoNum', 'haploFreq', 'alleleNum_sp'])
viewVars(pop.vars())

コード例 #7
0
ファイル: simtest.py プロジェクト: LZeitler/recsim
# create 3 subpops with different sizes
pop = sim.Population(size=[3, 4, 5], ploidy=1, loci=1, infoFields='x')
sim.dump(pop)

# a diploid population
pop = sim.Population(size=[10], ploidy=2, loci=10, infoFields='x')
sim.dump(pop)

# a tetraploid population
pop = sim.Population(size=[10], ploidy=4, loci=10, infoFields='x')
sim.dump(pop)

# something with frequencies
pop = sim.Population(10, ploidy=2, loci=[5])
sim.dump(pop)
sim.initGenotype(pop, freq=[0.2, 0.3, 0.5])
sim.dump(pop)

# access stuff
pop = sim.Population(size=[2, 3],
                     ploidy=2,
                     loci=[5, 10],
                     lociPos=list(range(0, 5)) + list(range(0, 20, 2)),
                     chromNames=['Chr1', 'Chr2'],
                     alleleNames=['A', 'C', 'T', 'G'])
pop.ploidy()
pop.popSize()
pop.alleleName(1)
pop.numChrom()
pop.chromBegin(1)
ind = pop.individual(2)  # access individual
コード例 #8
0
ファイル: saveCSV.py プロジェクト: sudorook/simuPOP
# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
from simuPOP.utils import saveCSV
pop = sim.Population(size=[10],
                     loci=[2, 3],
                     lociNames=['r11', 'r12', 'r21', 'r22', 'r23'],
                     alleleNames=['A', 'B'],
                     infoFields='age')
sim.initSex(pop)
sim.initInfo(pop, [2, 3, 4], infoFields='age')
sim.initGenotype(pop, freq=[0.4, 0.6])
sim.maPenetrance(pop, loci=0, penetrance=(0.2, 0.2, 0.4))
# no filename so output to standard output
saveCSV(pop, infoFields='age')
# change affection code and how to output genotype
saveCSV(pop,
        infoFields='age',
        affectionFormatter={
            True: 1,
            False: 2
        },
        genoFormatter={
            (0, 0): 'AA',
            (0, 1): 'AB',
            (1, 0): 'AB',
            (1, 1): 'BB'
コード例 #9
0
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
import random
pop = sim.Population(20, loci=1, infoFields='a')
pop.setVirtualSplitter(sim.InfoSplitter('a', cutoff=[3]))
sim.initGenotype(pop, freq=[0.2, 0.8])
pop.setIndInfo([random.randint(2, 5) for x in range(20)], 'a')
sim.infoEval(pop, 'a', subPops=[(0, 0)]);print(' ')
sim.infoEval(pop, 'ind.allele(0, 0)', exposeInd='ind');print(' ')
# use sim.population variables
pop.dvars().b = 5
sim.infoEval(pop, '"%d " % (a+b)');print(' ')

コード例 #10
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###################
# run simulations #
###################

for rep in range(1, 501):
    pop = sim.Population([popsize] * 3,
                         ploidy=2,
                         loci=[20],
                         lociPos=[
                             1, 1.1, 2, 3, 3.1, 4, 5, 5.1, 6, 7, 7.1, 8, 9,
                             9.1, 10, 11, 11.1, 12, 13, 13.1
                         ],
                         infoFields=['fitness', 'migrate_to'])

    # initiate genotypes in subpopulation 0 as fixed for '0' ancestry:
    sim.initGenotype(pop, genotype=[0] * 20, subPops=[0])

    # genotypes at subpopulation 1:
    #sim.initGenotype(pop, genotype=[0]*20+[1]*20, subPops=[1])    # all F1 hybrids

    sim.initGenotype(pop, genotype=[0] * 20, subPops=[1])  # or a mixture of
    for ind in random.sample(range(popsize, popsize * 2),
                             popsize / 2):  # both parental species.
        pop.individual(ind).setGenotype([1] * 20)

    # initiate genotypes in subpopulation 2 as fixed for '1' ancestry
    sim.initGenotype(pop, genotype=[1] * 20, subPops=[2])

    def printAlleleFreq(pop):
        'Print allele frequencies of all loci and populations'
コード例 #11
0
ファイル: MapPenetrance.py プロジェクト: sudorook/simuPOP
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
pop = sim.Population(size=2000, loci=2)
sim.initGenotype(pop, freq=[.2, .8])
sim.mapPenetrance(pop, loci=0, penetrance={(0, 0): 0, (0, 1): .2, (1, 1): .3})
sim.stat(pop, genoFreq=0, numOfAffected=1, vars='genoNum')
# number of affected individuals
pop.dvars().numOfAffected
# which should be roughly (#01 + #10) * 0.2 + #11 * 0.3
(pop.dvars().genoNum[0][(0,1)] + pop.dvars().genoNum[0][(1,0)]) * 0.2 \
+ pop.dvars().genoNum[0][(1,1)] * 0.3
コード例 #12
0
def do_forward_sims(sim_data, chrom_len, diploid_Ne, batchname, repilcates,
                    simupop_seed):
    print("start getting chromosomes positions")
    chromosome_positions = get_chromosome_positions(sim_data=sim_data,
                                                    chromsome_length=chrom_len)
    print("done getting chromosomes positions")

    haplotypes = get_haplotypes(sim_data)
    loci_per_chromsome = get_loci_per_chromosome(chromosome_positions)
    n_chrom = len(loci_per_chromsome)
    # set up the ancestral pop in simuPOP
    initial = simuPOP.Population(
        diploid_Ne,  # here is the diploid number
        loci=
        loci_per_chromsome,  # should be the number of loci on each chromosome
        lociPos=list(chromosome_positions),
        ploidy=2,
        infoFields=['father_idx', 'mother_idx', 'ind_id'],
        #alleleNames=['A', 'C', 'G', 'T'],
        lociNames=[
            'locus_{}'.format(x) for x in xrange(len(chromosome_positions))
        ])
    simuPOP.initGenotype(initial,
                         prop=[1.0 / len(haplotypes)] * len(haplotypes),
                         haplotypes=list(haplotypes))
    simuPOP.tagID(initial, reset=1)
    initial_export = get_export_genotypes(initial, initial.popSize())
    np.savetxt('./share/{}/Ne-{}_Chr-{}/Ne-{}_Chr-{}.inital.txt'.format(
        batchname, diploid_Ne, n_chrom, diploid_Ne, n_chrom),
               initial_export,
               delimiter='\t',
               fmt='%01d')

    # map-ped
    simuPOP.utils.export(
        initial,
        format='PED',
        output='./share/{}/Ne-{}_Chr-{}/Ne-{}_Chr-{}.inital.ped'.format(
            batchname, diploid_Ne, n_chrom, diploid_Ne, n_chrom),
        gui=False,
        idField='ind_id')
    simuPOP.utils.export(
        initial,
        format='MAP',
        output='./share/{}/Ne-{}_Chr-{}/Ne-{}_Chr-{}.inital.map'.format(
            batchname, diploid_Ne, n_chrom, diploid_Ne, n_chrom),
        gui=False)

    # Doesn't yet work!!
    # set the seed for simuPOP
    #simuPOP.setRNG(seed=simupop_seed)
    # and in Python
    #random.seed(simupop_seed)
    # and for numpy
    #np.random.seed(simupop_seed)

    print("initalizing the forward simulator")
    simu = simuPOP.Simulator(
        simuPOP.Population(
            diploid_Ne,  # here is the diploid number
            loci=get_loci_per_chromosome(
                chromosome_positions
            ),  # should be the number of loci on each chromosome
            lociPos=list(chromosome_positions),
            ploidy=2,
            infoFields=['ind_id', 'father_idx', 'mother_idx'],
            #alleleNames=['A', 'C', 'G', 'T'],
            lociNames=[
                'locus_{}'.format(x) for x in xrange(len(chromosome_positions))
            ]),
        rep=repilcates)

    print("Start evolving {} replicates".format(repilcates))
    simu.evolve(
        initOps=[
            simuPOP.InitSex(
                sex=[simuPOP.MALE, simuPOP.FEMALE]),  # alternate sex
            simuPOP.InitGenotype(prop=[1.0 / len(haplotypes)] *
                                 len(haplotypes),
                                 haplotypes=list(haplotypes))
        ],
        matingScheme=simuPOP.HomoMating(
            chooser=simuPOP.PyParentsChooser(fixedChooser),
            generator=simuPOP.OffspringGenerator(
                sexMode=(simuPOP.GLOBAL_SEQUENCE_OF_SEX, simuPOP.MALE,
                         simuPOP.FEMALE),
                ops=[
                    simuPOP.Recombinator(intensity=1.0 / chrom_len),
                    simuPOP.ParentsTagger()
                ]),
        ),
        postOps=[],
        gen=20)

    print("Done evolving {} replicates!".format(repilcates))

    # export the data
    print("Exporting data!".format(repilcates))
    for rep, pop in enumerate(simu.populations()):
        if diploid_Ne >= 200:
            pop_genotypes = get_export_genotypes(pop,
                                                 n_ind=200)  #  select 200 inds
        else:
            pop_genotypes = get_export_genotypes(
                pop, n_ind=diploid_Ne)  #  select 200 inds

        np.savetxt('./share/{}/Ne-{}_Chr-{}/Ne-{}_Chr-{}_Frep-{}.geno'.format(
            batchname, diploid_Ne, n_chrom, diploid_Ne, n_chrom,
            rep).format(rep),
                   pop_genotypes,
                   delimiter='\t',
                   fmt='%01d')
        if rep % 10 == 0:
            print "saved rep {}".format(rep)
コード例 #13
0
    return (1 / 2) * (xi_1 - yi_1)**2 / (
        (xi_1 + yi_1) / 2 - xi_1 * yi_1) + (1 / 2) * (xi_2 - yi_2)**2 / (
            (xi_2 + yi_2) / 2 - xi_2 * yi_2)


##########################

Ne_ests = []
FCs = []
for r in range(repeats):
    print(r + 1)

    popNe = sim.Population(size=[Ne], ploidy=2, loci=[1] * n_loci)
    popS = sim.Population(size=[S], ploidy=2, loci=[1] * n_loci)
    sim.initGenotype(popNe, freq=initial_frequencies)
    sim.initGenotype(popS, freq=initial_frequencies)

    sim.stat(popS, alleleFreq=range(0, n_loci), vars=['alleleFreq'])
    initial_allele_freqs = popS.vars()['alleleFreq']

    popNe.evolve(initOps=[sim.InitSex()],
                 matingScheme=sim.RandomMating(),
                 gen=gens)

    sample_pop = drawRandomSample(popNe, sizes=S)
    sim.stat(sample_pop, alleleFreq=range(0, n_loci), vars=['alleleFreq'])

    meanFC_repeat = 0
    countFC = 0
コード例 #14
0
ファイル: real.py プロジェクト: B-Rich/gsinghal_python_src
'''
Created on Oct 6, 2010

@author: Gaurav Singhal
'''

import simuPOP a

import simuPOP as sim

pop = sim.Population(size=1000, loci=[2])
pop.evolve(initOps = [sim.InitSex(),sim.initGenotype(pop, genotype=[1, 2, 2, 1])],  matingScheme=sim.RandomMating(ops=sim.Recombinator(rates=0.01)),
    postOps = [sim.stat(pop, LD=[0, 1]),sim.PyEval(r"'%.2f\n' % LD[0][1]", step=10),],gen=100)


コード例 #15
0
ファイル: statGenoFreq.py プロジェクト: sudorook/simuPOP
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
pop = sim.Population(
    100,
    loci=[1, 1, 1],
    lociNames=['A', 'X', 'Y'],
    chromTypes=[sim.AUTOSOME, sim.CHROMOSOME_X, sim.CHROMOSOME_Y])
sim.initGenotype(pop, freq=[0.01, 0.05, 0.94])
sim.stat(pop, genoFreq=['A', 'X'])  # both loci indexes and names can be used.
print('Available genotypes on autosome:', list(pop.dvars().genoFreq[0].keys()))
for i in range(3):
    for j in range(3):
        print('%d-%d: %.3f' % (i, j, pop.dvars().genoFreq[0][(i, j)]))

print('Genotype frequency on chromosome X:\n', \
    '\n'.join(['%s: %.3f' % (x,y) for x,y in pop.dvars().genoFreq[1].items()]))
コード例 #16
0
import simuPOP as sim


def calcNe(pop, param):
    'Calculated effective number of disease alleles at specified loci (param)'
    sim.stat(pop, alleleFreq=param)
    ne = {}
    for loc in param:
        freq = pop.dvars().alleleFreq[loc]
        sumFreq = 1 - pop.dvars().alleleFreq[loc][0]
        if sumFreq == 0:
            ne[loc] = 0
        else:
            ne[loc] = 1. / sum([(freq[x]/sumFreq)**2 \
                for x in list(freq.keys()) if x != 0])
    # save the result to the sim.Population.
    pop.dvars().ne = ne
    return True


pop = sim.Population(1000, loci=2)
sim.initGenotype(pop, freq=[0.9] + [0.01] * 10, loci=0)
sim.initGenotype(pop, freq=[0.9] + [0.05] + [0.005] * 10, loci=1)
calcNe(pop, param=[0, 1])
print(pop.dvars().ne)
コード例 #17
0
ファイル: reichstat.py プロジェクト: sudorook/simuPOP
    def __init__(self, loci, *args, **kwargs):
        self.loci = loci
        sim.PyOperator.__init__(self, func=self.calcNe, *args, **kwargs)

    #
    def calcNe(self, pop):
        sim.stat(pop, alleleFreq=self.loci)
        ne = {}
        for loc in self.loci:
            freq = pop.dvars().alleleFreq[loc]
            sumFreq = 1 - pop.dvars().alleleFreq[loc][0]
            if sumFreq == 0:
                ne[loc] = 0
            else:
                ne[loc] = 1. / sum([(freq[x] / sumFreq)**2
                                    for x in list(freq.keys()) if x != 0])
        # save the result to the sim.Population.
        pop.dvars().ne = ne
        return True


def Ne(pop, loci):
    '''Function form of operator ne'''
    ne(loci).apply(pop)
    return pop.dvars().ne


pop = sim.Population(100, loci=[10])
sim.initGenotype(pop, freq=[.2] * 5)
print(Ne(pop, loci=[2, 4]))
コード例 #18
0
ファイル: virtualSubPop.py プロジェクト: sudorook/simuPOP
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
import random
pop = sim.Population(10, loci=[2, 3], infoFields='Sex')
sim.initSex(pop)
pop.setVirtualSplitter(sim.SexSplitter())
# initialize male and females with different genotypes. 
sim.initGenotype(pop, genotype=[0]*5, subPops=[(0, 0)])
sim.initGenotype(pop, genotype=[1]*5, subPops=[(0, 1)])
# set Sex information field to 0 for all males, and 1 for all females
pop.setIndInfo([sim.MALE], 'Sex', [0, 0])
pop.setIndInfo([sim.FEMALE], 'Sex', [0, 1])
# Print individual genotypes, followed by values at information field Sex
sim.dump(pop, structure=False)

コード例 #19
0
ファイル: statLD.py プロジェクト: sudorook/simuPOP
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
pop = sim.Population([1000]*2, loci=3)
sim.initGenotype(pop, freq=[0.2, 0.8], subPops=0)
sim.initGenotype(pop, freq=[0.8, 0.2], subPops=1)
sim.stat(pop, LD=[[0, 1, 0, 0], [1, 2]],
    vars=['LD', 'LD_prime', 'R2', 'LD_ChiSq', 'LD_ChiSq_p', 'CramerV',
        'LD_prime_sp', 'LD_ChiSq_p_sp'])
from pprint import pprint
pprint(pop.vars())

コード例 #20
0
ファイル: extract.py プロジェクト: sudorook/simuPOP
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
import random
pop = sim.Population(size=[200, 200], loci=[5, 5], infoFields='age')
sim.initGenotype(pop, genotype=range(10))
sim.initInfo(pop, lambda: random.randint(0, 75), infoFields='age')
pop.setVirtualSplitter(sim.InfoSplitter(field='age', cutoff=[20, 60]))
# remove individuals
pop.removeIndividuals(indexes=range(0, 300, 10))
print(pop.subPopSizes())
# remove individuals using IDs
pop.setIndInfo([1, 2, 3, 4], field='age')
pop.removeIndividuals(IDs=[2, 4], idField='age')
# remove indiviuals using a filter function
sim.initSex(pop)
pop.removeIndividuals(filter=lambda ind: ind.sex() == sim.MALE)
print([pop.individual(x).sex() for x in range(8)])
#
# remove subpopulation
pop.removeSubPops(1)
コード例 #21
0
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
pop = sim.Population(size=[2000, 3000], loci=[5, 7])


# by allele frequency
def printFreq(pop, loci):
    sim.stat(pop, alleleFreq=loci)
    print(', '.join(
        ['{:.3f}'.format(pop.dvars().alleleFreq[x][0]) for x in loci]))


sim.initGenotype(pop, freq=[.4, .6])
sim.dump(pop, max=6, structure=False)
printFreq(pop, range(5))
# by proportion
sim.initGenotype(pop, prop=[0.4, 0.6])
printFreq(pop, range(5))
# by haplotype frequency
sim.initGenotype(pop, freq=[.4, .6], haplotypes=[[1, 1, 0, 1], [0, 0, 1]])
sim.dump(pop, max=6, structure=False)
printFreq(pop, range(5))
# by haplotype proportion
sim.initGenotype(pop, prop=[0.4, 0.6], haplotypes=[[1, 1, 0], [0, 0, 1, 1]])
printFreq(pop, range(5))
# by genotype
pop = sim.Population(size=[2, 3], loci=[5, 7])
sim.initGenotype(pop, genotype=[1] * 5 + [2] * 7 + [3] * 5 + [4] * 7)
コード例 #22
0
ファイル: popVars.py プロジェクト: sudorook/simuPOP
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
from pprint import pprint
pop = sim.Population(100, loci=2)
sim.initGenotype(pop, freq=[0.3, 0.7])
print(pop.vars())  # No variable now
pop.dvars().myVar = 21
print(pop.vars())
sim.stat(pop, popSize=1, alleleFreq=0)
# pprint prints in a less messy format
pprint(pop.vars())
# print number of allele 1 at locus 0
print(pop.vars()['alleleNum'][0][1])
# use the dvars() function to access dictionary keys as attributes
print(pop.dvars().alleleNum[0][1])
print(pop.dvars().alleleFreq[0])
コード例 #23
0
ファイル: Dumper.py プロジェクト: sudorook/simuPOP
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

# This script is an example in the simuPOP user's guide. Please refer to
# the user's guide (http://simupop.sourceforge.net/manual) for a detailed
# description of this example.
#

import simuPOP as sim
pop = sim.Population(size=[10, 10], loci=[20, 30], infoFields='gen',
    ancGen=-1)
sim.initSex(pop)
pop.setVirtualSplitter(sim.SexSplitter())
pop1 = pop.clone()
sim.initGenotype(pop, freq=[0]*20 + [0.1]*10)
pop.setIndInfo(1, 'gen')
sim.initGenotype(pop1, freq=[0]*50 + [0.1]*10)
pop1.setIndInfo(2, 'gen')
pop.push(pop1)
sim.dump(pop, width=3, loci=[5, 6, 30], subPops=([0, 0], [1, 1]),
    max=10, structure=False)
# list all male individuals in all subpopulations
sim.dump(pop, width=3, loci=[5, 6, 30], subPops=[(sim.ALL_AVAIL, 0)],
    max=10, structure=False)