Exemplos de Misc.make_data_dict em Python

Exemplo n.º 1

Arquivo: projections_calc_auto.py Projeto: jep-hub/Adaptive-pathways-of-coral-populations-on-the-Great-Barrier-Reef

#!/usr/bin/env python
import dadi
import pylab
import matplotlib.pyplot as plt
import numpy as np
from numpy import array
from dadi import Misc, Spectrum, Numerics, PhiManip, Integration, Demographics1D, Demographics2D
import sys
infile = sys.argv[1]
popid = [sys.argv[2]]
proj = range(int(sys.argv[3]), int(sys.argv[4]))
dd = Misc.make_data_dict(infile)
for p in range(len(proj)):
    data = Spectrum.from_data_dict(dd,
                                   pop_ids=popid,
                                   projections=[proj[p]],
                                   polarized=False)
    print proj[p], data.S()

Exemplo n.º 2

import numpy
import dadi
import Plotting_Functions
from dadi import Numerics, PhiManip, Integration, Misc
from dadi.Spectrum_mod import Spectrum

#===========================================================================
# Import data to create joint-site frequency spectrum
#===========================================================================

#**************
#path to your input file
snps = "/Users/portik/Documents/GitHub/dadi_pipeline/Two_Population_Pipeline/Example_Data/dadi_2pops_North_South_snps.txt"

#Create python dictionary from snps file
dd = Misc.make_data_dict(snps)

#**************
#pop_ids is a list which should match the populations headers of your SNPs file columns
pop_ids = ["North", "South"]

#**************
#projection sizes, in ALLELES not individuals
proj = [16, 32]

#Convert this dictionary into folded AFS object
#[polarized = False] creates folded spectrum object
fs = Spectrum.from_data_dict(dd,
                             pop_ids=pop_ids,
                             projections=proj,
                             polarized=False)