isaacovercast

Trashquatch:~ labuser$ conda install -c ipyrad ipyrad
Fetching package metadata: ......
Solving package specifications: ..........................................................
Package plan for installation in environment /Users/labuser/miniconda2:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libpng-1.6.17              |                0         184 KB

isaacovercast

def hill(p=.99, order=0):
    """ Obviously doesn't work for H1 """

    ## p is the frequency of the dominant species
    p = p
    q = 1-p

    abunds = np.array([p*p, p*q, p*q, q*q])
    ## Normalize abundances (not necessary here I guess)
    abunds = abunds/np.sum(abunds)

isaacovercast

def dadi_to_momi(infile, outfile=None, verbose=False):
    if outfile == None:
        outfile = infile.split(".sfs")[0] + "_momi.sfs"
    dat = open(infile).readlines()
    ## Get rid of comment lines
    dat = [x.strip() for x in dat if not x.startswith("#")]
    if not len(dat) == 3:
        raise Exception("Malformed dadi sfs {}.\n  Must have 3 lines, yours has {}".format(infile, len(dat)))

    ## Parse the info line into nsamps per pop (list of ints), folding flag, and pop names list (if they are given)