Not compatible with python 3?

[quarkmatter]

Your software uses xrange() instead of range(), but xrange() has been discontinued in python 3. Heres a screen shot of the error i get when trying to call your qvalues() function

[grenkoca]

It looks like you're using an old version of multipy, as it hasn't been updated on pip. Try installing manually and seeing if that fixes the issue:

git clone https://github.com/puolival/multipy.git
cd multipy/
ipython setup.py install

Then run your command again. If nothing else, try copying-and-pasting the code from source to define it locally in your program. This is what I did and it works for me:

import numpy as np
from scipy.interpolate import UnivariateSpline


def qvalue(pvals, threshold=0.05, verbose=True):
    """Function for estimating q-values from p-values using the Storey-
    Tibshirani q-value method (2003).

    Input arguments:
    ================
    pvals       - P-values corresponding to a family of hypotheses.
    threshold   - Threshold for deciding which q-values are significant.

    Output arguments:
    =================
    significant - An array of flags indicating which p-values are significant.
    qvals       - Q-values corresponding to the p-values.
    """


    """Count the p-values. Find indices for sorting the p-values into
    ascending order and for reversing the order back to original."""
    m, pvals = len(pvals), np.asarray(pvals)
    ind = np.argsort(pvals)
    rev_ind = np.argsort(ind)
    pvals = pvals[ind]


    # Estimate proportion of features that are truly null.
    kappa = np.arange(0, 0.96, 0.01)
    pik = [sum(pvals > k) / (m*(1-k)) for k in kappa]
    cs = UnivariateSpline(kappa, pik, k=3, s=None, ext=0)
    pi0 = float(cs(1.))
    if (verbose):
        print('The estimated proportion of truly null features is %.3f' % pi0)


    """The smoothing step can sometimes converge outside the interval [0, 1].
    This was noted in the published literature at least by Reiss and
    colleagues [4]. There are at least two approaches one could use to
    attempt to fix the issue:
    (1) Set the estimate to 1 if it is outside the interval, which is the
        assumption in the classic FDR method.
    (2) Assume that if pi0 > 1, it was overestimated, and if pi0 < 0, it
        was underestimated. Set to 0 or 1 depending on which case occurs.

    Here we have chosen the first option, since it is the more conservative
    one of the two.
    """
    if (pi0 < 0 or pi0 > 1):
        pi0 = 1
        print('Smoothing estimator did not converge in [0, 1]')


    # Compute the q-values.
    qvals = np.zeros(np.shape(pvals))
    qvals[-1] = pi0*pvals[-1]
    for i in np.arange(m-2, -1, -1):
        qvals[i] = min(pi0*m*pvals[i]/float(i+1), qvals[i+1])


    # Test which p-values are significant.
    significant = np.zeros(np.shape(pvals), dtype='bool')
    significant[ind] = qvals<threshold


    """Order the q-values according to the original order of the p-values."""
    qvals = qvals[rev_ind]
    return significant, qvals

[GDelevoye]

Same problem for me. Updating numpy did not solve the problem

Copy-paste the above snippet did not work either, but maybe this time it was due to pathologic p-values in my case