From 16fe152fd44e4b10b256f6d1a371581064215e85 Mon Sep 17 00:00:00 2001 From: Jeffrey Hsu Date: Mon, 22 May 2017 16:00:20 -0400 Subject: [PATCH 1/2] python 3 xrange compatibility fix --- qvalue/qvalue.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/qvalue/qvalue.py b/qvalue/qvalue.py index 8c50690..0b9ff76 100644 --- a/qvalue/qvalue.py +++ b/qvalue/qvalue.py @@ -47,11 +47,11 @@ def estimate(pv, m=None, verbose=False, lowmem=False, pi0=None): tck = interpolate.splrep(lam, pi0, k=3) pi0 = interpolate.splev(lam[-1], tck) if verbose: - print("qvalues pi0=%.3f, estimated proportion of null features " % pi0) + print(("qvalues pi0=%.3f, estimated proportion of null features " % pi0)) if pi0 > 1: if verbose: - print("got pi0 > 1 (%.3f) while estimating qvalues, setting it to 1" % pi0) + print(("got pi0 > 1 (%.3f) while estimating qvalues, setting it to 1" % pi0)) pi0 = 1.0 assert(pi0 >= 0 and pi0 <= 1), "pi0 is not between 0 and 1: %f" % pi0 @@ -63,7 +63,7 @@ def estimate(pv, m=None, verbose=False, lowmem=False, pi0=None): qv[last_pv] = (pi0*pv[last_pv]*m)/float(m) pv[last_pv] = -sp.inf prev_qv = last_pv - for i in xrange(int(len(pv))-2, -1, -1): + for i in range(int(len(pv))-2, -1, -1): cur_max = pv.argmax() qv_i = (pi0*m*pv[cur_max]/float(i+1)) pv[cur_max] = -sp.inf @@ -77,7 +77,7 @@ def estimate(pv, m=None, verbose=False, lowmem=False, pi0=None): qv = pi0 * m/len(pv) * pv qv[-1] = min(qv[-1], 1.0) - for i in xrange(len(pv)-2, -1, -1): + for i in range(len(pv)-2, -1, -1): qv[i] = min(pi0*m*pv[i]/(i+1.0), qv[i+1]) # reorder qvalues From 6d61704160ff67954053db688f2cc17a1491226d Mon Sep 17 00:00:00 2001 From: Jeffrey Hsu Date: Mon, 22 May 2017 16:07:44 -0400 Subject: [PATCH 2/2] fixes import for python 3 --- qvalue/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qvalue/__init__.py b/qvalue/__init__.py index 63f3a72..7e9eff3 100644 --- a/qvalue/__init__.py +++ b/qvalue/__init__.py @@ -1 +1 @@ -from qvalue import * +from .qvalue import *