Skip to content

python 3 compatibility changes #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jeffhsu3 wants to merge 2 commits into
base: master
Choose a base branch
from
Open

python 3 compatibility changes #4

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
16fe152
python 3 xrange compatibility fix
jeffhsu3 May 22, 2017
6d61704
fixes import for python 3
jeffhsu3 May 22, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion qvalue/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
from qvalue import *
from .qvalue import *
8 changes: 4 additions & 4 deletions qvalue/qvalue.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down