fixes for python3

dmnfarrell · Jan 13, 2018 · 0fa3fb6 · 0fa3fb6
1 parent 0447a36
commit 0fa3fb6
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/epitopepredict/base.py b/epitopepredict/base.py
@@ -12,6 +12,13 @@
 import time, io
 import operator as op
 import re, types
+try:
+ unicode = unicode
+except NameError:
+ #unicode is undefined, must be Python 3
+ str = str
+ unicode = str
+ basestring = (str,bytes)
 import math
 import subprocess
 from subprocess import CalledProcessError
@@ -103,7 +110,7 @@ def dbscan(B=None, x=None, dist=7, minsize=4):
  if len(B)==0:
  return
  x = sorted(B.pos.astype('int'))
- X = np.array(zip(x,np.zeros(len(x))), dtype=np.int)
+ X = np.array(list(zip(x,np.zeros(len(x)))), dtype=np.int)
  db = DBSCAN(eps=dist, min_samples=minsize)
  db.fit(X)
  labels = db.labels_

diff --git a/epitopepredict/config.py b/epitopepredict/config.py
@@ -134,7 +134,7 @@ def check_options(opts):
  """Check for missing default options in dict. Meant to handle
  incomplete config files"""
 
- sections = baseoptions.keys()
+ sections = list(baseoptions.keys())
  for s in sections:
  defaults = dict(baseoptions[s])
  for i in defaults: