Subject: fix some py3 transition
Description: fix some py2 to py3 port
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2020-02-08
Forwarded: no
--- a/pbsuite/honey/TGraf.py
+++ b/pbsuite/honey/TGraf.py
@@ -3,7 +3,6 @@
 import grp, logging, time, copy
 from tempfile import NamedTemporaryFile
 from collections import Counter, defaultdict
-from string import maketrans
 import pysam
 from pbsuite.utils.setupLogging import setupLogging
 
@@ -69,7 +68,7 @@
         self.epirem = getTag(read, "ES")
         #Choose higher quality or force epilog
         #     if we have an epi      and ((we want hq and  it's of higher quality)   or we want epi
-        if (self.epipos is not None) and ((log == 'h' and self.epimaq > self.promaq) or log == 'e'):
+        if (self.epipos is not None and self.promaq is not None) and ((log == 'h' and self.epimaq > self.promaq) or log == 'e'):
             foundBreak = True
             if self.epipos <= end:
                 s, e, a, b, uq, dq, uR, dR = (self.epipos, end, \
@@ -272,7 +271,7 @@
     
     def bpStr(self):
         def swap(a, b):
-            trans = maketrans("<>","><")
+            trans = str.maketrans("<>","><")
             if a in ['p','i','e']:
                 b = b.translate(trans)[::-1]
             elif b in ['p','i','e']:
--- a/pbsuite/utils/FileHandlers.py
+++ b/pbsuite/utils/FileHandlers.py
@@ -1,7 +1,6 @@
 import re, sys, os, bisect, logging, copy
 from collections import defaultdict
 from io import StringIO
-from string import maketrans
 
 from networkx import draw, write_gml, write_graphml, Graph
 
@@ -581,7 +580,7 @@
 
 """
 
-revComp = maketrans("ATCGNatcgn","TAGCNtagcn")
+revComp = str.maketrans("ATCGNatcgn","TAGCNtagcn")
 
 class M5File(list):
     
--- a/pbsuite/honey/HSpots.py
+++ b/pbsuite/honey/HSpots.py
@@ -554,16 +554,16 @@
             for svstart, svsize, svtype in expandCigar(align, args.minIndelErr, EXPLORECOLLAPSE):
                 if svstart >= offset and svstart <= offset + regsize:
                     if svtype == "MAT":#depricated
-                        begin = max(0, svstart - svsize - offset)
-                        end = min(begin - offset, container.shape[1])
+                        begin = int(max(0, svstart - svsize - offset))
+                        end = int(min(begin - offset, container.shape[1]))
                         container[MAT, begin:end] += BIGINTY(1)
                     elif svtype == "DEL":
-                        begin = max(0, svstart - offset)
-                        end = min(begin + svsize, container.shape[1])
+                        begin = int(max(0, svstart - offset))
+                        end = int(min(begin + svsize, container.shape[1]))
                         container[DEL, begin:end] += BIGINTY(1)
                     elif svtype == "INS":
-                        begin = max(0, svstart - (svsize/2) - offset)
-                        end = min(begin + (svsize/2), container.shape[1])
+                        begin = int(max(0, svstart - (svsize/2) - offset))
+                        end = int(min(begin + (svsize/2), container.shape[1]))
                         container[INS, begin:end] += BIGINTY(1)
                      
         logging.debug("%d reads filtered for low mapq in %s" % (mqFilt, self.groupName))