From: "Michael R. Crusoe" <crusoe@debian.org>
Date: Sun, 9 Feb 2020 12:45:16 +0100
Subject: convert all Python scripts to Python v3

Forwarded: https://github.com/vgteam/gfakluge/pull/7
Forwarded: https://github.com/benedictpaten/sonLib/pull/43
---
 deps/libbdsg/make_and_run_binder.py                |  2 +-
 deps/pinchesAndCacti/__init__.py                   |  2 +-
 .../externalTools/threeEdgeConnected/__init__.py   |  2 +-
 .../threeEdgeConnected/threeEdgeTests.py           |  2 +-
 .../document_listing/generate_collection.py        |  6 +-
 deps/sonLib/C/Makefile                             |  2 +-
 deps/sonLib/Makefile                               |  2 +-
 deps/sonLib/__init__.py                            |  2 +-
 deps/sonLib/allTests.py                            | 14 ++--
 deps/sonLib/bioio.py                               | 52 ++++++-------
 deps/sonLib/bioioTest.py                           | 88 +++++++++++-----------
 deps/sonLib/cigarsTest.py                          | 18 ++---
 deps/sonLib/kvdbTest.py                            |  2 +-
 deps/sonLib/misc.py                                |  2 +-
 deps/sonLib/nxnewick.py                            | 17 ++---
 deps/sonLib/nxnewickTest.py                        |  2 +-
 deps/sonLib/nxtree.py                              |  3 +-
 deps/sonLib/nxtreeTest.py                          |  2 +-
 deps/sonLib/setup.py                               |  2 +-
 deps/sonLib/sonLib_daemonize.py                    |  4 +-
 deps/sonLib/tree.py                                | 88 +++++++++++-----------
 deps/sonLib/treeTest.py                            | 48 ++++++------
 deps/sonLib/unitTest.py                            |  2 +-
 deps/xg/deps/gfakluge/scripts/fa_to_gfa.py         |  4 +-
 deps/xg/deps/gfakluge/scripts/gfa_to_cytoscape.py  |  2 +-
 25 files changed, 184 insertions(+), 186 deletions(-)

diff --git a/deps/libbdsg/make_and_run_binder.py b/deps/libbdsg/make_and_run_binder.py
index 15496fc..d779f04 100755
--- a/deps/libbdsg/make_and_run_binder.py
+++ b/deps/libbdsg/make_and_run_binder.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 import glob
 import os
diff --git a/deps/pinchesAndCacti/__init__.py b/deps/pinchesAndCacti/__init__.py
index 3483949..313c6b5 100644
--- a/deps/pinchesAndCacti/__init__.py
+++ b/deps/pinchesAndCacti/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2009-2011 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/pinchesAndCacti/externalTools/threeEdgeConnected/__init__.py b/deps/pinchesAndCacti/externalTools/threeEdgeConnected/__init__.py
index 3483949..313c6b5 100644
--- a/deps/pinchesAndCacti/externalTools/threeEdgeConnected/__init__.py
+++ b/deps/pinchesAndCacti/externalTools/threeEdgeConnected/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2009-2011 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/pinchesAndCacti/externalTools/threeEdgeConnected/threeEdgeTests.py b/deps/pinchesAndCacti/externalTools/threeEdgeConnected/threeEdgeTests.py
index ebbcbff..5db5c3f 100644
--- a/deps/pinchesAndCacti/externalTools/threeEdgeConnected/threeEdgeTests.py
+++ b/deps/pinchesAndCacti/externalTools/threeEdgeConnected/threeEdgeTests.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2009-2011 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/sdsl-lite/tutorial/document_listing/generate_collection.py b/deps/sdsl-lite/tutorial/document_listing/generate_collection.py
index 27b0325..e141946 100644
--- a/deps/sdsl-lite/tutorial/document_listing/generate_collection.py
+++ b/deps/sdsl-lite/tutorial/document_listing/generate_collection.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
 
 import fnmatch
 import sys
@@ -13,7 +13,7 @@ collection_path = "collection.txt"
 def main():
 
     if len(sys.argv) == 1:
-        print "Usage ./", sys.argv[0], "directory"
+        print("Usage ./", sys.argv[0], "directory")
         sys.exit(0)
     cur_dir = sys.argv[1]
     doc_paths = []
@@ -23,7 +23,7 @@ def main():
             doc_path = root+"/"+f
             doc_paths.append(doc_path)
 
-    print "Found ", len(doc_paths), "source files in", cur_dir
+    print("Found ", len(doc_paths), "source files in", cur_dir)
     collection_f = open(collection_path,'w')
     for doc_path in doc_paths:
         f = open(doc_path, 'r')
diff --git a/deps/sonLib/C/Makefile b/deps/sonLib/C/Makefile
index bbb2781..371b965 100644
--- a/deps/sonLib/C/Makefile
+++ b/deps/sonLib/C/Makefile
@@ -60,4 +60,4 @@ ${libPath}/sonLib.a : ${libSources} ${cppSources} $(foreach l, ${libHeaders}, ${
 	mv sonLib.a ${libPath}/
 
 test:
-	python allTests.py --testLength=SHORT --logLevel CRITICAL
+	python3 allTests.py --testLength=SHORT --logLevel CRITICAL
diff --git a/deps/sonLib/Makefile b/deps/sonLib/Makefile
index 35eb8b5..d60dd41 100644
--- a/deps/sonLib/Makefile
+++ b/deps/sonLib/Makefile
@@ -21,7 +21,7 @@ externalToolsP.clean :
 	cd externalTools && $(MAKE) clean
 
 test : all
-	PYTHONPATH=.. PATH=../../bin:$$PATH python allTests.py --testLength=SHORT --logLevel=CRITICAL
+	PYTHONPATH=.. PATH=../../bin:$$PATH python3 allTests.py --testLength=SHORT --logLevel=CRITICAL
 
 ${binPath}/sonLib_daemonize.py : sonLib_daemonize.py cP
 	cp sonLib_daemonize.py ${binPath}/sonLib_daemonize.py
diff --git a/deps/sonLib/__init__.py b/deps/sonLib/__init__.py
index 9d39579..ca1459a 100644
--- a/deps/sonLib/__init__.py
+++ b/deps/sonLib/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/sonLib/allTests.py b/deps/sonLib/allTests.py
index 04272fb..e398c02 100644
--- a/deps/sonLib/allTests.py
+++ b/deps/sonLib/allTests.py
@@ -1,20 +1,20 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
 #Released under the MIT license, see LICENSE.txt
 import unittest
 
-import bioioTest
-import cigarsTest
-import treeTest
-import kvdbTest
+from . import bioioTest
+from . import cigarsTest
+from . import treeTest
+from . import kvdbTest
 import socket
 try:
     import networkx as NX
     networkx_installed = True
-    import nxtreeTest
-    import nxnewickTest
+    from . import nxtreeTest
+    from . import nxnewickTest
 except ImportError:
     networkx_installed = False
 
diff --git a/deps/sonLib/bioio.py b/deps/sonLib/bioio.py
index 3b1070a..ae17ce5 100644
--- a/deps/sonLib/bioio.py
+++ b/deps/sonLib/bioio.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
@@ -16,8 +16,8 @@ import math
 import shutil
 from argparse import ArgumentParser
 from optparse import OptionParser, OptionContainer, OptionGroup
-from tree import BinaryTree
-from misc import close
+from .tree import BinaryTree
+from .misc import close
 import subprocess
 import array
 import string
@@ -421,14 +421,14 @@ def nameValue(name, value, valueType=str, quotes=False):
 def getRandomAlphaNumericString(length=10):
     """Returns a random alpha numeric string of the given length.
     """
-    return "".join([ random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz') for i in xrange(0, length) ])
+    return "".join([ random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz') for i in range(0, length) ])
 
 def makeSubDir(dirName):
     """Makes a given subdirectory if it doesn't already exist, making sure it us public.
     """
     if not os.path.exists(dirName):
         os.mkdir(dirName)
-        os.chmod(dirName, 0777)
+        os.chmod(dirName, 0o777)
     return dirName
 
 def getTempFile(suffix="", rootDir=None):
@@ -441,7 +441,7 @@ def getTempFile(suffix="", rootDir=None):
     else:
         tmpFile = os.path.join(rootDir, "tmp_" + getRandomAlphaNumericString() + suffix)
         open(tmpFile, 'w').close()
-        os.chmod(tmpFile, 0777) #Ensure everyone has access to the file.
+        os.chmod(tmpFile, 0o777) #Ensure everyone has access to the file.
         return tmpFile
 
 def getTempDirectory(rootDir=None):
@@ -468,7 +468,7 @@ def getTempDirectory(rootDir=None):
                 break
                 
         os.mkdir(tmpDir)
-        os.chmod(tmpDir, 0777) #Ensure everyone has access to the file.
+        os.chmod(tmpDir, 0o777) #Ensure everyone has access to the file.
         return tmpDir
 
 class TempFileTree:
@@ -744,7 +744,7 @@ def fastaWrite(fileHandleOrFile, name, seq, mode="w"):
     fileHandle = _getFileHandle(fileHandleOrFile, mode)
     valid_chars = {x for x in string.ascii_letters + "-"}
     try:
-        assert any([isinstance(seq, unicode), isinstance(seq, str)])
+        assert any([isinstance(seq, str), isinstance(seq, str)])
     except AssertionError:
         raise RuntimeError("Sequence is not unicode or string")
     try:
@@ -754,7 +754,7 @@ def fastaWrite(fileHandleOrFile, name, seq, mode="w"):
         raise RuntimeError("Invalid FASTA character(s) see in fasta sequence: {}".format(bad_chars))
     fileHandle.write(">%s\n" % name)
     chunkSize = 100
-    for i in xrange(0, len(seq), chunkSize):
+    for i in range(0, len(seq), chunkSize):
         fileHandle.write("%s\n" % seq[i:i+chunkSize])
     if isinstance(fileHandleOrFile, "".__class__):
         fileHandle.close()
@@ -849,23 +849,23 @@ def fastaAlignmentRead(fasta, mapFn=(lambda x : x), l=None):
     else:
         l = l[:]
     seqNo = len(l)
-    for i in xrange(0, seqNo):
+    for i in range(0, seqNo):
         j = open(fasta, 'r')
         j.seek(l[i])
         l[i] = j
-    column = [sys.maxint]*seqNo
+    column = [sys.maxsize]*seqNo
     if seqNo != 0:
         while True:
-            for j in xrange(0, seqNo):
+            for j in range(0, seqNo):
                 i = l[j].read(1)
                 while i == '\n':
                     i = l[j].read(1)
                 column[j] = i
             if column[0] == '>' or column[0] == '':
-                for j in xrange(1, seqNo):
+                for j in range(1, seqNo):
                     assert column[j] == '>' or column[j] == ''
                 break
-            for j in xrange(1, seqNo):
+            for j in range(1, seqNo):
                  assert column[j] != '>' and column[j] != ''
                  column[j] = mapFn(column[j])
             yield column[:]
@@ -878,8 +878,8 @@ def fastaAlignmentWrite(columnAlignment, names, seqNo, fastaFile,
     Writes out column alignment to given file multi-fasta format
     """
     fastaFile = open(fastaFile, 'w')
-    columnAlignment = [ i for i in columnAlignment if filter(i) ]
-    for seq in xrange(0, seqNo):
+    columnAlignment = [ i for i in columnAlignment if list(filter(i)) ]
+    for seq in range(0, seqNo):
         fastaFile.write(">%s\n" % names[seq])
         for column in columnAlignment:
             fastaFile.write(column[seq])
@@ -890,10 +890,10 @@ def getRandomSequence(length=500):
     """Generates a random name and sequence.
     """
     fastaHeader = ""
-    for i in xrange(int(random.random()*100)):
+    for i in range(int(random.random()*100)):
         fastaHeader = fastaHeader + random.choice([ 'A', 'C', '0', '9', ' ', '\t' ])
     return (fastaHeader, \
-            "".join([ random.choice([ 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'N' ]) for i in xrange((int)(random.random() * length))]))
+            "".join([ random.choice([ 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'N' ]) for i in range((int)(random.random() * length))]))
 
 def _expLength(i=0, prob=0.95):
     if random.random() >= prob:
@@ -1043,9 +1043,9 @@ def pWMRead(fileHandle, alphabetSize=4):
     for line in lines[1:]:
         l2 = [ float(i) for i in line.split() ]
         assert len(l) == len(l2)
-        for i in xrange(0, len(l)):
+        for i in range(0, len(l)):
             l[i].append(l2[i])
-    for i in xrange(0, len(l)):
+    for i in range(0, len(l)):
         j = sum(l[i]) + 0.0
         l[i] = [ k/j for k in l[i] ]
     return l
@@ -1053,8 +1053,8 @@ def pWMRead(fileHandle, alphabetSize=4):
 def pWMWrite(fileHandle, pWM, alphabetSize=4):
     """Writes file in standard PWM format, is reverse of pWMParser
     """
-    for i in xrange(0, alphabetSize):
-        fileHandle.write("%s\n" % ' '.join([ str(pWM[j][i]) for j in xrange(0, len(pWM)) ]))
+    for i in range(0, alphabetSize):
+        fileHandle.write("%s\n" % ' '.join([ str(pWM[j][i]) for j in range(0, len(pWM)) ]))
 
 #########################################################
 #########################################################
@@ -1229,8 +1229,8 @@ def cigarWrite(fileHandle, pairwiseAlignment, withProbs=True):
 
 def _getRandomSegment():
     contig = random.choice([ "one", "two", "three", "four" ])
-    start = random.choice(xrange(0, 10000))
-    end = start + random.choice(xrange(0, 1000))
+    start = random.choice(range(0, 10000))
+    end = start + random.choice(range(0, 1000))
     strand = random.choice([ True, False ])
     if not strand:
         start, end = end, start
@@ -1244,7 +1244,7 @@ def getRandomOperationList(xLength, yLength, operationMaxLength=100):
         if operationMaxLength == 1:
             length = 1
         else:
-            length = random.choice(xrange(1, operationMaxLength))
+            length = random.choice(range(1, operationMaxLength))
         if opType != PairwiseAlignment.PAIRWISE_INDEL_Y and xLength - length < 0:
             continue
         if opType != PairwiseAlignment.PAIRWISE_INDEL_X and yLength - length < 0:
@@ -1262,7 +1262,7 @@ def getRandomPairwiseAlignment():
     """
     i, j, k, l = _getRandomSegment()
     m, n, o, p = _getRandomSegment()
-    score = random.choice(xrange(-1000, 1000))
+    score = random.choice(range(-1000, 1000))
     return PairwiseAlignment(i, j, k, l, m, n, o, p, score, getRandomOperationList(abs(k - j), abs(o - n)))
 
 #########################################################
diff --git a/deps/sonLib/bioioTest.py b/deps/sonLib/bioioTest.py
index c7404d1..4b74176 100644
--- a/deps/sonLib/bioioTest.py
+++ b/deps/sonLib/bioioTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
@@ -11,32 +11,32 @@ import sys
 import random
 import math
 
-from bioio import getTempFile
-from bioio import getTempDirectory
-from bioio import TempFileTree
-from bioio import getRandomAlphaNumericString
+from .bioio import getTempFile
+from .bioio import getTempDirectory
+from .bioio import TempFileTree
+from .bioio import getRandomAlphaNumericString
 
-from bioio import fastaRead
-from bioio import fastaWrite 
-from bioio import fastqRead
-from bioio import fastqWrite 
-from bioio import getRandomSequence
+from .bioio import fastaRead
+from .bioio import fastaWrite 
+from .bioio import fastqRead
+from .bioio import fastqWrite 
+from .bioio import getRandomSequence
 
-from bioio import pWMRead
-from bioio import pWMWrite
+from .bioio import pWMRead
+from .bioio import pWMWrite
 
-from bioio import newickTreeParser
-from bioio import printBinaryTree
+from .bioio import newickTreeParser
+from .bioio import printBinaryTree
 
-from bioio import cigarRead
-from bioio import cigarWrite
-from bioio import PairwiseAlignment
-from bioio import getRandomPairwiseAlignment
+from .bioio import cigarRead
+from .bioio import cigarWrite
+from .bioio import PairwiseAlignment
+from .bioio import getRandomPairwiseAlignment
 
 from sonLib.bioio import TestStatus
 
-from bioio import system
-from bioio import logger
+from .bioio import system
+from .bioio import logger
 
 class TestCase(unittest.TestCase):
     
@@ -61,12 +61,12 @@ class TestCase(unittest.TestCase):
     #########################################################
     
     def testTempFileTree(self):
-        for test in xrange(100): #self.testNo):
-            levels = random.choice(xrange(1, 4))
-            fileNo = random.choice(xrange(1, 6))
+        for test in range(100): #self.testNo):
+            levels = random.choice(range(1, 4))
+            fileNo = random.choice(range(1, 6))
             maxTempFiles = int(math.pow(fileNo, levels))
             
-            print "Got %s levels, %s fileNo and %s maxTempFiles" % (levels, fileNo, maxTempFiles)
+            print("Got %s levels, %s fileNo and %s maxTempFiles" % (levels, fileNo, maxTempFiles))
             
             tempFileTreeRootDir = os.path.join(self.tempDir, getRandomAlphaNumericString())
             tempFileTree = TempFileTree(tempFileTreeRootDir, fileNo, levels)
@@ -74,7 +74,7 @@ class TestCase(unittest.TestCase):
             tempFiles = []
             tempDirs = []
             #Check we can mac number of temp files.
-            for i in xrange(maxTempFiles):
+            for i in range(maxTempFiles):
                 if random.random() > 0.5:
                     tempFile = tempFileTree.getTempFile()
                     assert os.path.isfile(tempFile)
@@ -132,9 +132,9 @@ class TestCase(unittest.TestCase):
     def testFastaReadWrite(self):
         tempFile = getTempFile()
         self.tempFiles.append(tempFile)
-        for test in xrange(0, self.testNo):
-            fastaNumber = random.choice(xrange(10))
-            l = [ getRandomSequence() for i in xrange(fastaNumber) ]
+        for test in range(0, self.testNo):
+            fastaNumber = random.choice(range(10))
+            l = [ getRandomSequence() for i in range(fastaNumber) ]
             fileHandle = open(tempFile, 'w')
             for name, seq in l:
                 fastaWrite(fileHandle, name, seq)
@@ -150,9 +150,9 @@ class TestCase(unittest.TestCase):
     def testFastqReadWrite(self):
         tempFile = getTempFile()
         self.tempFiles.append(tempFile)
-        for test in xrange(0, self.testNo):
-            fastaNumber = random.choice(xrange(10))
-            fastqs = [ (name, seq, [ random.randint(33, 126) for i in range(len(seq)) ]) for name, seq in [ getRandomSequence() for i in xrange(fastaNumber) ]]
+        for test in range(0, self.testNo):
+            fastaNumber = random.choice(range(10))
+            fastqs = [ (name, seq, [ random.randint(33, 126) for i in range(len(seq)) ]) for name, seq in [ getRandomSequence() for i in range(fastaNumber) ]]
             fH = open(tempFile, 'w')
             for name, seq, quals in fastqs:
                 fastqWrite(fH, name, seq, quals)
@@ -170,9 +170,9 @@ class TestCase(unittest.TestCase):
         self.tempFiles.append(tempFile)
         tempFile2 = getTempFile()
         self.tempFiles.append(tempFile2)
-        for test in xrange(0, self.testNo):
-            fastaNumber = random.choice(xrange(10))
-            l = [ getRandomSequence() for i in xrange(fastaNumber) ]
+        for test in range(0, self.testNo):
+            fastaNumber = random.choice(range(10))
+            l = [ getRandomSequence() for i in range(fastaNumber) ]
             fileHandle = open(tempFile, 'w')
             for name, seq in l:
                 fastaWrite(fileHandle, name, seq)
@@ -180,7 +180,7 @@ class TestCase(unittest.TestCase):
             
             command = "sonLib_fastaCTest %s %s" % (tempFile, tempFile2)
             
-            print command
+            print(command)
             
             system(command)
             
@@ -205,12 +205,12 @@ class TestCase(unittest.TestCase):
             d = '((human,baboon),chimp);'
             e = newickTreeParser(d)
             f = printBinaryTree(e, False)
-            print d, f
+            print(d, f)
             assert d == f
     
     def testNewickTreeParser_UnaryNodes(self):
         #tests with unary nodes 
-        for test in xrange(0, self.testNo):
+        for test in range(0, self.testNo):
             tree = getRandomTreeString()
             logger.debug("tree to try\t", tree)
             tree2 = newickTreeParser(tree, reportUnaryNodes=True)
@@ -229,7 +229,7 @@ class TestCase(unittest.TestCase):
     def testPWMParser(self):
         tempFile = getTempFile()
         self.tempFiles.append(tempFile)
-        for test in xrange(0, self.testNo):
+        for test in range(0, self.testNo):
             pWM = getRandomPWM()
             
             fileHandle = open(tempFile, 'w')
@@ -240,7 +240,7 @@ class TestCase(unittest.TestCase):
             pWM2 = pWMRead(fileHandle)
             fileHandle.close()
             
-            for i in xrange(0, len(pWM)):  
+            for i in range(0, len(pWM)):  
                 pWM[i] == pWM2[i]
     
     #########################################################
@@ -254,9 +254,9 @@ class TestCase(unittest.TestCase):
     def testCigarReadWrite(self):
         tempFile = getTempFile()
         self.tempFiles.append(tempFile)
-        for test in xrange(0, self.testNo):
-            cigarNumber = random.choice(xrange(10))
-            l = [ getRandomPairwiseAlignment() for i in xrange(cigarNumber) ]
+        for test in range(0, self.testNo):
+            cigarNumber = random.choice(range(10))
+            l = [ getRandomPairwiseAlignment() for i in range(cigarNumber) ]
             fileHandle = open(tempFile, 'w')
             for cigar in l:
                 cigarWrite(fileHandle, cigar)
@@ -292,10 +292,10 @@ def getRandomPWM(length=-1):
     if length == -1:
         length = 1 + int(random.random()*10)
     def fn():
-        l = [ random.random()*100 for i in xrange(0, 4) ]
+        l = [ random.random()*100 for i in range(0, 4) ]
         i = sum(l)
         return [ j/i for j in l ]
-    return [ fn() for i in xrange(0, length) ]
+    return [ fn() for i in range(0, length) ]
         
 if __name__ == '__main__':
     unittest.main()
diff --git a/deps/sonLib/cigarsTest.py b/deps/sonLib/cigarsTest.py
index 5339fb4..ad7b5b2 100644
--- a/deps/sonLib/cigarsTest.py
+++ b/deps/sonLib/cigarsTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
@@ -10,12 +10,12 @@ import os
 import sys
 import random
 
-from bioio import getTempFile
+from .bioio import getTempFile
 
-from bioio import cigarRead
-from bioio import cigarWrite
-from bioio import getRandomPairwiseAlignment
-from bioio import system
+from .bioio import cigarRead
+from .bioio import cigarWrite
+from .bioio import getRandomPairwiseAlignment
+from .bioio import system
 from sonLib.bioio import TestStatus
 from sonLib.bioio import logger
 
@@ -36,9 +36,9 @@ class TestCase(unittest.TestCase):
         """
         tempFile = getTempFile()
         self.tempFiles.append(tempFile)
-        for test in xrange(0, self.testNo):
-            pairwiseAlignmentNumber = random.choice(xrange(10))
-            l = [ getRandomPairwiseAlignment() for i in xrange(pairwiseAlignmentNumber) ]
+        for test in range(0, self.testNo):
+            pairwiseAlignmentNumber = random.choice(range(10))
+            l = [ getRandomPairwiseAlignment() for i in range(pairwiseAlignmentNumber) ]
             fileHandle = open(tempFile, 'w')
             
             keepProbs = random.random() > 0.5
diff --git a/deps/sonLib/kvdbTest.py b/deps/sonLib/kvdbTest.py
index ae0de1d..cc5b8a6 100644
--- a/deps/sonLib/kvdbTest.py
+++ b/deps/sonLib/kvdbTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/sonLib/misc.py b/deps/sonLib/misc.py
index 4c3af55..a8bcd41 100644
--- a/deps/sonLib/misc.py
+++ b/deps/sonLib/misc.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/sonLib/nxnewick.py b/deps/sonLib/nxnewick.py
index 65223dc..9005a92 100644
--- a/deps/sonLib/nxnewick.py
+++ b/deps/sonLib/nxnewick.py
@@ -1,9 +1,8 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Glenn Hickey
 #
 #Released under the MIT license, see LICENSE.txt
-#!/usr/bin/env python
 
 """read and write newick trees to and from networkx graphs (as wrapped by nxtree). 
 """
@@ -14,7 +13,7 @@ import math
 import random
 from string import whitespace as ws
 from sonLib.misc import close
-import bioio
+from . import bioio
 import networkx as NX
 from optparse import OptionParser
 from sonLib.nxtree import NXTree
@@ -187,15 +186,15 @@ def main():
     parser.parseFile(args[0])
     NX.drawing.nx_agraph.write_dot(parser.nxTree.nxDg, args[1])
     parser.writeFile(args[2])
-    print "PRE"
+    print("PRE")
     for i in parser.nxTree.preOrderTraversal():
-        print ("%d %s" % (i, parser.nxTree.getName(i)))
-    print "POST"
+        print(("%d %s" % (i, parser.nxTree.getName(i))))
+    print("POST")
     for i in parser.nxTree.postOrderTraversal():
-        print ("%d %s" % (i, parser.nxTree.getName(i)))
-    print "BFS"
+        print(("%d %s" % (i, parser.nxTree.getName(i))))
+    print("BFS")
     for i in parser.nxTree.breadthFirstTraversal():
-        print ("%d %s" % (i, parser.nxTree.getName(i)))
+        print(("%d %s" % (i, parser.nxTree.getName(i))))
     return 0
 
 if __name__ == '__main__':    
diff --git a/deps/sonLib/nxnewickTest.py b/deps/sonLib/nxnewickTest.py
index b38bd25..63953bc 100644
--- a/deps/sonLib/nxnewickTest.py
+++ b/deps/sonLib/nxnewickTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 011 by Glenn Hickey
 #
diff --git a/deps/sonLib/nxtree.py b/deps/sonLib/nxtree.py
index 3fe82b8..02392a9 100644
--- a/deps/sonLib/nxtree.py
+++ b/deps/sonLib/nxtree.py
@@ -1,9 +1,8 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Glenn Hickey
 #
 #Released under the MIT license, see LICENSE.txt
-#!/usr/bin/env python
 
 """A more general (ie arbitrary degree) tree to replace the BinaryTree
 in sonLib.tree.py.  Implemented as a lightweight wrapper over a 
diff --git a/deps/sonLib/nxtreeTest.py b/deps/sonLib/nxtreeTest.py
index d7600c1..1cd0c67 100644
--- a/deps/sonLib/nxtreeTest.py
+++ b/deps/sonLib/nxtreeTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 011 by Glenn Hickey
 #
diff --git a/deps/sonLib/setup.py b/deps/sonLib/setup.py
index 17503b2..a749737 100755
--- a/deps/sonLib/setup.py
+++ b/deps/sonLib/setup.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 from setuptools import setup
 import subprocess
diff --git a/deps/sonLib/sonLib_daemonize.py b/deps/sonLib/sonLib_daemonize.py
index 9e146e0..080d166 100644
--- a/deps/sonLib/sonLib_daemonize.py
+++ b/deps/sonLib/sonLib_daemonize.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # Glenn Hickey 2011
 #
@@ -66,7 +66,7 @@ else:
    
 if __name__ == '__main__':
     if len(sys.argv) != 2:
-        raise Exception, "%s: Wrong number of arguments" % sys.argv[0]
+        raise Exception("%s: Wrong number of arguments" % sys.argv[0])
     
     pid = os.fork()
     if pid > 0:
diff --git a/deps/sonLib/tree.py b/deps/sonLib/tree.py
index 0818c8c..d37c670 100644
--- a/deps/sonLib/tree.py
+++ b/deps/sonLib/tree.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
@@ -69,7 +69,7 @@ def binaryTree_depthFirstNumbers(binaryTree, labelTree=True, dontStopAtID=True):
         return mid+1, leafNo+1
     traverse(binaryTree)
     if labelTree:
-        for binaryTree in traversalIDs.keys():
+        for binaryTree in list(traversalIDs.keys()):
             binaryTree.traversalID = traversalIDs[binaryTree]
     return traversalIDs
 
@@ -164,18 +164,18 @@ def transformByDistance(wV, subModel, alphabetSize=4):
     transform wV by given substitution matrix
     """
     nc = [0.0]*alphabetSize
-    for i in xrange(0, alphabetSize):
+    for i in range(0, alphabetSize):
         j = wV[i]
         k = subModel[i]
-        for l in xrange(0, alphabetSize):
+        for l in range(0, alphabetSize):
             nc[l] += j * k[l]
     return nc
 
 def multiplyWV(wVX, wVY, alphabetSize=4):
-    return [ wVX[i] * wVY[i] for i in xrange(0, alphabetSize) ]
+    return [ wVX[i] * wVY[i] for i in range(0, alphabetSize) ]
 
 def sumWV(wVX, wVY, alphabetSize=4):
-    return [ wVX[i] + wVY[i] for i in xrange(0, alphabetSize) ]
+    return [ wVX[i] + wVY[i] for i in range(0, alphabetSize) ]
     
 def normaliseWV(wV, normFac=1.0):
     """
@@ -187,7 +187,7 @@ def normaliseWV(wV, normFac=1.0):
 def sumWVA(wVA, alphabetSize=4):
     totals = [0.0]*alphabetSize
     for wV in wVA:
-        for i in xrange(0, alphabetSize):
+        for i in range(0, alphabetSize):
             totals[i] += wV[i]
     return totals
 
@@ -222,7 +222,7 @@ def felsensteins(binaryTree, subMatrices, ancestorProbs, leaves, alphabetSize):
 def calculateCharacterFrequencies(seq, map, alphabetSize):
     counts = [0.0]*alphabetSize
     for i in seq:
-        counts[map(i)] += 1
+        counts[list(map(i))] += 1
     return counts
     
 #########################################################
@@ -261,9 +261,9 @@ def calculateDNADistanceMatrix(seqNo, fastaIter, transitionTransversionRatio=2.0
     transversions = [0.1]*seqNo*seqNo
     counts = [1.0]*seqNo*seqNo
     for column in fastaIter:
-        for i in xrange(0, seqNo):
+        for i in range(0, seqNo):
             if column[i] in [ 'A', 'C', 'T', 'G' ]:
-                for j in xrange(i+1, seqNo):
+                for j in range(i+1, seqNo):
                     if column[j] in [ 'A', 'C', 'T', 'G' ]:
                         counts[i*seqNo + j] += 1
                         if column[i] != column[j]:
@@ -277,9 +277,9 @@ def calculateDNADistanceMatrix(seqNo, fastaIter, transitionTransversionRatio=2.0
                                     transversions[i*seqNo + j] += 1
                                 else:
                                     transitions[i*seqNo + j] += 1
-    distanceMatrix = [ [None]*seqNo for i in xrange(0, seqNo) ]
-    for i in xrange(0, seqNo*seqNo):
-        for j in xrange(i+1, seqNo):
+    distanceMatrix = [ [None]*seqNo for i in range(0, seqNo) ]
+    for i in range(0, seqNo*seqNo):
+        for j in range(i+1, seqNo):
             k = i * seqNo + j
             distanceMatrix[i][j] = -0.75*math.log(1 - (4/3)*((transitions[k]+transversions[k])/counts[k])) #jukes cantor correction
             distanceMatrix[j][i] = distanceMatrix[i][j]
@@ -288,10 +288,10 @@ def calculateDNADistanceMatrix(seqNo, fastaIter, transitionTransversionRatio=2.0
     return distanceMatrix
 
 def makeDistancePairs(distanceMatrix, iDs, seqNo):
-    binaryTrees = [ BinaryTree(0.0, False, None, None, iDs[i]) for i in xrange(0, seqNo) ]
+    binaryTrees = [ BinaryTree(0.0, False, None, None, iDs[i]) for i in range(0, seqNo) ]
     distancePairs = []
-    for i in xrange(0, seqNo):
-        for j in xrange(i+1, seqNo): 
+    for i in range(0, seqNo):
+        for j in range(i+1, seqNo): 
             distancePairs.append(DistancePair(distanceMatrix[i][j], binaryTrees[i], 1, binaryTrees[j], 1))
             distancePairs.append(DistancePair(distanceMatrix[i][j], binaryTrees[j], 1, binaryTrees[i], 1))
     return distancePairs
@@ -327,10 +327,10 @@ def upgmaI(distancePairs, leafNo):
             holder1[i.leaf2] = i
         if i.leaf1 == distancePair.leaf2 and i.leaf2 != distancePair.leaf1:
             holder2[i.leaf2] = i
-    assert len(holder1.keys()) == leafNo-2
-    assert len(holder2.keys()) == leafNo-2
+    assert len(list(holder1.keys())) == leafNo-2
+    assert len(list(holder2.keys())) == leafNo-2
     assert set(holder1.keys()) == set(holder2.keys())
-    for i in holder1.keys():
+    for i in list(holder1.keys()):
         j = holder1[i]
         k = holder2[i]
         newDistance = (j.distance*j.leafNo1 + k.distance*k.leafNo1)/(j.leafNo1 + k.leafNo1)
@@ -346,7 +346,7 @@ def nj(distanceMatrix, iDs, leafNo):
 
 def getMinPair(distancePairs, rValues, leafNo):
     j = None
-    k = sys.maxint
+    k = sys.maxsize
     for i in distancePairs:
         adjustD = i.distance - (rValues[i.leaf1] + rValues[i.leaf2])/(leafNo-2)
         #print "the adjusted value ", adjustD, i.distance, rValues[i.leaf1]/(leafNo-2), rValues[i.leaf2]/(leafNo-2)
@@ -359,11 +359,11 @@ def getMinPair(distancePairs, rValues, leafNo):
 def calculateRValues(distancePairs, leafNo):
     j = {}
     for i in distancePairs:
-        if j.has_key(i.leaf1):
+        if i.leaf1 in j:
             j[i.leaf1] += i.distance
         else:
             j[i.leaf1] = i.distance
-    assert len(j.keys()) == leafNo
+    assert len(list(j.keys())) == leafNo
     return j
 
 def njI(distancePairs, leafNo):
@@ -391,10 +391,10 @@ def njI(distancePairs, leafNo):
             holder1[i.leaf2] = i
         if i.leaf1 == distancePair.leaf2 and i.leaf2 != distancePair.leaf1:
             holder2[i.leaf2] = i
-    assert len(holder1.keys()) == leafNo-2
-    assert len(holder2.keys()) == leafNo-2
+    assert len(list(holder1.keys())) == leafNo-2
+    assert len(list(holder2.keys())) == leafNo-2
     assert set(holder1.keys()) == set(holder2.keys())
-    for i in holder1.keys():
+    for i in list(holder1.keys()):
         j = holder1[i]
         k = holder2[i]
         assert j.leaf2 == k.leaf2
@@ -416,13 +416,13 @@ def njI(distancePairs, leafNo):
 
 def checkMatrix(m, fV, AS=4, reversible=True):
     #print m
-    for i in xrange(0, AS):
+    for i in range(0, AS):
         j = sum(m[i])
         #print "AAAAA", j
         assert j <= 1.0001
         assert j >= 0.9999
         if reversible:
-            for k in xrange(0, AS):
+            for k in range(0, AS):
                 #print "comp2", (fV[i] * m[i][k]), (fV[k] * m[k][i] )
                 assert close(fV[i] * m[i][k], fV[k] * m[k][i], 0.00001)
     
@@ -436,9 +436,9 @@ def checkMatrix(m, fV, AS=4, reversible=True):
     assert close(i, j, 0.00001)
     
 def reverseSubMatrix(m, AS=4):
-    k = [ [None]*AS for i in xrange(0, AS) ]
-    for i in xrange(0, AS):
-        for j in xrange(0, AS):
+    k = [ [None]*AS for i in range(0, AS) ]
+    for i in range(0, AS):
+        for j in range(0, AS):
             k[j][i] = m[i][j]
     return k
     
@@ -476,7 +476,7 @@ def subMatrix_TamuraNei(d, fA, fC, fG, fT, alphaPur, alphaPyr, beta):
     AS = 4
     freq = ( fA, fC, fG, fT )
     alpha = ( alphaPur, alphaPyr, alphaPur, alphaPyr )
-    matrix = [ [ 0.0 ]*AS for i in xrange(0, AS) ]
+    matrix = [ [ 0.0 ]*AS for i in range(0, AS) ]
     #see page 203 of Felsenstein's Inferring Phylogenies for explanation of calculations
     def watKro(j, k):
         if (j % 2) == (k % 2):
@@ -486,10 +486,10 @@ def subMatrix_TamuraNei(d, fA, fC, fG, fT, alphaPur, alphaPyr, beta):
         if i == j:
             return 1.0
         return 0.0
-    for i in xrange(0, AS): #long winded, totally unoptimised method for calculating matrix
-        for j in xrange(0, AS):
+    for i in range(0, AS): #long winded, totally unoptimised method for calculating matrix
+        for j in range(0, AS):
             l = 0.0
-            for k in xrange(0, AS):
+            for k in range(0, AS):
                 l += watKro(j, k) * freq[k]
             matrix[i][j] =\
             math.exp(-(alpha[i] + beta) * d) * kroenickerDelta(i, j) + \
@@ -516,9 +516,9 @@ def subMatrix_HKY(d, fA, fC, fG, fT, transitionTransversionR):
 def subMatrix_HalpernBruno(d, freqColumn, subMatrix, AS=4):
     #return subMatrix_HKY(d, freqColumn[0], freqColumn[1], freqColumn[2], freqColumn[3], 2.0)
     #return subMatrix
-    matrix = [ [ 0.0 ]*AS for i in xrange(0, AS) ]
-    for i in xrange(0, AS):
-        for j in xrange(0, AS):
+    matrix = [ [ 0.0 ]*AS for i in range(0, AS) ]
+    for i in range(0, AS):
+        for j in range(0, AS):
             a = freqColumn[i] * subMatrix[i][j]
             b = freqColumn[j] * subMatrix[j][i]
             if not close(a, b, 0.0001):
@@ -580,8 +580,8 @@ def mapTraversalIDsBetweenTrees(oldTree, newTree):
             internalMap[(fn(oldTree), fn(oldTree.left))] = fn(oldTree.right)
             internalMap[(fn(oldTree.left), fn(oldTree))] = fn(oldTree.right)
     fn3(oldTree)
-    print leafMap
-    print internalMap
+    print(leafMap)
+    print(internalMap)
     def fn4(newTree):
         if newTree.internal:
             fn4(newTree.left)
@@ -596,7 +596,7 @@ def remodelTreeRemovingRoot(root, node):
     """
     Node is mid order number
     """
-    import bioio
+    from . import bioio
     assert root.traversalID.mid != node
     hash = {}
     def fn(bT):
@@ -632,7 +632,7 @@ def moveRoot(root, branch):
     """
     Removes the old root and places the new root at the mid point along the given branch
     """
-    import bioio
+    from . import bioio
     if root.traversalID.mid == branch:
         return bioio.newickTreeParser(bioio.printBinaryTree(root, True))
     def fn2(tree, seq):
@@ -703,7 +703,7 @@ def calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID):
             if nodes.issubset(a[speciesTree.right.traversalID.mid]):
                 return fn2(nodes, speciesTree.right)
         return speciesTree.traversalID.mid
-    for iD in b.keys():
+    for iD in list(b.keys()):
         nodes = b[iD]
         b[iD] = fn2(nodes, speciesTree)
     dups = []
@@ -725,7 +725,7 @@ def calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID):
                 nodes.append((node, losses+1))
         return nodes
     for node, losses in fn4(speciesTree):
-        lossMap[(sys.maxint, node)] = losses+1
+        lossMap[(sys.maxsize, node)] = losses+1
     losses = [0]
     def fn5(geneTree, ancestor):
         if geneTree.internal:
@@ -745,7 +745,7 @@ def calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID):
         if speciesTree.internal:
             fn6(speciesTree.left, speciesTree.traversalID.mid, node)
             fn6(speciesTree.right, speciesTree.traversalID.mid, node)
-    ancestor = fn6(speciesTree, sys.maxint, b[geneTree.traversalID.mid])
+    ancestor = fn6(speciesTree, sys.maxsize, b[geneTree.traversalID.mid])
     assert ancestorHolder[0] is not None
     fn5(geneTree, ancestorHolder[0])
     return len(dups), losses[0]
diff --git a/deps/sonLib/treeTest.py b/deps/sonLib/treeTest.py
index e7c6c9a..7301b25 100644
--- a/deps/sonLib/treeTest.py
+++ b/deps/sonLib/treeTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
@@ -7,16 +7,16 @@
 import unittest
 import random
 
-from tree import remodelTreeRemovingRoot
-from tree import binaryTree_depthFirstNumbers
-from tree import mapTraversalIDsBetweenTrees
-from tree import BinaryTree
-from bioio import printBinaryTree
-from bioio import newickTreeParser
-from misc import close
-from tree import moveRoot
-from tree import calculateDupsAndLossesByReconcilingTrees
-from tree import calculateProbableRootOfGeneTree
+from .tree import remodelTreeRemovingRoot
+from .tree import binaryTree_depthFirstNumbers
+from .tree import mapTraversalIDsBetweenTrees
+from .tree import BinaryTree
+from .bioio import printBinaryTree
+from .bioio import newickTreeParser
+from .misc import close
+from .tree import moveRoot
+from .tree import calculateDupsAndLossesByReconcilingTrees
+from .tree import calculateProbableRootOfGeneTree
 from sonLib.bioio import TestStatus
 
 class TestCase(unittest.TestCase):
@@ -29,29 +29,29 @@ class TestCase(unittest.TestCase):
         unittest.TestCase.tearDown(self)
         
     def testRemodelTreeRemovingRoot(self):
-        for test in xrange(0, self.testNo):
+        for test in range(0, self.testNo):
             binaryTree = getRandomTree()
             binaryTree_depthFirstNumbers(binaryTree) 
             node = getRandomLeafNode(binaryTree)
             remodTree = remodelTreeRemovingRoot(binaryTree, node.traversalID.mid)
-            print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)
+            print("test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True))
             binaryTree_depthFirstNumbers(remodTree)
             distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
             d = getDistancesBetweenLeaves(binaryTree)
             d2 = getDistancesBetweenLeaves(remodTree)
-            print d
-            print d2
+            print(d)
+            print(d2)
             for key in d2:
                 assert close(d2[key], d[key], 0.0001)
                 
     def testMoveRoot(self):
-        for test in xrange(0, self.testNo):
+        for test in range(0, self.testNo):
             binaryTree = getRandomTree()
             binaryTree_depthFirstNumbers(binaryTree)
             node = getRandomNode(binaryTree)
-            print "before", printBinaryTree(binaryTree, True), printBinaryTree(node, True)
+            print("before", printBinaryTree(binaryTree, True), printBinaryTree(node, True))
             remodTree = moveRoot(binaryTree, node.traversalID.mid)
-            print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)
+            print("test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True))
             binaryTree_depthFirstNumbers(remodTree)
             #distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)
             #d = getDistancesBetweenLeaves(binaryTree)
@@ -62,7 +62,7 @@ class TestCase(unittest.TestCase):
             #    assert close(d2[key], d[key], 0.0001)
     
     def testCalculateDupsAndLossesByReconcilingTrees(self):
-        for test in xrange(0, self.testNo):
+        for test in range(0, self.testNo):
             speciesTree = getRandomTree()
             binaryTree_depthFirstNumbers(speciesTree)
             geneTree = getRandomTree()
@@ -102,13 +102,13 @@ class TestCase(unittest.TestCase):
         geneStrings = [ geneString1, geneString2, geneString3, geneString4, \
                         geneString5, geneString6, geneString7, geneString8,
                         geneString9, geneString10, geneString11 ]
-        print ""
+        print("")
         for geneString, dupCount, lossCount in geneStrings:
             geneTree = newickTreeParser(geneString)
             binaryTree_depthFirstNumbers(geneTree)
-            print printBinaryTree(geneTree, True), printBinaryTree(speciesTree, True)
+            print(printBinaryTree(geneTree, True), printBinaryTree(speciesTree, True))
             dupCount2, lossCount2 = calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID=lambda x : x)
-            print geneString, "dups", dupCount, dupCount2, "losses", lossCount, lossCount2
+            print(geneString, "dups", dupCount, dupCount2, "losses", lossCount, lossCount2)
             assert dupCount == dupCount2
             assert lossCount == lossCount2
             
@@ -144,11 +144,11 @@ class TestCase(unittest.TestCase):
             rootedGeneTree = newickTreeParser(geneString)
             binaryTree_depthFirstNumbers(geneTree)
             rootedGeneTree2, dupCount, lossCount = calculateProbableRootOfGeneTree(speciesTree, geneTree)
-            print "rootedGeneTree", rootedGeneString, dupCount, lossCount, printBinaryTree(rootedGeneTree2, False)
+            print("rootedGeneTree", rootedGeneString, dupCount, lossCount, printBinaryTree(rootedGeneTree2, False))
             #assert printBinaryTree(rootedGeneTree, False) == printBinaryTree(rootedGeneTree2, False)
     
     def testCalculateProbableRootOfGeneTree(self):
-        for test in xrange(0, self.testNo):
+        for test in range(0, self.testNo):
             speciesTree = getRandomTree()
             binaryTree_depthFirstNumbers(speciesTree)
             geneTree = getRandomTree()
diff --git a/deps/sonLib/unitTest.py b/deps/sonLib/unitTest.py
index b561105..11c99ee 100644
--- a/deps/sonLib/unitTest.py
+++ b/deps/sonLib/unitTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)
 #
diff --git a/deps/xg/deps/gfakluge/scripts/fa_to_gfa.py b/deps/xg/deps/gfakluge/scripts/fa_to_gfa.py
index e94c672..6f0e521 100644
--- a/deps/xg/deps/gfakluge/scripts/fa_to_gfa.py
+++ b/deps/xg/deps/gfakluge/scripts/fa_to_gfa.py
@@ -3,10 +3,10 @@ import sys
 if __name__ == "__main__":
 
     id_ctr = 0
-    print "\t".join(["H", "VZ:i:2.0"])
+    print("\t".join(["H", "VZ:i:2.0"]))
     with open(sys.argv[1],"r") as ifi:
         for line in ifi:
             if not line.startswith(">"):
                 id_ctr += 1
-                print "\t".join(["S", str(id_ctr), str(len(line.strip())), line.strip(), ""])
+                print("\t".join(["S", str(id_ctr), str(len(line.strip())), line.strip(), ""]))
 
diff --git a/deps/xg/deps/gfakluge/scripts/gfa_to_cytoscape.py b/deps/xg/deps/gfakluge/scripts/gfa_to_cytoscape.py
index 9d5d2eb..858f41c 100644
--- a/deps/xg/deps/gfakluge/scripts/gfa_to_cytoscape.py
+++ b/deps/xg/deps/gfakluge/scripts/gfa_to_cytoscape.py
@@ -15,7 +15,7 @@ if __name__ == "__main__":
                 name_to_seq[tokens[1]] = tokens[3]
             elif line.startswith("E"):
                 tokens = line.split("\t")
-                print tokens[2][0:-1], tokens[3][0:-1]
+                print(tokens[2][0:-1], tokens[3][0:-1])
 
     with open(node_file_name, "w") as ofi:
         for i in name_to_seq: