[med-svn] [python-pbcore] 01/07: Provide python3 package
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Jun 28 19:12:06 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit 10e0d945ecf58734d7dd45d64489bc52af58be1a
Author: عفيف الغراوي <afif at ghraoui.name>
Date: Sun Jun 28 11:19:28 2015 -0700
Provide python3 package
This patch
- Adds code to modernize the source
- Splits the package further into -doc and -data packages
that are Python-version-independent.
---
debian/control | 61 +-
debian/patches/doc-theme.patch | 4 +-
debian/patches/modernize-python.patch | 1780 ++++++++++++++++++++++++
debian/patches/remove-convenience-script.patch | 2 +-
debian/patches/series | 1 +
debian/rules | 7 +-
6 files changed, 1845 insertions(+), 10 deletions(-)
diff --git a/debian/control b/debian/control
index f7f9e34..a3b8cf0 100644
--- a/debian/control
+++ b/debian/control
@@ -5,10 +5,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Afif Elghraoui <afif at ghraoui.name>
Build-Depends: debhelper (>= 9),
dh-python,
- python,
+ python-all,
python-setuptools,
+ python3-all,
+ python3-setuptools,
python-sphinx
Standards-Version: 3.9.6
+X-Python-Version: >= 2.7
+X-Python3-Version: >= 3.2
Homepage: https://github.com/PacificBiosciences/pbcore
Vcs-Git: git://anonscm.debian.org/debian-med/python-pbcore.git
Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
@@ -17,13 +21,60 @@ Package: python-pbcore
Architecture: all
Depends: ${misc:Depends},
${python:Depends},
- libjs-jquery,
- libjs-underscore
-Description: Python library for processing PacBio data files
+ python-six
+Suggests: python-pbcore-doc
+Description: Python library for processing PacBio data files (Python 2)
The pbcore package provides Python modules for processing Pacific Biosciences
data files and building PacBio bioinformatics applications. These modules
include tools to read/write PacBio data formats, sample data files for
testing and debugging, base classes, and utilities for building bioinformatics
applications.
.
- This package is part of the SMRTAnalysis suite.
+ This package is part of the SMRTAnalysis suite. It provides the Python2
+ module
+
+Package: python3-pbcore
+Architecture: all
+Depends: ${misc:Depends},
+ ${python3:Depends},
+ python3-six
+Suggests: python-pbcore-doc
+Description: Python library for processing PacBio data files (Python 3)
+ The pbcore package provides Python modules for processing Pacific Biosciences
+ data files and building PacBio bioinformatics applications. These modules
+ include tools to read/write PacBio data formats, sample data files for
+ testing and debugging, base classes, and utilities for building bioinformatics
+ applications.
+ .
+ This package is part of the SMRTAnalysis suite. It provides the Python3
+ module.
+
+Package: python-pbcore-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: Python library for processing PacBio data files (data)
+ The pbcore package provides Python modules for processing Pacific Biosciences
+ data files and building PacBio bioinformatics applications. These modules
+ include tools to read/write PacBio data formats, sample data files for
+ testing and debugging, base classes, and utilities for building bioinformatics
+ applications.
+ .
+ pbcore is part of the SMRTAnalysis suite. This package provides sample
+ data files.
+
+Package: python-pbcore-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+ ${sphinxdoc:Depends},
+# libjs-jquery,
+# libjs-underscore
+Description: Python library for processing PacBio data files (documentation)
+ The pbcore package provides Python modules for processing Pacific Biosciences
+ data files and building PacBio bioinformatics applications. These modules
+ include tools to read/write PacBio data formats, sample data files for
+ testing and debugging, base classes, and utilities for building bioinformatics
+ applications.
+ .
+ pbcore is part of the SMRTAnalysis suite. This package provides the common
+ documentation package.
diff --git a/debian/patches/doc-theme.patch b/debian/patches/doc-theme.patch
index 32e597f..a733994 100644
--- a/debian/patches/doc-theme.patch
+++ b/debian/patches/doc-theme.patch
@@ -9,7 +9,7 @@ Last-Update: 2015-06-21
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-pbcore.orig/doc/conf.py
+++ python-pbcore/doc/conf.py
-@@ -98,7 +98,7 @@
+@@ -99,7 +99,7 @@
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
@@ -18,7 +18,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
-@@ -107,7 +107,6 @@
+@@ -108,7 +108,6 @@
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
diff --git a/debian/patches/modernize-python.patch b/debian/patches/modernize-python.patch
new file mode 100644
index 0000000..f1400a5
--- /dev/null
+++ b/debian/patches/modernize-python.patch
@@ -0,0 +1,1780 @@
+Description: Modernize Python code
+ These patches were mostly generated by running
+ python-modernize on the source tree. setup.py was then
+ slightly modified by hand.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-06-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pbcore.orig/doc/conf.py
++++ python-pbcore/doc/conf.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ # -*- coding: utf-8 -*-
+ #
+ # pbcore documentation build configuration file, created by
+@@ -13,7 +14,7 @@
+
+ import sys, os
+ globals = {}
+-execfile("../pbcore/__init__.py", globals)
++exec(compile(open("../pbcore/__init__.py").read(), "../pbcore/__init__.py", 'exec'), globals)
+ __VERSION__ = globals["__VERSION__"]
+
+
+--- python-pbcore.orig/pbcore/chemistry/chemistry.py
++++ python-pbcore/pbcore/chemistry/chemistry.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -54,7 +55,7 @@
+ mappings[(bindingKit, sequencingKit, softwareVersion)] = sequencingChemistry
+ return mappings
+ except:
+- raise ChemistryLookupError, "Error loading chemistry mapping xml"
++ raise ChemistryLookupError("Error loading chemistry mapping xml")
+
+ def _loadBarcodeMappings():
+ mappingFname = resource_filename(Requirement.parse('pbcore'),'pbcore/chemistry/resources/mapping.xml')
+@@ -80,8 +81,7 @@
+ instrumentControlVersion = ".".join(verComponents)
+ return (bindingKit, sequencingKit, instrumentControlVersion)
+ except Exception as e:
+- raise ChemistryLookupError, \
+- ("Could not find, or extract chemistry information from, %s" % (metadataXmlPath,))
++ raise ChemistryLookupError("Could not find, or extract chemistry information from, %s" % (metadataXmlPath,))
+
+ def decodeTriple(bindingKit, sequencingKit, softwareVersion):
+ """
+--- python-pbcore.orig/pbcore/data/__init__.py
++++ python-pbcore/pbcore/data/__init__.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -29,6 +30,8 @@
+ #################################################################################
+
+ from pkg_resources import Requirement, resource_filename
++from six.moves import map
++from six.moves import range
+
+ DATA_FILES = {'aligned_reads_1.cmp.h5':
+ ['m110818_075520_42141_c100129202555500000315043109121112_s1_p0.bas.h5',
+@@ -79,8 +82,8 @@
+ cmp.h5 file.
+ '''
+ return [{'cmph5' : _getAbsPath(cmph5),
+- 'bash5s': map(_getAbsPath, bash5s)}
+- for cmph5, bash5s in DATA_FILES.items()]
++ 'bash5s': list(map(_getAbsPath, bash5s))}
++ for cmph5, bash5s in list(DATA_FILES.items())]
+
+ def getCmpH5AndBas():
+ '''
+@@ -137,11 +140,11 @@
+ """
+ Returns a list of FOFN files
+ """
+- return map(_getAbsPath,
++ return list(map(_getAbsPath,
+ ["1.4_bas_files.fofn",
+ "2.0_bax_files.fofn",
+ "2.1_bax_files.fofn",
+- "2.1_ccs_files.fofn"])
++ "2.1_ccs_files.fofn"]))
+
+ def getBcFofn():
+ return _getAbsPath("bc_files.fofn")
+--- python-pbcore.orig/pbcore/io/BarcodeH5Reader.py
++++ python-pbcore/pbcore/io/BarcodeH5Reader.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################$$
+ # Copyright (c) 2011,2012, Pacific Biosciences of California, Inc.
+ #
+@@ -31,6 +32,9 @@
+ import numpy as n
+
+ from pbcore.io.FofnIO import readFofn
++import six
++from six.moves import range
++from functools import reduce
+
+ BARCODE_DELIMITER = "--"
+ BC_DS_PATH = "BarcodeCalls/best"
+@@ -99,7 +103,7 @@
+ """Write a barcode file from a list of labeled ZMWs. In addition
+ to labeledZmws, this function takes a
+ pbbarcode.BarcodeLabeler."""
+- bestScores = map(lambda z: z.toBestRecord(), labeledZmws)
++ bestScores = [z.toBestRecord() for z in labeledZmws]
+ outDta = n.vstack(bestScores)
+ outH5 = h5.File(outFile, 'a')
+
+@@ -127,9 +131,9 @@
+ def makeRecord(lZmw):
+ zmws = makeArray(nBarcodes * lZmw.nScored, lZmw.holeNumber)
+ adapters = n.concatenate([makeArray(nBarcodes, i) for i in \
+- xrange(1, lZmw.nScored + 1)])
+- idxs = n.concatenate([range(0, nBarcodes) for i in \
+- xrange(0, lZmw.nScored)])
++ range(1, lZmw.nScored + 1)])
++ idxs = n.concatenate([list(range(0, nBarcodes)) for i in \
++ range(0, lZmw.nScored)])
+ scores = n.concatenate(lZmw.allScores)
+ return n.transpose(n.vstack((zmws, adapters, idxs, scores)))
+
+@@ -163,12 +167,12 @@
+ self._movieName = self.bestDS.attrs['movieName']
+ # zmw => LabeledZmw
+ labeledZmws = [LabeledZmw.fromBestRecord(self.bestDS[i,:]) for i in
+- xrange(0, self.bestDS.shape[0])]
++ range(0, self.bestDS.shape[0])]
+ self.labeledZmws = dict([(lZmw.holeNumber, lZmw) for lZmw in labeledZmws])
+
+ # barcode => LabeledZmws
+ self.bcLabelToLabeledZmws = {l:[] for l in self.barcodeLabels}
+- for lZmw in self.labeledZmws.values():
++ for lZmw in list(self.labeledZmws.values()):
+ d = self.bcLabelToLabeledZmws[self.barcodeLabels[lZmw.bestIdx]]
+ d.append(lZmw)
+
+@@ -211,7 +215,7 @@
+ return (n.min(x), n.max(x))
+ # these aren't the ranges of ZMWs, but the ranges for the
+ # scored ZMWs.
+- self._bins = map(lambda z : rng(z.holeNumbers), self._parts)
++ self._bins = [rng(z.holeNumbers) for z in self._parts]
+
+ def choosePart(self, holeNumber):
+ for i,b in enumerate(self._bins):
+@@ -239,8 +243,7 @@
+
+ def labeledZmwsFromBarcodeLabel(self, bcLabel):
+ lzmws = reduce(lambda x,y: x + y,
+- map(lambda z: z.labeledZmwsFromBarcodeLabel(bcLabel),
+- self._parts))
++ [z.labeledZmwsFromBarcodeLabel(bcLabel) for z in self._parts])
+ return sorted(lzmws, key=lambda z: z.holeNumber)
+
+ def __iter__(self):
+@@ -256,7 +259,7 @@
+ return self.labeledZmwsFromBarcodeLabel(item)
+ elif isinstance(item, slice):
+ return [ self.labeledZmwFromHoleNumber(self, item)
+- for r in xrange(*item.indices(len(self)))]
++ for r in range(*item.indices(len(self)))]
+ elif isinstance(item, list) or isinstance(item, n.ndarray):
+ if len(item) == 0:
+ return []
+@@ -266,7 +269,7 @@
+ return [ self.labeledZmwFromHoleNumber(r) for r in item ]
+ elif entryType == bool or issubclass(entryType, n.bool_):
+ return [ self.labeledZmwFromHoleNumber(r) for r in n.flatnonzero(item) ]
+- raise TypeError, "Invalid type for BasH5Reader slicing"
++ raise TypeError("Invalid type for BasH5Reader slicing")
+
+
+ class BarcodeH5Fofn(object):
+@@ -290,7 +293,7 @@
+ self._byMovie[bc.movieName].append(bc)
+
+ self.mpReaders = { movieName: parts[0] if len(parts) == 1 else MPBarcodeH5Reader(parts)
+- for movieName, parts in self._byMovie.iteritems() }
++ for movieName, parts in six.iteritems(self._byMovie) }
+
+ @property
+ def holeNumbers(self):
+@@ -298,7 +301,7 @@
+ for hn in reader.holeNumbers])
+ @property
+ def movieNames(self):
+- return self.mpReaders.keys()
++ return list(self.mpReaders.keys())
+ @property
+ def barcodeLabels(self):
+ return self._bcH5s[0].barcodeLabels
+@@ -309,8 +312,7 @@
+
+ def labeledZmwsFromBarcodeLabel(self, item):
+ lzmws = reduce(lambda x,y: x + y,
+- map(lambda z: z.labeledZmwsFromBarcodeLabel(item),
+- self._bcH5s))
++ [z.labeledZmwsFromBarcodeLabel(item) for z in self._bcH5s])
+ return sorted(lzmws, key=lambda z: z.holeNumber )
+
+ def labeledZmwFromName(self, item):
+--- python-pbcore.orig/pbcore/io/BasH5IO.py
++++ python-pbcore/pbcore/io/BasH5IO.py
+@@ -1,3 +1,8 @@
++from __future__ import absolute_import
++import six
++from six.moves import map
++from six.moves import range
++from six.moves import zip
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -58,7 +63,7 @@
+ return e - b
+
+ def removeNones(lst):
+- return filter(lambda x: x!=None, lst)
++ return [x for x in lst if x!=None]
+
+ # ZMW hole Types
+ SEQUENCING_ZMW = 0
+@@ -215,7 +220,7 @@
+ insert, used to forming the CCS consensus.
+ """
+ if not self.baxH5.hasConsensusBasecalls:
+- raise ValueError, "No CCS reads in this file"
++ raise ValueError("No CCS reads in this file")
+ return self.baxH5._ccsNumPasses[self.index]
+
+ #
+@@ -228,7 +233,7 @@
+ specified extent of the polymerase read.
+ """
+ if not self.baxH5.hasRawBasecalls:
+- raise ValueError, "No raw reads in this file"
++ raise ValueError("No raw reads in this file")
+ hqStart, hqEnd = self.hqRegion
+ readStart = hqStart if readStart is None else readStart
+ readEnd = hqEnd if readEnd is None else readEnd
+@@ -248,7 +253,7 @@
+ HQ region.
+ """
+ if not self.baxH5.hasRawBasecalls:
+- raise ValueError, "No raw reads in this file"
++ raise ValueError("No raw reads in this file")
+ offsets = self.baxH5._offsetsByHole[self.holeNumber]
+ numEvent = offsets[1] - offsets[0]
+ polymeraseBegin = 0
+@@ -269,7 +274,7 @@
+ HQ region.
+ """
+ if not self.baxH5.hasRawBasecalls:
+- raise ValueError, "No raw reads in this file"
++ raise ValueError("No raw reads in this file")
+ return [ self.read(readStart, readEnd)
+ for (readStart, readEnd) in self.unclippedInsertRegions ]
+
+@@ -281,7 +286,7 @@
+ production code.
+ """
+ if not self.baxH5.hasRawBasecalls:
+- raise ValueError, "No raw reads in this file"
++ raise ValueError("No raw reads in this file")
+ return [ self.read(readStart, readEnd)
+ for (readStart, readEnd) in self.insertRegions ]
+
+@@ -294,7 +299,7 @@
+ by production code.
+ """
+ if not self.baxH5.hasRawBasecalls:
+- raise ValueError, "No raw reads in this file"
++ raise ValueError("No raw reads in this file")
+ return [ self.read(readStart, readEnd)
+ for (readStart, readEnd) in self.adapterRegions ]
+
+@@ -311,14 +316,14 @@
+ HQ region.
+ """
+ if not self.baxH5.hasRawBasecalls:
+- raise ValueError, "No raw reads in this file"
++ raise ValueError("No raw reads in this file")
+ return [ self.read(readStart, readEnd)
+ for (readStart, readEnd) in self.unclippedAdapterRegions ]
+
+ @property
+ def ccsRead(self):
+ if not self.baxH5.hasConsensusBasecalls:
+- raise ValueError, "No CCS reads in this file"
++ raise ValueError("No CCS reads in this file")
+ baseOffset = self.baxH5._ccsOffsetsByHole[self.holeNumber]
+ if (baseOffset[1] - baseOffset[0]) <= 0:
+ return None
+@@ -356,7 +361,7 @@
+ self.offsetBegin <=
+ self.offsetEnd <=
+ zmwOffsetEnd):
+- raise IndexError, "Invalid slice of Zmw!"
++ raise IndexError("Invalid slice of Zmw!")
+
+ def _getBasecallsGroup(self):
+ return self.baxH5._basecallsGroup
+@@ -424,18 +429,18 @@
+ holeNumber = h5Group["ZMW/HoleNumber"].value
+ endOffset = np.cumsum(numEvent)
+ beginOffset = np.hstack(([0], endOffset[0:-1]))
+- offsets = zip(beginOffset, endOffset)
+- return dict(zip(holeNumber, offsets))
++ offsets = list(zip(beginOffset, endOffset))
++ return dict(list(zip(holeNumber, offsets)))
+
+ def _makeRegionTableIndex(regionTableHoleNumbers):
+ # returns a dict: holeNumber -> (startRow, endRow)
+ diffs = np.ediff1d(regionTableHoleNumbers,
+ to_begin=[1], to_end=[1])
+ changepoints = np.flatnonzero(diffs)
+- startsAndEnds = zip(changepoints[:-1],
+- changepoints[1:])
+- return dict(zip(np.unique(regionTableHoleNumbers),
+- startsAndEnds))
++ startsAndEnds = list(zip(changepoints[:-1],
++ changepoints[1:]))
++ return dict(list(zip(np.unique(regionTableHoleNumbers),
++ startsAndEnds)))
+
+ class BaxH5Reader(object):
+ """
+@@ -447,7 +452,7 @@
+ self.filename = op.abspath(op.expanduser(filename))
+ self.file = h5py.File(self.filename, "r")
+ except IOError:
+- raise IOError, ("Invalid or nonexistent bax/bas file %s" % filename)
++ raise IOError("Invalid or nonexistent bax/bas file %s" % filename)
+
+ #
+ # Raw base calls?
+@@ -493,7 +498,7 @@
+ it to the ZMW data.
+ """
+ holeNumbers = self._mainBasecallsGroup["ZMW/HoleNumber"].value
+- self._holeNumberToIndex = dict(zip(holeNumbers, range(len(holeNumbers))))
++ self._holeNumberToIndex = dict(list(zip(holeNumbers, list(range(len(holeNumbers))))))
+
+ #
+ # Region table
+@@ -544,7 +549,7 @@
+ try:
+ fh = h5py.File(op.abspath(op.expanduser(regionH5Filename)), "r")
+ except IOError:
+- raise IOError, ("Invalid or nonexistent file %s" % regionH5Filename)
++ raise IOError("Invalid or nonexistent file %s" % regionH5Filename)
+
+ self._loadRegions(fh)
+ fh.close()
+@@ -556,7 +561,7 @@
+ if not np.in1d(rgnHoleNumbers, baxHoleNumbers).all():
+ msg = "Region file (%s) does not contain the same hole numbers as " \
+ "bas/bax file (%s)"
+- raise IOError, (msg % (regionH5Filename, self.filename))
++ raise IOError(msg % (regionH5Filename, self.filename))
+
+ @property
+ def sequencingZmws(self):
+@@ -619,7 +624,7 @@
+ else:
+ movieNameString = movieNameAttr
+
+- if not isinstance(movieNameString, basestring):
++ if not isinstance(movieNameString, six.string_types):
+ raise TypeError("Unsupported movieName {m} of type {t}."
+ .format(m=movieNameString,
+ t=type(movieNameString)))
+@@ -661,7 +666,7 @@
+ if triple:
+ return triple
+ else:
+- raise ChemistryLookupError, "Could not find chemistry barcodes in file or companion metadata.xml"
++ raise ChemistryLookupError("Could not find chemistry barcodes in file or companion metadata.xml")
+
+ @property
+ def sequencingChemistry(self):
+@@ -682,7 +687,7 @@
+ if tripleFromXML is not None:
+ self._sequencingChemistry = decodeTriple(*tripleFromXML)
+ else:
+- raise ChemistryLookupError, "Chemistry information could not be found for this file"
++ raise ChemistryLookupError("Chemistry information could not be found for this file")
+ return self._sequencingChemistry
+
+ def __len__(self):
+@@ -700,7 +705,7 @@
+ self.close()
+
+ def listZmwMetrics(self):
+- return self._basecallsGroup["ZMWMetrics"].keys()
++ return list(self._basecallsGroup["ZMWMetrics"].keys())
+
+ def zmwMetric(self, name, index):
+ # we are going to cache these lazily because it is very likely
+@@ -795,7 +800,7 @@
+ self.filename = op.abspath(op.expanduser(filename))
+ self.file = h5py.File(self.filename, "r")
+ except IOError:
+- raise IOError, ("Invalid or nonexistent bas/bax file %s" % filename)
++ raise IOError("Invalid or nonexistent bas/bax file %s" % filename)
+
+
+ # Is this a multi-part or single-part?
+@@ -814,7 +819,7 @@
+ self.file = None
+ self._parts = [ BaxH5Reader(fn) for fn in partFilenames ]
+ holeLookupDict = { hn : (i + 1)
+- for i in xrange(len(self._parts))
++ for i in range(len(self._parts))
+ for hn in self._parts[i]._holeNumberToIndex }
+ self._holeLookup = lambda hn: holeLookupDict[hn]
+ self._sequencingZmws = np.concatenate([ part.sequencingZmws
+@@ -883,7 +888,7 @@
+ return self._getitemScalar(holeNumbers)
+ elif isinstance(holeNumbers, slice):
+ return [ self._getitemScalar(r)
+- for r in xrange(*holeNumbers.indices(len(self)))]
++ for r in range(*holeNumbers.indices(len(self)))]
+ elif isinstance(holeNumbers, list) or isinstance(holeNumbers, np.ndarray):
+ if len(holeNumbers) == 0:
+ return []
+@@ -893,7 +898,7 @@
+ return [ self._getitemScalar(r) for r in holeNumbers ]
+ elif entryType == bool or issubclass(entryType, np.bool_):
+ return [ self._getitemScalar(r) for r in np.flatnonzero(holeNumbers) ]
+- raise TypeError, "Invalid type for BasH5Reader slicing"
++ raise TypeError("Invalid type for BasH5Reader slicing")
+
+ @property
+ def movieName(self):
+@@ -964,7 +969,7 @@
+ else:
+ basFilenames.append(arg)
+
+- movieNames = map(sniffMovieName, basFilenames)
++ movieNames = list(map(sniffMovieName, basFilenames))
+ movieNamesAndFiles = sorted(zip(movieNames, basFilenames))
+
+ self.readers = OrderedDict(
+@@ -973,7 +978,7 @@
+
+ @property
+ def movieNames(self):
+- return self.readers.keys()
++ return list(self.readers.keys())
+
+ def __getitem__(self, key):
+ """
+@@ -998,7 +1003,7 @@
+ if indices[2] == "ccs":
+ result = result.ccsRead
+ else:
+- start, end = map(int, indices[2].split("_"))
++ start, end = list(map(int, indices[2].split("_")))
+ result = result.read(start, end)
+ return result
+
+@@ -1007,20 +1012,20 @@
+ #
+
+ def __iter__(self):
+- for reader in self.readers.values():
++ for reader in list(self.readers.values()):
+ for zmw in reader: yield zmw
+
+ def reads(self):
+- for reader in self.readers.values():
++ for reader in list(self.readers.values()):
+ for read in reader.reads():
+ yield read
+
+ def subreads(self):
+- for reader in self.readers.values():
++ for reader in list(self.readers.values()):
+ for read in reader.subreads():
+ yield read
+
+ def ccsReads(self):
+- for reader in self.readers.values():
++ for reader in list(self.readers.values()):
+ for read in reader.ccsReads():
+ yield read
+--- python-pbcore.orig/pbcore/io/FastaIO.py
++++ python-pbcore/pbcore/io/FastaIO.py
+@@ -33,6 +33,9 @@
+ """
+ Streaming I/O support for FASTA files.
+ """
++from __future__ import absolute_import
++from six.moves import map
++from six.moves import range
+
+ __all__ = [ "FastaRecord",
+ "FastaReader",
+@@ -273,7 +276,7 @@
+ ##
+ def wrap(s, columns):
+ return "\n".join(s[start:start+columns]
+- for start in xrange(0, len(s), columns))
++ for start in range(0, len(s), columns))
+
+
+
+@@ -298,7 +301,7 @@
+ # only "id" makes it into the fai.
+ offsetEnd = 0
+ for line in open(faidxFilename):
+- length, offset, lineWidth, blen = map(int, line.split()[-4:])
++ length, offset, lineWidth, blen = list(map(int, line.split()[-4:]))
+ newlineWidth = blen - lineWidth # 2 for DOS, 1 for UNIX
+ header_ = fastaView[offsetEnd:offset]
+ assert (header_[0] == ">" and header_[-1] == "\n")
+@@ -333,7 +336,7 @@
+ if isinstance(spec, slice):
+ start, stop, stride = spec.indices(len(self))
+ if stride != 1:
+- raise ValueError, "Unsupported stride"
++ raise ValueError("Unsupported stride")
+ elif spec < 0:
+ start = self.faiRecord.length + spec
+ stop = start + 1
+@@ -343,7 +346,7 @@
+ stop = start + 1
+ stride = 1
+ if not (0 <= start <= stop <= self.faiRecord.length):
+- raise IndexError, "Out of bounds"
++ raise IndexError("Out of bounds")
+ startOffset = fileOffset(self.faiRecord, start)
+ endOffset = fileOffset(self.faiRecord, stop)
+ snip = self.view[startOffset:endOffset].translate(None, "\r\n")
+@@ -441,16 +444,16 @@
+ key = len(self) + key
+
+ if isinstance(key, slice):
+- indices = xrange(*key.indices(len(self)))
++ indices = range(*key.indices(len(self)))
+ return [ IndexedFastaRecord(self.view, self.contigLookup[i])
+ for i in indices ]
+ elif key in self.contigLookup:
+ return IndexedFastaRecord(self.view, self.contigLookup[key])
+ else:
+- raise IndexError, "Contig not in FastaTable"
++ raise IndexError("Contig not in FastaTable")
+
+ def __iter__(self):
+- return (self[i] for i in xrange(len(self)))
++ return (self[i] for i in range(len(self)))
+
+ def __len__(self):
+ return len(self.fai)
+--- python-pbcore.orig/pbcore/io/FastqIO.py
++++ python-pbcore/pbcore/io/FastqIO.py
+@@ -33,6 +33,8 @@
+ """
+ I/O support for FASTQ files
+ """
++from __future__ import absolute_import
++from six.moves import range
+
+ __all__ = [ "FastqRecord",
+ "FastqReader",
+@@ -205,7 +207,7 @@
+ One-shot iteration support
+ """
+ while True:
+- lines = [next(self.file) for i in xrange(4)]
++ lines = [next(self.file) for i in range(4)]
+ yield FastqRecord(lines[0][1:-1],
+ lines[1][:-1],
+ qualityString=lines[3][:-1])
+--- python-pbcore.orig/pbcore/io/FofnIO.py
++++ python-pbcore/pbcore/io/FofnIO.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -33,6 +34,7 @@
+ from pbcore.io.base import getFileHandle
+ from os.path import dirname, isabs, join, abspath, expanduser
+ import xml.etree.ElementTree as ET
++import six
+
+
+ __all__ = [ "readFofn",
+@@ -48,7 +50,7 @@
+ FOFN that are relative (i.e., do not contain a leading '/') will
+ be reckoned from the directory containing the FOFN.
+ """
+- if isinstance(f, basestring):
++ if isinstance(f, six.string_types):
+ fofnRoot = dirname(abspath(expanduser(f)))
+ else:
+ fofnRoot = None
+@@ -62,7 +64,7 @@
+ elif fofnRoot is not None:
+ yield join(fofnRoot, path)
+ else:
+- raise IOError, "Cannot handle relative paths in StringIO FOFN"
++ raise IOError("Cannot handle relative paths in StringIO FOFN")
+
+ def readInputXML(fname):
+ tree = ET.parse(fname)
+--- python-pbcore.orig/pbcore/io/GffIO.py
++++ python-pbcore/pbcore/io/GffIO.py
+@@ -36,6 +36,9 @@
+ The specification for the GFF format is available at
+ http://www.sequenceontology.org/gff3.shtml
+ """
++from __future__ import absolute_import
++import six
++from six.moves import map
+
+ __all__ = [ "Gff3Record",
+ "GffReader",
+@@ -105,7 +108,7 @@
+ columns = s.rstrip().rstrip(";").split("\t")
+ try:
+ assert len(columns) == len(cls._GFF_COLUMNS)
+- attributes = map(tupleFromGffAttribute, columns[-1].split(";"))
++ attributes = list(map(tupleFromGffAttribute, columns[-1].split(";")))
+ (_seqid, _source, _type, _start,
+ _end, _score, _strand, _phase) = columns[:-1]
+ return Gff3Record(_seqid, int(_start), int(_end), _type,
+@@ -124,7 +127,7 @@
+ def __str__(self):
+ formattedAttributes = ";".join(
+ ("%s=%s" % (k, self._formatField(v))
+- for (k, v) in self.attributes.iteritems()))
++ for (k, v) in six.iteritems(self.attributes)))
+ formattedFixedColumns = "\t".join(
+ self._formatField(getattr(self, k))
+ for k in self._GFF_COLUMNS[:-1])
+--- python-pbcore.orig/pbcore/io/_utils.py
++++ python-pbcore/pbcore/io/_utils.py
+@@ -29,8 +29,10 @@
+ #################################################################################
+
+ from __future__ import absolute_import
++from __future__ import print_function
+ import h5py, numpy as np
+ from cStringIO import StringIO
++import six
+
+
+ def arrayFromDataset(ds, offsetBegin, offsetEnd):
+@@ -75,7 +77,7 @@
+
+ def is_string_like(obj):
+ 'Return True if *obj* looks like a string'
+- if isinstance(obj, (str, unicode)): return True
++ if isinstance(obj, (str, six.text_type)): return True
+ # numpy strings are subclass of str, ma strings are not
+ if ma.isMaskedArray(obj):
+ if obj.ndim == 0 and obj.dtype.kind in 'SU':
+@@ -189,8 +191,8 @@
+ newrec[name] = 0
+
+ if jointype != 'inner' and defaults is not None: # fill in the defaults enmasse
+- newrec_fields = newrec.dtype.fields.keys()
+- for k, v in defaults.items():
++ newrec_fields = list(newrec.dtype.fields.keys())
++ for k, v in list(defaults.items()):
+ if k in newrec_fields:
+ newrec[k] = v
+
+@@ -234,7 +236,7 @@
+ """
+ Pretty-print a recarray
+ """
+- print "foo"
++ print("foo")
+
+
+ class CommonEqualityMixin(object):
+--- python-pbcore.orig/pbcore/io/align/BamAlignment.py
++++ python-pbcore/pbcore/io/align/BamAlignment.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -36,6 +37,7 @@
+ from pbcore.sequence import reverseComplement
+ from ._BamSupport import *
+ from ._AlignmentMixin import AlignmentRecordMixin
++from six.moves import range
+
+ __all__ = [ "BamAlignment" ]
+
+@@ -67,7 +69,7 @@
+ @wraps(method)
+ def f(bamAln, *args, **kwargs):
+ if not bamAln.bam.isReferenceLoaded:
+- raise UnavailableFeature, "this feature requires loaded reference sequence"
++ raise UnavailableFeature("this feature requires loaded reference sequence")
+ else:
+ return method(bamAln, *args, **kwargs)
+ return f
+@@ -76,7 +78,7 @@
+ @wraps(method)
+ def f(bamAln, *args, **kwargs):
+ if bamAln.rowNumber is None:
+- raise UnavailableFeature, "this feature requires a PacBio BAM index"
++ raise UnavailableFeature("this feature requires a PacBio BAM index")
+ else:
+ return method(bamAln, *args, **kwargs)
+ return f
+@@ -85,7 +87,7 @@
+ @wraps(method)
+ def f(bamAln, *args, **kwargs):
+ if bamAln.isUnmapped:
+- raise UnavailableFeature, "this feature requires a *mapped* BAM record"
++ raise UnavailableFeature("this feature requires a *mapped* BAM record")
+ else:
+ return method(bamAln, *args, **kwargs)
+ return f
+@@ -180,7 +182,7 @@
+ if (refStart >= refEnd or
+ refStart >= self.tEnd or
+ refEnd <= self.tStart):
+- raise IndexError, "Clipping query does not overlap alignment"
++ raise IndexError("Clipping query does not overlap alignment")
+
+ # The clipping region must intersect the alignment, though it
+ # does not have to be contained wholly within it.
+@@ -305,7 +307,7 @@
+ @requiresReference
+ def reference(self, aligned=True, orientation="native"):
+ if not (orientation == "native" or orientation == "genomic"):
+- raise ValueError, "Bad `orientation` value"
++ raise ValueError("Bad `orientation` value")
+ tSeq = self.bam.referenceFasta[self.referenceName].sequence[self.tStart:self.tEnd]
+ shouldRC = orientation == "native" and self.isReverseStrand
+ tSeqOriented = reverseComplement(tSeq) if shouldRC else tSeq
+@@ -401,10 +403,9 @@
+ oriented genomically in the file.
+ """
+ if not (orientation == "native" or orientation == "genomic"):
+- raise ValueError, "Bad `orientation` value"
++ raise ValueError("Bad `orientation` value")
+ if self.isUnmapped and (orientation != "native" or aligned == True):
+- raise UnavailableFeature, \
+- "Cannot get genome oriented/aligned features from unmapped BAM record"
++ raise UnavailableFeature("Cannot get genome oriented/aligned features from unmapped BAM record")
+ # 1. Extract in native orientation
+ tag, kind_, dtype_ = PULSE_FEATURE_TAGS[featureName]
+ data_ = self.peer.opt(tag)
+@@ -477,10 +478,9 @@
+
+ def read(self, aligned=True, orientation="native"):
+ if not (orientation == "native" or orientation == "genomic"):
+- raise ValueError, "Bad `orientation` value"
++ raise ValueError("Bad `orientation` value")
+ if self.isUnmapped and (orientation != "native" or aligned == True):
+- raise UnavailableFeature, \
+- "Cannot get genome oriented/aligned features from unmapped BAM record"
++ raise UnavailableFeature("Cannot get genome oriented/aligned features from unmapped BAM record")
+ data = np.fromstring(self.peer.seq, dtype=np.int8)
+ s = self.aStart - self.qStart
+ e = self.aEnd - self.qStart
+@@ -520,7 +520,7 @@
+ transcript = self.transcript(style="exonerate+")
+ refPos = self.referencePositions()
+ refPosString = "".join([str(pos % 10) for pos in refPos])
+- for i in xrange(0, len(alignedRef), COLUMNS):
++ for i in range(0, len(alignedRef), COLUMNS):
+ val += "\n"
+ val += " " + refPosString[i:i+COLUMNS] + "\n"
+ val += " " + alignedRef [i:i+COLUMNS] + "\n"
+@@ -540,7 +540,7 @@
+ if key in self.bam.pbi.columnNames:
+ return self.bam.pbi[self.rowNumber][key]
+ else:
+- raise AttributeError, "no such column in pbi index"
++ raise AttributeError("no such column in pbi index")
+
+ def __dir__(self):
+ if self.bam.pbi is not None:
+--- python-pbcore.orig/pbcore/io/align/BamIO.py
++++ python-pbcore/pbcore/io/align/BamIO.py
+@@ -1,3 +1,7 @@
++from __future__ import absolute_import
++from six.moves import map
++from six.moves import range
++from six.moves import zip
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -52,7 +56,7 @@
+ @wraps(method)
+ def f(bamReader, *args, **kwargs):
+ if not bamReader.peer._hasIndex():
+- raise UnavailableFeature, "this feature requires an standard BAM index file (bam.bai)"
++ raise UnavailableFeature("this feature requires an standard BAM index file (bam.bai)")
+ else:
+ return method(bamReader, *args, **kwargs)
+ return f
+@@ -71,11 +75,11 @@
+ refNames = [r["SN"] for r in refRecords]
+ refLengths = [r["LN"] for r in refRecords]
+ refMD5s = [r["M5"] for r in refRecords]
+- refIds = map(self.peer.gettid, refNames)
++ refIds = list(map(self.peer.gettid, refNames))
+ nRefs = len(refRecords)
+
+ if nRefs > 0:
+- self._referenceInfoTable = np.rec.fromrecords(zip(
++ self._referenceInfoTable = np.rec.fromrecords(list(zip(
+ refIds,
+ refIds,
+ refNames,
+@@ -83,14 +87,14 @@
+ refLengths,
+ refMD5s,
+ np.zeros(nRefs, dtype=np.uint32),
+- np.zeros(nRefs, dtype=np.uint32)),
++ np.zeros(nRefs, dtype=np.uint32))),
+ dtype=[('ID', '<i8'), ('RefInfoID', '<i8'),
+ ('Name', 'O'), ('FullName', 'O'),
+ ('Length', '<i8'), ('MD5', 'O'),
+ ('StartRow', '<u4'), ('EndRow', '<u4')])
+ self._referenceDict = {}
+- self._referenceDict.update(zip(refIds, self._referenceInfoTable))
+- self._referenceDict.update(zip(refNames, self._referenceInfoTable))
++ self._referenceDict.update(list(zip(refIds, self._referenceInfoTable)))
++ self._referenceDict.update(list(zip(refNames, self._referenceInfoTable)))
+ else:
+ self._referenceInfoTable = None
+ self._referenceDict = None
+@@ -98,7 +102,7 @@
+ def _loadReadGroupInfo(self):
+ rgs = self.peer.header["RG"]
+ readGroupTable_ = []
+- pulseFeaturesInAll_ = frozenset(PULSE_FEATURE_TAGS.keys())
++ pulseFeaturesInAll_ = frozenset(list(PULSE_FEATURE_TAGS.keys()))
+ for rg in rgs:
+ rgID = rgAsInt(rg["ID"])
+ rgName = rg["PU"]
+@@ -110,7 +114,7 @@
+ rgChem = decodeTriple(*triple)
+ rgReadType = ds["READTYPE"]
+ readGroupTable_.append((rgID, rgName, rgReadType, rgChem))
+- pulseFeaturesInAll_ = pulseFeaturesInAll_.intersection(ds.keys())
++ pulseFeaturesInAll_ = pulseFeaturesInAll_.intersection(list(ds.keys()))
+
+ self._readGroupTable = np.rec.fromrecords(
+ readGroupTable_,
+@@ -147,7 +151,7 @@
+ fastaIdsAndLens = set((c.id, len(c)) for c in ft)
+ bamIdsAndLens = set((c.Name, c.Length) for c in self.referenceInfoTable)
+ if not bamIdsAndLens.issubset(fastaIdsAndLens):
+- raise ReferenceMismatch, "FASTA file must contain superset of reference contigs in BAM"
++ raise ReferenceMismatch("FASTA file must contain superset of reference contigs in BAM")
+ self.referenceFasta = ft
+
+ def _checkFileCompatibility(self):
+@@ -172,7 +176,7 @@
+ self.referenceFasta = None
+ if referenceFastaFname is not None:
+ if self.isUnmapped:
+- raise ValueError, "Unmapped BAM file--reference FASTA should not be given as argument to BamReader"
++ raise ValueError("Unmapped BAM file--reference FASTA should not be given as argument to BamReader")
+ self._loadReferenceFasta(referenceFastaFname)
+
+ @property
+@@ -343,7 +347,7 @@
+ if exists(pbiFname):
+ self.pbi = PacBioBamIndex(pbiFname)
+ else:
+- raise IOError, "IndexedBamReader requires bam.pbi index file"
++ raise IOError("IndexedBamReader requires bam.pbi index file")
+
+ def atRowNumber(self, rn):
+ offset = self.pbi.virtualFileOffset[rn]
+@@ -360,7 +364,7 @@
+ return self[ix]
+
+ def __iter__(self):
+- for rn in xrange(len(self.pbi)):
++ for rn in range(len(self.pbi)):
+ yield self.atRowNumber(rn)
+
+ def __len__(self):
+@@ -372,7 +376,7 @@
+ return self.atRowNumber(rowNumbers)
+ elif isinstance(rowNumbers, slice):
+ return [ self.atRowNumber(r)
+- for r in xrange(*rowNumbers.indices(len(self)))]
++ for r in range(*rowNumbers.indices(len(self)))]
+ elif isinstance(rowNumbers, list) or isinstance(rowNumbers, np.ndarray):
+ if len(rowNumbers) == 0:
+ return []
+@@ -382,13 +386,13 @@
+ return [ self.atRowNumber(r) for r in rowNumbers ]
+ elif entryType == bool or issubclass(entryType, np.bool_):
+ return [ self.atRowNumber(r) for r in np.flatnonzero(rowNumbers) ]
+- raise TypeError, "Invalid type for IndexedBamReader slicing"
++ raise TypeError("Invalid type for IndexedBamReader slicing")
+
+ def __getattr__(self, key):
+ if key in self.pbi.columnNames:
+ return self.pbi[key]
+ else:
+- raise AttributeError, "no such column in pbi index"
++ raise AttributeError("no such column in pbi index")
+
+ def __dir__(self):
+ return self.pbi.columnNames
+--- python-pbcore.orig/pbcore/io/align/BlasrIO.py
++++ python-pbcore/pbcore/io/align/BlasrIO.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+--- python-pbcore.orig/pbcore/io/align/CmpH5IO.py
++++ python-pbcore/pbcore/io/align/CmpH5IO.py
+@@ -1,3 +1,8 @@
++from __future__ import absolute_import
++import six
++from six.moves import map
++from six.moves import range
++from six.moves import zip
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -69,9 +74,9 @@
+ _basemapArray = np.ndarray(shape=(max(_basemap.keys()) + 1,), dtype=np.byte)
+ _cBasemapArray = np.ndarray(shape=(max(_basemap.keys()) + 1,), dtype=np.byte)
+
+-for (e, v) in _basemap.iteritems():
++for (e, v) in six.iteritems(_basemap):
+ _basemapArray[e] = v
+-for (e, v) in _cBasemap.iteritems():
++for (e, v) in six.iteritems(_cBasemap):
+ _cBasemapArray[e] = v
+
+ _baseEncodingToInt = np.array([-1]*16)
+@@ -163,7 +168,7 @@
+ elif dtype == np.int8:
+ return a[a != ord("-")]
+ else:
+- raise Exception, "Invalid pulse array type"
++ raise Exception("Invalid pulse array type")
+
+
+
+@@ -281,7 +286,7 @@
+ if (refStart >= refEnd or
+ refStart >= self.tEnd or
+ refEnd <= self.tStart):
+- raise IndexError, "Clipping query does not overlap alignment"
++ raise IndexError("Clipping query does not overlap alignment")
+ else:
+ return ClippedCmpH5Alignment(self, refStart, refEnd)
+
+@@ -588,7 +593,7 @@
+ transcript = self.transcript(style="exonerate+")
+ refPos = self.referencePositions()
+ refPosString = "".join([str(pos % 10) for pos in refPos])
+- for i in xrange(0, len(alignedRef), COLUMNS):
++ for i in range(0, len(alignedRef), COLUMNS):
+ val += "\n"
+ val += " " + refPosString[i:i+COLUMNS] + "\n"
+ val += " " + alignedRef [i:i+COLUMNS] + "\n"
+@@ -719,7 +724,7 @@
+ self.filename = abspath(expanduser(filenameOrH5File))
+ self.file = h5py.File(self.filename, "r")
+ except IOError:
+- raise IOError, ("Invalid or nonexistent cmp.h5 file %s" % filenameOrH5File)
++ raise IOError("Invalid or nonexistent cmp.h5 file %s" % filenameOrH5File)
+
+ self._loadAlignmentInfo(sharedAlignmentIndex)
+ self._loadMovieInfo()
+@@ -753,7 +758,7 @@
+ for (alnGroupId, alnGroupPath) in zip(self.file["/AlnGroup/ID"],
+ self.file["/AlnGroup/Path"]):
+ alnGroup = self.file[alnGroupPath]
+- self._alignmentGroupById[alnGroupId] = dict(alnGroup.items())
++ self._alignmentGroupById[alnGroupId] = dict(list(alnGroup.items()))
+
+
+ def _loadMovieInfo(self):
+@@ -767,10 +772,10 @@
+ timeScale = [1.0] * numMovies
+
+ self._movieInfoTable = np.rec.fromrecords(
+- zip(self.file["/MovieInfo/ID"],
++ list(zip(self.file["/MovieInfo/ID"],
+ self.file["/MovieInfo/Name"],
+ frameRate,
+- timeScale),
++ timeScale)),
+ dtype=[("ID" , int),
+ ("Name" , object),
+ ("FrameRate" , float),
+@@ -787,10 +792,10 @@
+ # missing chemistry info.
+ assert (self._readGroupTable is None) and (self._readGroupDict is None)
+ self._readGroupTable = np.rec.fromrecords(
+- zip(self._movieInfoTable.ID,
++ list(zip(self._movieInfoTable.ID,
+ self._movieInfoTable.Name,
+ [self.readType] * len(self._movieInfoTable.ID),
+- self.sequencingChemistry),
++ self.sequencingChemistry)),
+ dtype=[("ID" , np.int32),
+ ("MovieName" , "O"),
+ ("ReadType" , "O"),
+@@ -800,18 +805,18 @@
+
+ def _loadReferenceInfo(self):
+ _referenceGroupTbl = np.rec.fromrecords(
+- zip(self.file["/RefGroup/ID"],
++ list(zip(self.file["/RefGroup/ID"],
+ self.file["/RefGroup/RefInfoID"],
+- [path[1:] for path in self.file["/RefGroup/Path"]]),
++ [path[1:] for path in self.file["/RefGroup/Path"]])),
+ dtype=[("ID" , int),
+ ("RefInfoID", int),
+ ("Name" , object)])
+
+ _referenceInfoTbl = np.rec.fromrecords(
+- zip(self.file["/RefInfo/ID"],
++ list(zip(self.file["/RefInfo/ID"],
+ self.file["/RefInfo/FullName"],
+ self.file["/RefInfo/Length"],
+- self.file["/RefInfo/MD5"]) ,
++ self.file["/RefInfo/MD5"])) ,
+ dtype=[("RefInfoID", int),
+ ("FullName" , object),
+ ("Length" , int),
+@@ -840,7 +845,7 @@
+ record.Name in self._referenceDict or
+ record.FullName in self._referenceDict or
+ record.MD5 in self._referenceDict):
+- raise ValueError, "Duplicate reference contig sequence or identifier"
++ raise ValueError("Duplicate reference contig sequence or identifier")
+ else:
+ self._referenceDict[shortName] = record
+ self._referenceDict[record.ID] = record
+@@ -859,10 +864,10 @@
+
+ if "Barcode" in self.file["/AlnInfo"]:
+ # Build forward and backwards id<->label lookup tables
+- self._barcodeName = OrderedDict(zip(self.file["/BarcodeInfo/ID"],
+- self.file["/BarcodeInfo/Name"]))
+- self._barcode = OrderedDict(zip(self.file["/BarcodeInfo/Name"],
+- self.file["/BarcodeInfo/ID"]))
++ self._barcodeName = OrderedDict(list(zip(self.file["/BarcodeInfo/ID"],
++ self.file["/BarcodeInfo/Name"])))
++ self._barcode = OrderedDict(list(zip(self.file["/BarcodeInfo/Name"],
++ self.file["/BarcodeInfo/ID"])))
+ # Barcode ID per row
+ self._barcodes = self.file["/AlnInfo/Barcode"].value[:,1]
+
+@@ -890,7 +895,7 @@
+ # Old way
+ self._sequencingChemistry = mi["SequencingChemistry"].value
+ else:
+- raise ChemistryLookupError, "Chemistry information could not be found in cmp.h5!"
++ raise ChemistryLookupError("Chemistry information could not be found in cmp.h5!")
+ return self._sequencingChemistry
+
+
+@@ -1032,8 +1037,8 @@
+ >>> c.versionAtLeast("1.3.0")
+ False
+ """
+- myVersionTuple = map(int, self.version.split(".")[:3])
+- minimalVersionTuple = map(int, minimalVersion.split(".")[:3])
++ myVersionTuple = list(map(int, self.version.split(".")[:3]))
++ minimalVersionTuple = list(map(int, minimalVersion.split(".")[:3]))
+ return myVersionTuple >= minimalVersionTuple
+
+ def softwareVersion(self, programName):
+@@ -1041,8 +1046,8 @@
+ Return the version of program `programName` that processed
+ this file.
+ """
+- filelog = dict(zip(self.file["/FileLog/Program"],
+- self.file["/FileLog/Version"]))
++ filelog = dict(list(zip(self.file["/FileLog/Program"],
++ self.file["/FileLog/Version"])))
+ return filelog.get(programName, None)
+
+ @property
+@@ -1062,7 +1067,7 @@
+
+ @property
+ def movieNames(self):
+- return set([mi.Name for mi in self._movieDict.values()])
++ return set([mi.Name for mi in list(self._movieDict.values())])
+
+ @property
+ def ReadGroupID(self):
+@@ -1152,7 +1157,7 @@
+ """
+
+ if not self.isSorted:
+- raise Exception, "CmpH5 is not sorted"
++ raise Exception("CmpH5 is not sorted")
+ rowNumbers = self._readLocatorByKey[refKey](refStart, refEnd, justIndices=True)
+ if justIndices:
+ return rowNumbers
+@@ -1173,8 +1178,8 @@
+ False
+
+ """
+- return all(featureName in alnGroup.keys()
+- for alnGroup in self._alignmentGroupById.values())
++ return all(featureName in list(alnGroup.keys())
++ for alnGroup in list(self._alignmentGroupById.values()))
+
+ def pulseFeaturesAvailable(self):
+ """
+@@ -1186,9 +1191,9 @@
+ [u'QualityValue', u'IPD', u'PulseWidth', u'InsertionQV', u'DeletionQV']
+
+ """
+- pulseFeaturesByMovie = [ alnGroup.keys()
+- for alnGroup in self._alignmentGroupById.values() ]
+- pulseFeaturesAvailableAsSet = set.intersection(*map(set, pulseFeaturesByMovie))
++ pulseFeaturesByMovie = [ list(alnGroup.keys())
++ for alnGroup in list(self._alignmentGroupById.values()) ]
++ pulseFeaturesAvailableAsSet = set.intersection(*list(map(set, pulseFeaturesByMovie)))
+ pulseFeaturesAvailableAsSet.discard("AlnArray")
+ return list(pulseFeaturesAvailableAsSet)
+
+@@ -1239,7 +1244,7 @@
+ return CmpH5Alignment(self, rowNumbers)
+ elif isinstance(rowNumbers, slice):
+ return [CmpH5Alignment(self, r)
+- for r in xrange(*rowNumbers.indices(len(self)))]
++ for r in range(*rowNumbers.indices(len(self)))]
+ elif isinstance(rowNumbers, list) or isinstance(rowNumbers, np.ndarray):
+ if len(rowNumbers) == 0:
+ return []
+@@ -1249,10 +1254,10 @@
+ return [CmpH5Alignment(self, r) for r in rowNumbers]
+ elif entryType == bool or issubclass(entryType, np.bool_):
+ return [CmpH5Alignment(self, r) for r in np.flatnonzero(rowNumbers)]
+- raise TypeError, "Invalid type for CmpH5Reader slicing"
++ raise TypeError("Invalid type for CmpH5Reader slicing")
+
+ def __iter__(self):
+- return (self[i] for i in xrange(len(self)))
++ return (self[i] for i in range(len(self)))
+
+ def __len__(self):
+ return len(self.alignmentIndex)
+--- python-pbcore.orig/pbcore/io/align/PacBioBamIndex.py
++++ python-pbcore/pbcore/io/align/PacBioBamIndex.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -35,6 +36,9 @@
+ from os.path import abspath, expanduser
+ from functools import wraps
+ from collections import namedtuple
++import six
++from six.moves import range
++from six.moves import zip
+
+ class PacBioBamIndex(object):
+ """
+@@ -54,8 +58,8 @@
+ """
+ def _loadColumns(self, f):
+ g = f["PacBioBamIndex/Columns"]
+- columnNamesAndColumns = sorted([ (k, v[:]) for (k, v) in g.iteritems() ])
+- columnNames, columns = zip(*columnNamesAndColumns)
++ columnNamesAndColumns = sorted([ (k, v[:]) for (k, v) in six.iteritems(g) ])
++ columnNames, columns = list(zip(*columnNamesAndColumns))
+ return np.rec.fromarrays(columns, names=columnNames)
+
+ def _loadVersion(self, f):
+@@ -72,7 +76,7 @@
+ self._columns = self._loadColumns(f)
+ self._offsets = self._loadOffsets(f)
+ except Exception as e:
+- raise IOError, "Malformed bam.pbi file: " + str(e)
++ raise IOError("Malformed bam.pbi file: " + str(e))
+
+
+ @property
+@@ -87,7 +91,7 @@
+ if columnName in self.columnNames:
+ return self._columns[columnName]
+ else:
+- raise AttributeError, "pbi has no column named '%s'" % columnName
++ raise AttributeError("pbi has no column named '%s'" % columnName)
+
+ def __getitem__(self, rowNumber):
+ return self._columns[rowNumber]
+@@ -100,7 +104,7 @@
+ return len(self._columns)
+
+ def __iter__(self):
+- for i in xrange(len(self)):
++ for i in range(len(self)):
+ yield self[i]
+
+ def rangeQuery(self, winId, winStart, winEnd):
+--- python-pbcore.orig/pbcore/io/align/_AlignmentMixin.py
++++ python-pbcore/pbcore/io/align/_AlignmentMixin.py
+@@ -1,3 +1,5 @@
++from __future__ import absolute_import
++from six.moves import map
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -86,8 +88,8 @@
+ elif readName.endswith("ccs"):
+ return False
+ else:
+- q = map(int, rQuery.split("_"))
+- r = map(int, readName.split("/")[-1].split("_"))
++ q = list(map(int, rQuery.split("_")))
++ r = list(map(int, readName.split("/")[-1].split("_")))
+ return rangeOverlap(q, r)
+
+ fields = query.split("/")
+--- python-pbcore.orig/pbcore/io/align/_BamSupport.py
++++ python-pbcore/pbcore/io/align/_BamSupport.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -31,6 +32,8 @@
+ # Author: David Alexander
+
+ import numpy as np
++from six.moves import range
++from six.moves import zip
+
+ class UnavailableFeature(Exception): pass
+ class Unimplemented(Exception): pass
+@@ -103,9 +106,9 @@
+ for i, (fl, fu) in enumerate(zip(framepoints, framepoints[1:])):
+ if (fu > fl + 1):
+ m = (fl + fu)/2
+- for f in xrange(fl, m):
++ for f in range(fl, m):
+ frameToCode[f] = i
+- for f in xrange(m, fu):
++ for f in range(m, fu):
+ frameToCode[f] = i + 1
+ else:
+ frameToCode[fl] = i
+--- python-pbcore.orig/pbcore/io/align/__init__.py
++++ python-pbcore/pbcore/io/align/__init__.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -28,7 +29,7 @@
+ # POSSIBILITY OF SUCH DAMAGE.
+ #################################################################################
+
+-from CmpH5IO import *
+-from BamIO import *
+-from BamAlignment import *
+-from BlasrIO import *
++from .CmpH5IO import *
++from .BamIO import *
++from .BamAlignment import *
++from .BlasrIO import *
+--- python-pbcore.orig/pbcore/io/base.py
++++ python-pbcore/pbcore/io/base.py
+@@ -34,6 +34,7 @@
+ from __future__ import absolute_import
+ import gzip
+ from os.path import abspath, expanduser
++import six
+
+ __all__ = [ "ReaderBase", "WriterBase" ]
+
+@@ -53,7 +54,7 @@
+ """
+ assert mode in ("r", "w")
+
+- if isinstance(filenameOrFile, basestring):
++ if isinstance(filenameOrFile, six.string_types):
+ filename = abspath(expanduser(filenameOrFile))
+ if filename.endswith(".gz"):
+ return gzip.open(filename, mode)
+--- python-pbcore.orig/pbcore/io/opener.py
++++ python-pbcore/pbcore/io/opener.py
+@@ -1,3 +1,5 @@
++from __future__ import absolute_import
++from __future__ import print_function
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -54,7 +56,7 @@
+ elif fname.endswith("bam"):
+ return IndexedBamReader(fname, referenceFasta)
+ else:
+- raise ValueError, "Invalid alignment file suffix"
++ raise ValueError("Invalid alignment file suffix")
+
+ def openAlignmentFile(fname, referenceFasta=None):
+ """
+@@ -97,7 +99,7 @@
+ elif ext == "fofn": return BasH5Collection
+ elif ext == "bam": return openAlignmentFile
+ else:
+- raise ValueError, ("No known opener class for extension %s" % ext)
++ raise ValueError("No known opener class for extension %s" % ext)
+
+ def _extension(fname):
+ parts = fname.split(".")
+@@ -119,7 +121,7 @@
+ import sys, code
+
+ if len(sys.argv) < 2:
+- print "Requires at least one argument!"
++ print("Requires at least one argument!")
+ return 1
+
+ fname = sys.argv[1]
+--- python-pbcore.orig/pbcore/io/rangeQueries.py
++++ python-pbcore/pbcore/io/rangeQueries.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -31,6 +32,7 @@
+ import h5py as h
+ import numpy as n
+ import bisect
++from six.moves import zip
+
+ def rightmostBinSearch(vec, val):
+ """
+@@ -127,7 +129,7 @@
+ Return a function which can be called iteratively to find reads
+ quickly.
+ """
+- if not cmpH5.isSorted: raise Exception, "CmpH5 is not sorted"
++ if not cmpH5.isSorted: raise Exception("CmpH5 is not sorted")
+ offsets = cmpH5.file["/RefGroup/OffsetTable"].value
+ offStart, offEnd = offsets[offsets[:,0] == refSeq, 1:3].ravel()
+
+@@ -163,7 +165,7 @@
+ cmpH5 is an hdf5 object representing a pointer to a sorted cmp.h5
+ file.
+ """
+- if not cmpH5.isSorted: raise Exception, "CmpH5 is not sorted"
++ if not cmpH5.isSorted: raise Exception("CmpH5 is not sorted")
+ return makeReadLocator(cmpH5, coords[0])(coords[1], coords[2], justIndices)
+
+ def getCoverageInRange(cmpH5, coords, rowNumbers=None):
+@@ -172,7 +174,7 @@
+ element represents the number of reads overlapping that position
+ in the cmp.h5 file.
+ """
+- if not cmpH5.isSorted: raise Exception, "CmpH5 is not sorted"
++ if not cmpH5.isSorted: raise Exception("CmpH5 is not sorted")
+ if rowNumbers==None:
+ rowNumbers = getReadsInRange(cmpH5, coords, justIndices=True)
+ if (len(rowNumbers))==0:
+--- python-pbcore.orig/pbcore/sequence.py
++++ python-pbcore/pbcore/sequence.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+--- python-pbcore.orig/pbcore/util/Process.py
++++ python-pbcore/pbcore/util/Process.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+--- python-pbcore.orig/pbcore/util/ToolRunner.py
++++ python-pbcore/pbcore/util/ToolRunner.py
+@@ -1,3 +1,5 @@
++from __future__ import absolute_import
++from __future__ import print_function
+ #################################################################################
+ # Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+ #
+@@ -95,7 +97,7 @@
+ try:
+ import ipdb
+ except ImportError:
+- print "--debug requires module 'ipdb'"
++ print("--debug requires module 'ipdb'")
+ return -1
+ with ipdb.launch_ipdb_on_exception():
+ self.run()
+--- python-pbcore.orig/pbcore/util/decorators.py
++++ python-pbcore/pbcore/util/decorators.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ import warnings
+
+ def deprecated(func):
+--- python-pbcore.orig/setup.py
++++ python-pbcore/setup.py
+@@ -1,12 +1,9 @@
++from __future__ import absolute_import
+ from setuptools import setup, Extension, find_packages
+ import sys
+
+-if ("install" in sys.argv) and sys.version_info < (2, 7, 0):
+- print "pbcore requires Python 2.7"
+- sys.exit(-1)
+-
+ globals = {}
+-execfile("pbcore/__init__.py", globals)
++exec(compile(open("pbcore/__init__.py").read(), "pbcore/__init__.py", 'exec'), globals)
+ __VERSION__ = globals["__VERSION__"]
+
+ setup(
+--- python-pbcore.orig/tests/test_pbcore_data.py
++++ python-pbcore/tests/test_pbcore_data.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal
+ from pbcore import data
+
+--- python-pbcore.orig/tests/test_pbcore_io_AlnFileReaders.py
++++ python-pbcore/tests/test_pbcore_io_AlnFileReaders.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from numpy.testing import (assert_array_almost_equal as ASIM,
+ assert_array_equal as AEQ)
+ from nose.tools import (nottest,
+@@ -14,6 +15,8 @@
+ from pbcore.io import CmpH5Reader, BamReader, IndexedBamReader
+ from pbcore.sequence import reverseComplement as RC
+ from pbcore.chemistry import ChemistryLookupError
++from six.moves import range
++from six.moves import zip
+
+
+ class _BasicAlnFileReaderTests(object):
+@@ -151,7 +154,7 @@
+ EQ(985, ac1.referenceEnd)
+ EQ([(983, 'A', '-'),
+ (984, 'C', 'C')],
+- zip(ac1.referencePositions(), ac1.reference(), ac1.read()))
++ list(zip(ac1.referencePositions(), ac1.reference(), ac1.read())))
+
+ ac2 = a.clippedTo(982, 986)
+ EQ(982, ac2.referenceStart)
+@@ -161,13 +164,13 @@
+ (984, 'C', 'C'),
+ (985, '-', 'G'),
+ (985, 'T', 'T')],
+- zip(ac2.referencePositions(), ac2.reference(), ac2.read()))
++ list(zip(ac2.referencePositions(), ac2.reference(), ac2.read())))
+
+ ac3 = a.clippedTo(984, 985)
+ EQ(984, ac3.referenceStart)
+ EQ(985, ac3.referenceEnd)
+ EQ([(984, 'C', 'C')],
+- zip(ac3.referencePositions(), ac3.reference(), ac3.read()))
++ list(zip(ac3.referencePositions(), ac3.reference(), ac3.read())))
+
+ # Get a more interesting (more gappy) rev strand aln
+ b = self.alns[3]
+@@ -192,7 +195,7 @@
+ (2210, 'C', 'C'),
+ (2209, 'T', 'T'),
+ (2208, 'G', '-')],
+- zip(bc1.referencePositions(), bc1.reference(), bc1.read()))
++ list(zip(bc1.referencePositions(), bc1.reference(), bc1.read())))
+
+ bc2 = b.clippedTo(2207, 2215)
+ EQ([(2214, 'C', 'C'),
+@@ -203,7 +206,7 @@
+ (2209, 'T', 'T'),
+ (2208, 'G', '-'),
+ (2207, 'G', 'G')],
+- zip(bc2.referencePositions(), bc2.reference(), bc2.read()))
++ list(zip(bc2.referencePositions(), bc2.reference(), bc2.read())))
+
+ bc3 = b.clippedTo(2209, 2214)
+ EQ([(2213, 'A', 'A'),
+@@ -211,7 +214,7 @@
+ (2211, 'G', 'G'),
+ (2210, 'C', 'C'),
+ (2209, 'T', 'T')],
+- zip(bc3.referencePositions(), bc3.reference(), bc3.read()))
++ list(zip(bc3.referencePositions(), bc3.reference(), bc3.read())))
+
+
+ # Test clipping in a large deletion
+@@ -259,15 +262,15 @@
+ def testClippingsVsBaxData(self):
+ self.f.attach(self.BAX_FILE)
+ for aln in [self.alns[52], self.alns[8]]:
+- for cS in xrange(aln.tStart, aln.tEnd + 1):
+- for cE in xrange(cS + 1, min(aln.tEnd, cS + 10)):
++ for cS in range(aln.tStart, aln.tEnd + 1):
++ for cE in range(cS + 1, min(aln.tEnd, cS + 10)):
+ ca = aln.clippedTo(cS, cE)
+ EQ(ca.zmwRead.basecalls(),
+ ca.read(aligned=False, orientation="native"))
+
+ def testReadsInRange(self):
+ wLen = 1000
+- for wStart in xrange(0, 50000, wLen):
++ for wStart in range(0, 50000, wLen):
+ wEnd = wStart + wLen
+ expectedNames = set([ a.readName for a in self.alns
+ if (a.referenceName == "lambda_NEB3011" and
+--- python-pbcore.orig/tests/test_pbcore_io_BarcodeH5Reader.py
++++ python-pbcore/tests/test_pbcore_io_BarcodeH5Reader.py
+@@ -1,3 +1,5 @@
++from __future__ import absolute_import
++from __future__ import print_function
+ import nose.tools
+ import numpy
+ import numpy.testing
+@@ -6,6 +8,7 @@
+
+ from pbcore.data import MOVIE_NAME_BC
+ from pbcore.io.BarcodeH5Reader import BarcodeH5Reader, BarcodeH5Fofn, MPBarcodeH5Reader, LabeledZmw
++from six.moves import map
+
+ class TestBarcodeH5Reader(object):
+ """Tests of BarcodeH5Reader against a generic BarcodeH5 file
+@@ -13,8 +16,8 @@
+
+ def __init__(self):
+ bcFiles = pbcore.data.getBcH5s()
+- print bcFiles
+- self.bc1, self.bc2, self.bc3 = map(BarcodeH5Reader, bcFiles)
++ print(bcFiles)
++ self.bc1, self.bc2, self.bc3 = list(map(BarcodeH5Reader, bcFiles))
+
+ def test_BarcodeH5Reader_basicTest(self):
+ """Test that BcH5Reader correctly sets movie name, barcode labels, and hole numbers
+@@ -48,15 +51,15 @@
+ """Test that BcH5Reader correctly iterates over it's labeled ZMWs
+ """
+
+- labeledZmws1 = [ lZmw for lZmw in self.bc1.labeledZmws.values() ]
++ labeledZmws1 = [ lZmw for lZmw in list(self.bc1.labeledZmws.values()) ]
+ sortedZmws1 = sorted(labeledZmws1, key=lambda z: z.holeNumber)
+ nose.tools.assert_equal(sortedZmws1, list(self.bc1))
+
+- labeledZmws2 = [ lZmw for lZmw in self.bc2.labeledZmws.values() ]
++ labeledZmws2 = [ lZmw for lZmw in list(self.bc2.labeledZmws.values()) ]
+ sortedZmws2 = sorted(labeledZmws2, key=lambda z: z.holeNumber)
+ nose.tools.assert_equal(sortedZmws2, list(self.bc2))
+
+- labeledZmws3 = [ lZmw for lZmw in self.bc3.labeledZmws.values() ]
++ labeledZmws3 = [ lZmw for lZmw in list(self.bc3.labeledZmws.values()) ]
+ sortedZmws3 = sorted(labeledZmws3, key=lambda z: z.holeNumber)
+ nose.tools.assert_equal(sortedZmws3, list(self.bc3))
+
+@@ -66,9 +69,9 @@
+
+ def __init__(self):
+ bcFofn = pbcore.data.getBcFofn()
+- print bcFofn
++ print(bcFofn)
+ self.bcFofn = BarcodeH5Fofn(bcFofn)
+- print self.bcFofn
++ print(self.bcFofn)
+
+ def test_BasH5Fofn_basicTest(self):
+ """Test that BcH5Fofn correctly sets movie name, barcode labels, and hole numbers
+--- python-pbcore.orig/tests/test_pbcore_io_BasH5Collection.py
++++ python-pbcore/tests/test_pbcore_io_BasH5Collection.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal, assert_true, assert_false
+ from numpy.testing import assert_array_equal
+ from StringIO import StringIO
+--- python-pbcore.orig/tests/test_pbcore_io_BasH5Reader.py
++++ python-pbcore/tests/test_pbcore_io_BasH5Reader.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ import inspect
+ import os
+
+@@ -10,6 +11,8 @@
+
+ from pbcore.io.BasH5IO import BasH5Reader, Zmw, ZmwRead, CCSZmwRead
+ from pbcore.chemistry import ChemistryLookupError
++from six.moves import map
++from six.moves import zip
+
+ class TestBasH5Reader_14:
+ """Tests of BasH5Reader against a 1.4 bas.h5 file, no multipart with
+@@ -19,7 +22,7 @@
+ def __init__(self):
+ self.cmpH5 = pbcore.io.CmpH5Reader(pbcore.data.getCmpH5())
+ basFiles = pbcore.data.getBasH5s()
+- self.bas1, self.bas2 = map(pbcore.io.BasH5Reader, basFiles)
++ self.bas1, self.bas2 = list(map(pbcore.io.BasH5Reader, basFiles))
+
+ def test_BasH5Reader_basicTest(self):
+ """Test that BasH5Reader correctly sets moviename, identifies the
+@@ -344,8 +347,8 @@
+ productivities = {}
+ for filename in self.baxh5_filenames:
+ f = h5py.File(filename, 'r')
+- hn_to_prod = dict(zip(f["PulseData/BaseCalls/ZMW/HoleNumber"],
+- f["PulseData/BaseCalls/ZMWMetrics/Productivity"]))
++ hn_to_prod = dict(list(zip(f["PulseData/BaseCalls/ZMW/HoleNumber"],
++ f["PulseData/BaseCalls/ZMWMetrics/Productivity"])))
+ productivities.update(hn_to_prod)
+ f.close()
+
+--- python-pbcore.orig/tests/test_pbcore_io_BlasrIO.py
++++ python-pbcore/tests/test_pbcore_io_BlasrIO.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+
+ from pbcore.io import M4Reader, M5Reader
+ import pbcore.data as D
+--- python-pbcore.orig/tests/test_pbcore_io_FastaIO.py
++++ python-pbcore/tests/test_pbcore_io_FastaIO.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal, assert_true, assert_false
+ from pbcore import data
+ from pbcore.io import FastaReader, FastaWriter, FastaRecord
+--- python-pbcore.orig/tests/test_pbcore_io_FastaTable.py
++++ python-pbcore/tests/test_pbcore_io_FastaTable.py
+@@ -1,6 +1,8 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal, assert_true, assert_false
+ from pbcore import data
+ from pbcore.io import FastaReader, FastaWriter, IndexedFastaReader
++from six.moves import zip
+
+
+ class TestIndexedFastaReader:
+--- python-pbcore.orig/tests/test_pbcore_io_FastqIO.py
++++ python-pbcore/tests/test_pbcore_io_FastqIO.py
+@@ -1,9 +1,11 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal, assert_true, assert_false
+ from numpy.testing import assert_array_equal
+ from pbcore import data
+ from StringIO import StringIO
+
+ from pbcore.io.FastqIO import *
++from six.moves import range
+
+
+ # Test QV <-> string conversion routines
+@@ -12,7 +14,7 @@
+ self.ascii = \
+ "!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`" + \
+ "abcdefghijklmnopqrstuvwxyz{|}~"
+- self.qvs = range(0, 94)
++ self.qvs = list(range(0, 94))
+
+ def testAsciiFromQvs(self):
+ assert_equal(self.ascii, asciiFromQvs(self.qvs))
+@@ -107,7 +109,7 @@
+ def test_eq(self):
+ header = 'r1'
+ seq = 'ACGT'
+- qvs = list(xrange(10, 10 + len(seq)))
++ qvs = list(range(10, 10 + len(seq)))
+ r1 = FastqRecord(header, seq, qvs)
+ r2 = FastqRecord(header, seq, qvs)
+ assert_true(r1 == r2)
+@@ -116,7 +118,7 @@
+ def test_not_equal(self):
+ header = 'r1'
+ seq = 'ACGT'
+- qvs = list(xrange(10, 10 + len(seq)))
++ qvs = list(range(10, 10 + len(seq)))
+ r1 = FastqRecord(header, seq, qvs)
+ r2 = FastqRecord('r2', seq, qvs)
+ assert_true(r1 != r2)
+@@ -138,12 +140,12 @@
+ def test_readFastq1(self):
+ r1 = FastqReader(self.fastq1)
+ l = list(r1)
+- assert_equal([FastqRecord("seq1", "GATTACA", range(22, 29))], l)
++ assert_equal([FastqRecord("seq1", "GATTACA", list(range(22, 29)))], l)
+
+ def test_readFastq2(self):
+ r2 = FastqReader(self.fastq2)
+ l = list(r2)
+- assert_equal([FastqRecord("seq1", "GATTACA", range(22, 29)),
++ assert_equal([FastqRecord("seq1", "GATTACA", list(range(22, 29))),
+ FastqRecord("seq2", "CATTAGA", [31]*7) ],
+ l)
+
+--- python-pbcore.orig/tests/test_pbcore_io_FofnIO.py
++++ python-pbcore/tests/test_pbcore_io_FofnIO.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal, assert_true, assert_false
+ from numpy.testing import assert_array_equal
+ from StringIO import StringIO
+--- python-pbcore.orig/tests/test_pbcore_io_GffIO.py
++++ python-pbcore/tests/test_pbcore_io_GffIO.py
+@@ -1,7 +1,9 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal, assert_raises
+ from StringIO import StringIO
+ from pbcore.io import GffWriter, Gff3Record, GffReader
+ from pbcore import data
++from six.moves import zip
+
+ class TestGff3Record:
+
+--- python-pbcore.orig/tests/test_pbcore_io_rangeQueries.py
++++ python-pbcore/tests/test_pbcore_io_rangeQueries.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from nose.tools import assert_equal
+ from numpy.testing import assert_array_equal
+
+@@ -7,6 +8,7 @@
+
+ import bisect
+ from numpy import *
++from six.moves import range
+
+ def brute_force_lm_search(vec, val):
+ if (val not in vec):
+@@ -56,7 +58,7 @@
+ # This is a brute force check that reads in range returns the
+ # right answer for 50-base windows of lambda
+ for BLOCKSIZE in [50, 77]:
+- for winStart in xrange(0, 45000, BLOCKSIZE):
++ for winStart in range(0, 45000, BLOCKSIZE):
+ winEnd = winStart + BLOCKSIZE
+ assert_array_equal(brute_force_reads_in_range(winStart, winEnd, self.cmpH5.tStart, self.cmpH5.tEnd),
+ self.cmpH5.readsInRange(1, winStart, winEnd, justIndices=True))
+@@ -65,7 +67,7 @@
+
+ def test_coverage_in_range2(self):
+ # Brute force over lambda
+- for winStart in xrange(0, 45000, 50):
++ for winStart in range(0, 45000, 50):
+ winEnd = winStart + 1
+ assert_array_equal([len(brute_force_reads_in_range(winStart, winEnd, self.cmpH5.tStart, self.cmpH5.tEnd))],
+ RQ.getCoverageInRange(self.cmpH5, (1, winStart, winEnd)))
+--- python-pbcore.orig/tests/test_pbcore_io_unaligned_bam.py
++++ python-pbcore/tests/test_pbcore_io_unaligned_bam.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ from numpy.testing import (assert_array_almost_equal as ASIM,
+ assert_array_equal as AEQ)
+ from nose.tools import (nottest,
+--- python-pbcore.orig/tests/test_pbcore_util_sequences.py
++++ python-pbcore/tests/test_pbcore_util_sequences.py
+@@ -1,3 +1,4 @@
++from __future__ import absolute_import
+ import nose
+ from nose.tools import assert_equal, assert_true, assert_false
+ from pbcore import sequence
diff --git a/debian/patches/remove-convenience-script.patch b/debian/patches/remove-convenience-script.patch
index 6b39f09..7feca2c 100644
--- a/debian/patches/remove-convenience-script.patch
+++ b/debian/patches/remove-convenience-script.patch
@@ -9,7 +9,7 @@ Last-Update: 2015-06-07
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-pbcore.orig/setup.py
+++ python-pbcore/setup.py
-@@ -24,7 +24,6 @@
+@@ -21,7 +21,6 @@
'chemistry/resources/*.xml']
},
zip_safe = False,
diff --git a/debian/patches/series b/debian/patches/series
index 8003af8..3b9561b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+modernize-python.patch
remove-convenience-script.patch
doc-theme.patch
diff --git a/debian/rules b/debian/rules
index 823d09b..7f125e4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,9 +6,10 @@ include /usr/share/dpkg/default.mk
# debhelper doesn't appear to define DESTDIR for debian/rules
# call it "ROOT" here so it doesn't conflict with DESTDIR (it shouldn't anyway)
ROOT=`pwd`/debian/$(DEB_SOURCE)
+export PYBUILD_NAME = pbcore
%:
- LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
+ LC_ALL=C.UTF-8 dh $@ --with python2,python3 --buildsystem=pybuild
override_dh_auto_build:
dh_auto_build
@@ -16,7 +17,9 @@ override_dh_auto_build:
override_dh_fixperms:
dh_fixperms
- chmod -x $(ROOT)/usr/lib/python2.7/dist-packages/pbcore/data/*.h5
+ # TODO: Not hardcoding this would be nice
+# chmod -x $(ROOT)/usr/lib/python2.7/dist-packages/pbcore/data/*.h5
+# chmod -x $(ROOT)/usr/lib/python3/dist-packages/pbcore/data/*.h5
override_dh_installdocs:
dh_installdocs -X _source
--
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