trim six usage

flye/assembly/assemble.py

@@ -6,7 +6,6 @@
 Runs assemble binary
 """
 
-from __future__ import absolute_import
 import subprocess
 import logging
 import os

flye/assembly/repeat_graph.py

@@ -6,7 +6,6 @@
 Runs repeat/contigger binary
 """
 
-from __future__ import absolute_import
 import subprocess
 import logging
 import os

flye/assembly/scaffolder.py

@@ -6,8 +6,6 @@
 Final output generator
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import logging
 
 import flye.utils.fasta_parser as fp

flye/config/configurator.py

@@ -6,8 +6,6 @@
 Sets up some parameters for the run based on input
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import logging
 
 import flye.utils.fasta_parser as fp

flye/config/py_cfg.py

@@ -6,7 +6,6 @@
 Configuration file for the Python part of the pipeline
 """
 
-from __future__ import absolute_import
 import os
 
 vals = {

flye/main.py

@@ -6,8 +6,6 @@
 Main logic of the package
 """
 
-from __future__ import print_function
-from __future__ import absolute_import
 import sys
 import os
 import logging
@@ -33,7 +31,6 @@
 #import flye.trestle.trestle as tres
 #import flye.trestle.graph_resolver as tres_graph
 from flye.repeat_graph.repeat_graph import RepeatGraph
-from flye.six.moves import range
 
 if sys.version_info[0] == 2:
     raise Exception("Python 2 is unsupported")

flye/polishing/alignment.py

@@ -6,8 +6,6 @@
 Runs Minimap2 and parses its output
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import os
 from collections import namedtuple
 import subprocess
@@ -19,7 +17,6 @@
 from flye.utils.utils import which, get_median
 from flye.utils.sam_parser import AlignmentException
 from flye.six import iteritems
-from flye.six.moves import range
 
 
 logger = logging.getLogger()

flye/polishing/bubbles.py

@@ -6,11 +6,8 @@
 Separates alignment into small bubbles for further correction
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import logging
 from bisect import bisect
-from flye.six.moves import range
 from collections import defaultdict
 from queue import Queue
 
@@ -22,7 +19,6 @@
 from flye.polishing.alignment import shift_gaps, get_uniform_alignments
 from flye.utils.sam_parser import SynchronizedSamReader, SynchonizedChunkManager
 from flye.utils.utils import process_in_parallel, get_median
-from flye.six.moves import zip
 
 
 logger = logging.getLogger()

flye/polishing/consensus.py

@@ -6,11 +6,8 @@
 Quick and dirty alignment consensus
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import logging
 from collections import defaultdict
-from flye.six.moves import range
 from flye.six import itervalues
 
 import multiprocessing
@@ -21,7 +18,6 @@
 import flye.config.py_cfg as cfg
 import flye.utils.fasta_parser as fp
 from flye.utils.utils import process_in_parallel
-from flye.six.moves import zip
 
 logger = logging.getLogger()
 

flye/polishing/polish.py

@@ -6,8 +6,6 @@
 Runs polishing binary in parallel and concatentes output
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import logging
 import subprocess, multiprocessing
 import os
@@ -22,7 +20,6 @@
 from flye.utils.utils import which
 import flye.config.py_cfg as cfg
 from flye.six import iteritems
-from flye.six.moves import range
 
 
 POLISH_BIN = "flye-modules"

flye/repeat_graph/graph_alignment.py

@@ -8,7 +8,6 @@
 """
 
 
-from __future__ import division
 class OverlapRange(object):
     __slots__ = ("cur_id", "cur_len", "cur_start", "cur_end",
                  "ext_id", "ext_len", "ext_start", "ext_end",

flye/repeat_graph/repeat_graph.py

@@ -8,7 +8,6 @@
 as well as some basic operations
 """
 
-from __future__ import division
 class RgEdge(object):
     __slots__ = ("node_left", "node_right", "edge_id", "repetitive",
                  "self_complement", "resolved", "mean_coverage",

flye/short_plasmids/circular_sequences.py

@@ -3,14 +3,12 @@
 #Released under the BSD license (see LICENSE file)
 
 
-from __future__ import absolute_import
 import flye.short_plasmids.utils as utils
 import flye.short_plasmids.unmapped_reads as unmapped
 import flye.utils.fasta_parser as fp
 from flye.utils.sam_parser import read_paf, read_paf_grouped
 import logging
 from flye.six import iteritems
-from flye.six.moves import range
 
 logger = logging.getLogger()
 

flye/short_plasmids/plasmids.py

@@ -2,7 +2,6 @@
 #This file is a part of Flye program.
 #Released under the BSD license (see LICENSE file)
 
-from __future__ import absolute_import
 import os
 import logging
 

flye/short_plasmids/unmapped_reads.py

@@ -3,14 +3,11 @@
 #Released under the BSD license (see LICENSE file)
 
 
-from __future__ import absolute_import
-from __future__ import division
 import flye.utils.fasta_parser as fp
 from flye.utils.sam_parser import read_paf_grouped
 import logging
 from collections import defaultdict
 from flye.six import iteritems
-from flye.six.moves import range
 
 logger = logging.getLogger()
 

flye/short_plasmids/utils.py

@@ -2,8 +2,6 @@
 #This file is a part of Flye program.
 #Released under the BSD license (see LICENSE file)
 
-from flye.six.moves import range
-
 def find_connected_components(graph):
     def dfs(start_vertex, connected_components_counter):
         dfs_stack = [start_vertex]

flye/six.py

@@ -20,8 +20,6 @@
 
 """Utilities for writing code that runs on Python 2 and 3"""
 
-from __future__ import absolute_import
-
 import functools
 import itertools
 import operator

flye/tests/test_toy.py

@@ -8,9 +8,6 @@
 Runs simple toy test
 """
 
-
-from __future__ import print_function
-
 import os
 import sys
 import subprocess

flye/trestle/divergence.py

@@ -8,11 +8,8 @@
 @author: jeffrey_yuan
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import logging
 from collections import defaultdict
-from flye.six.moves import range
 
 import multiprocessing
 import os.path
@@ -22,7 +19,6 @@
 import flye.utils.fasta_parser as fp
 from flye.utils.utils import process_in_parallel
 import flye.config.py_cfg as config
-from flye.six.moves import zip
 
 logger = logging.getLogger()
 

flye/trestle/graph_resolver.py

@@ -6,15 +6,13 @@
 Modifies repeat graph using the Tresle output
 """
 
-from __future__ import absolute_import
 import logging
 from itertools import chain
 from collections import defaultdict
 
 import flye.utils.fasta_parser as fp
 from flye.repeat_graph.graph_alignment import iter_alignments
 from flye.six import iteritems
-from flye.six.moves import zip
 
 logger = logging.getLogger()
 

flye/trestle/trestle.py

@@ -8,8 +8,6 @@
 @author: jeffrey_yuan
 """
 
-from __future__ import absolute_import
-from __future__ import division
 import os
 import logging
 from itertools import combinations, product
@@ -25,8 +23,6 @@
 
 import flye.trestle.divergence as div
 import flye.trestle.trestle_config as trestle_config
-from flye.six.moves import range
-from flye.six.moves import zip
 
 logger = logging.getLogger()
 

flye/utils/bytes2human.py

@@ -8,7 +8,6 @@
 """
 
 # see: http://goo.gl/kTQMs
-from __future__ import division
 SYMBOLS = {
     'customary'     : ('B', 'K', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y'),
     'customary_ext' : ('byte', 'kilo', 'mega', 'giga', 'tera', 'peta', 'exa',

flye/utils/fasta_parser.py

@@ -6,7 +6,6 @@
 This module provides some basic FASTA I/O
 """
 
-from __future__ import absolute_import
 import logging
 import gzip
 import io
@@ -23,8 +22,6 @@
     _STR = bytes.decode
     _BYTES = str.encode
 
-from flye.six.moves import range
-
 
 logger = logging.getLogger()
 

flye/utils/sam_parser.py

@@ -6,9 +6,6 @@
 Provides multithreaded parser for SAM files
 """
 
-from __future__ import absolute_import
-from __future__ import division
-
 import os
 import re
 import sys
@@ -32,7 +29,6 @@
     _STR = bytes.decode
     _BYTES = str.encode
 
-from flye.six.moves import range
 from flye.six import iteritems
 
 import flye.utils.fasta_parser as fp

flye/utils/utils.py

@@ -2,7 +2,6 @@
 #This file is a part of ABruijn program.
 #Released under the BSD license (see LICENSE file)
 
-from __future__ import absolute_import
 import os
 import signal
 import multiprocessing

setup.py

@@ -2,8 +2,6 @@
 #This file is a part of the Flye package
 #Released under the BSD license (see LICENSE file)
 
-from __future__ import print_function
-
 import os
 import sys
 import subprocess