drop unused imports due to deepblue drop, flake fixes

deeptools/bigwigAverage.py

@@ -1,9 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import argparse  # to parse command line arguments
+import argparse
 import sys
-import multiprocessing
-import os
 import numpy as np
 from deeptools import parserCommon
 from deeptools import writeBedGraph_bam_and_bw

deeptools/bigwigCompare.py

@@ -1,9 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import argparse  # to parse command line arguments
-import sys
-import multiprocessing
-import os
+import argparse
 from deeptools import parserCommon
 from deeptools.getRatio import getRatio
 from deeptools import writeBedGraph_bam_and_bw

deeptools/computeMatrix.py

@@ -3,9 +3,6 @@
 
 import argparse
 import sys
-import os
-import multiprocessing
-
 from deeptools.parserCommon import writableFile, numberOfProcessors
 from deeptools import parserCommon
 from deeptools import heatmapper
@@ -47,11 +44,12 @@ def parse_arguments(args=None):
     subparsers.add_parser(
         'scale-regions',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        parents=[computeMatrixRequiredArgs(),
-                 computeMatrixOutputArgs(),
-                 computeMatrixOptArgs(case='scale-regions'),
-                 parserCommon.gtf_options()
-                ],
+        parents=[
+            computeMatrixRequiredArgs(),
+            computeMatrixOutputArgs(),
+            computeMatrixOptArgs(case='scale-regions'),
+            parserCommon.gtf_options()
+        ],
         help="In the scale-regions mode, all regions in the BED file are "
         "stretched or shrunken to the length (in bases) indicated by the user.",
         usage='An example usage is:\n  computeMatrix scale-regions -S '
@@ -421,4 +419,3 @@ def main(args=None):
 
     if args.outFileSortedRegions:
         hm.save_BED(args.outFileSortedRegions)
-

deeptools/multiBigwigSummary.py

@@ -5,7 +5,6 @@
 import argparse
 import os.path
 import numpy as np
-import multiprocessing
 from deeptools import parserCommon
 from deeptools.utilities import smartLabels
 import deeptools.getScorePerBigWigBin as score_bw
@@ -54,10 +53,11 @@ def parse_arguments(args=None):
     subparsers.add_parser(
         'bins',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        parents=[multiBigwigSummaryArgs(case='bins'),
-                 parent_parser,
-                 parserCommon.gtf_options(suppress=True)
-                ],
+        parents=[
+            multiBigwigSummaryArgs(case='bins'),
+            parent_parser,
+            parserCommon.gtf_options(suppress=True)
+        ],
         help="The average score is based on equally sized bins "
              "(10 kilobases by default), which consecutively cover the "
              "entire genome. The only exception is the last bin of a chromosome, which "
@@ -73,10 +73,11 @@ def parse_arguments(args=None):
     subparsers.add_parser(
         'BED-file',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        parents=[multiBigwigSummaryArgs(case='BED-file'),
-                 parent_parser,
-                 parserCommon.gtf_options()
-                ],
+        parents=[
+            multiBigwigSummaryArgs(case='BED-file'),
+            parent_parser,
+            parserCommon.gtf_options()
+        ],
         help="The user provides a BED file that contains all regions "
              "that should be considered for the analysis. A "
              "common use is to compare scores (e.g. ChIP-seq scores) between "
@@ -278,4 +279,3 @@ def main(args=None):
                 args.outRawCounts.write(fmt.format(*tuple(row)))
         """
         f.close()
-

deeptools/parserCommon.py

@@ -861,6 +861,7 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]):
                           action='store_true')
     return parser
 
+
 def requiredLength(minL, maxL):
     """
     This is an optional action that can be given to argparse.add_argument(..., nargs='+')