Author: Steffen Möller
Last-Update: 2020-01-15 00:46:37 +0100
Description: Use python3 as interpreter

--- a/bin/alignmentSieve
+++ b/bin/alignmentSieve
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/bamCompare
+++ b/bin/bamCompare
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/bamCoverage
+++ b/bin/bamCoverage
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/bamPEFragmentSize
+++ b/bin/bamPEFragmentSize
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/bigwigCompare
+++ b/bin/bigwigCompare
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/computeGCBias
+++ b/bin/computeGCBias
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/computeMatrix
+++ b/bin/computeMatrix
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/computeMatrixOperations
+++ b/bin/computeMatrixOperations
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/correctGCBias
+++ b/bin/correctGCBias
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/deeptools
+++ b/bin/deeptools
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/estimateReadFiltering
+++ b/bin/estimateReadFiltering
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/estimateScaleFactor
+++ b/bin/estimateScaleFactor
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/multiBamSummary
+++ b/bin/multiBamSummary
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/multiBigwigSummary
+++ b/bin/multiBigwigSummary
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/plotCorrelation
+++ b/bin/plotCorrelation
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/plotCoverage
+++ b/bin/plotCoverage
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/plotEnrichment
+++ b/bin/plotEnrichment
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/plotFingerprint
+++ b/bin/plotFingerprint
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/plotHeatmap
+++ b/bin/plotHeatmap
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/bin/plotPCA
+++ b/bin/plotPCA
@@ -1,7 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
-import deeptools.misc
+from  deeptools import misc
 from deeptools.plotPCA import main
 import sys
 
--- a/bin/plotProfile
+++ b/bin/plotProfile
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
 import deeptools.misc
--- a/deeptools/plotPCA.py
+++ b/deeptools/plotPCA.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- a/deeptools/SES_scaleFactor.py
+++ b/deeptools/SES_scaleFactor.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- a/deeptools/alignmentSieve.py
+++ b/deeptools/alignmentSieve.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 import argparse
 import pysam
 import os
@@ -380,6 +380,7 @@ def main(args=None):
     total = mapped + unmapped
     chrom_sizes = [(x, y) for x, y in zip(bam.references, bam.lengths)]
     chromDict = {x: y for x, y in zip(bam.references, bam.lengths)}
+    bam.close()
 
     # Filter, writing the results to a bunch of temporary files
     res = mapReduce([args, chromDict],
--- a/deeptools/bamCompare.py
+++ b/deeptools/bamCompare.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse  # to parse command line arguments
--- a/deeptools/bamCoverage.py
+++ b/deeptools/bamCoverage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 # own tools
--- a/deeptools/bamPEFragmentSize.py
+++ b/deeptools/bamPEFragmentSize.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse
--- a/deeptools/bigwigCompare.py
+++ b/deeptools/bigwigCompare.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 import argparse  # to parse command line arguments
 import sys
--- a/deeptools/computeGCBias.py
+++ b/deeptools/computeGCBias.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import time
--- a/deeptools/computeMatrix.py
+++ b/deeptools/computeMatrix.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse
--- a/deeptools/computeMatrixOperations.py
+++ b/deeptools/computeMatrixOperations.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 import deeptools.heatmapper as heatmapper
 import deeptoolsintervals.parse as dti
 import numpy as np
--- a/deeptools/correctGCBias.py
+++ b/deeptools/correctGCBias.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- a/deeptools/deepBlue.py
+++ b/deeptools/deepBlue.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 try:
     # python 2
     import xmlrpclib
--- a/deeptools/deeptools_list_tools.py
+++ b/deeptools/deeptools_list_tools.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse
--- a/deeptools/estimateReadFiltering.py
+++ b/deeptools/estimateReadFiltering.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 import argparse
 import sys
 
--- a/deeptools/getScaleFactor.py
+++ b/deeptools/getScaleFactor.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import numpy as np
--- a/deeptools/multiBamSummary.py
+++ b/deeptools/multiBamSummary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- a/deeptools/multiBigwigSummary.py
+++ b/deeptools/multiBigwigSummary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- a/deeptools/plotCorrelation.py
+++ b/deeptools/plotCorrelation.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- a/deeptools/plotCoverage.py
+++ b/deeptools/plotCoverage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- a/deeptools/plotEnrichment.py
+++ b/deeptools/plotEnrichment.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- a/deeptools/plotFingerprint.py
+++ b/deeptools/plotFingerprint.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import numpy as np
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 from __future__ import division
 
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 
--- a/deeptools/writeBedGraph_bam_and_bw.py
+++ b/deeptools/writeBedGraph_bam_and_bw.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- a/scripts/convertChromsBigWig.py
+++ b/scripts/convertChromsBigWig.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import sys
 import pyBigWig
--- a/scripts/split_bed_into_multiple_files.py
+++ b/scripts/split_bed_into_multiple_files.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 """