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

--- python-deeptools.orig/deeptools/plotPCA.py
+++ python-deeptools/deeptools/plotPCA.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- python-deeptools.orig/deeptools/SES_scaleFactor.py
+++ python-deeptools/deeptools/SES_scaleFactor.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- python-deeptools.orig/deeptools/alignmentSieve.py
+++ python-deeptools/deeptools/alignmentSieve.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 import argparse
 import pysam
 import os
@@ -388,6 +388,7 @@
     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],
--- python-deeptools.orig/deeptools/bamCompare.py
+++ python-deeptools/deeptools/bamCompare.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse  # to parse command line arguments
--- python-deeptools.orig/deeptools/bamCoverage.py
+++ python-deeptools/deeptools/bamCoverage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 # own tools
--- python-deeptools.orig/deeptools/bamPEFragmentSize.py
+++ python-deeptools/deeptools/bamPEFragmentSize.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse
--- python-deeptools.orig/deeptools/bigwigCompare.py
+++ python-deeptools/deeptools/bigwigCompare.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 import argparse
 from deeptools import parserCommon
--- python-deeptools.orig/deeptools/computeGCBias.py
+++ python-deeptools/deeptools/computeGCBias.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import time
--- python-deeptools.orig/deeptools/computeMatrix.py
+++ python-deeptools/deeptools/computeMatrix.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse
--- python-deeptools.orig/deeptools/computeMatrixOperations.py
+++ python-deeptools/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
--- python-deeptools.orig/deeptools/correctGCBias.py
+++ python-deeptools/deeptools/correctGCBias.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- python-deeptools.orig/deeptools/deeptools_list_tools.py
+++ python-deeptools/deeptools/deeptools_list_tools.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse
--- python-deeptools.orig/deeptools/estimateReadFiltering.py
+++ python-deeptools/deeptools/estimateReadFiltering.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 import argparse
 import sys
 
--- python-deeptools.orig/deeptools/getScaleFactor.py
+++ python-deeptools/deeptools/getScaleFactor.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import numpy as np
--- python-deeptools.orig/deeptools/multiBamSummary.py
+++ python-deeptools/deeptools/multiBamSummary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- python-deeptools.orig/deeptools/multiBigwigSummary.py
+++ python-deeptools/deeptools/multiBigwigSummary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- python-deeptools.orig/deeptools/plotCorrelation.py
+++ python-deeptools/deeptools/plotCorrelation.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- python-deeptools.orig/deeptools/plotCoverage.py
+++ python-deeptools/deeptools/plotCoverage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- python-deeptools.orig/deeptools/plotEnrichment.py
+++ python-deeptools/deeptools/plotEnrichment.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- python-deeptools.orig/deeptools/plotFingerprint.py
+++ python-deeptools/deeptools/plotFingerprint.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import numpy as np
--- python-deeptools.orig/deeptools/plotHeatmap.py
+++ python-deeptools/deeptools/plotHeatmap.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 from __future__ import division
 
--- python-deeptools.orig/deeptools/plotProfile.py
+++ python-deeptools/deeptools/plotProfile.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 
--- python-deeptools.orig/deeptools/writeBedGraph_bam_and_bw.py
+++ python-deeptools/deeptools/writeBedGraph_bam_and_bw.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import os
--- python-deeptools.orig/scripts/convertChromsBigWig.py
+++ python-deeptools/scripts/convertChromsBigWig.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import sys
 import pyBigWig
--- python-deeptools.orig/scripts/split_bed_into_multiple_files.py
+++ python-deeptools/scripts/split_bed_into_multiple_files.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 """
--- python-deeptools.orig/deeptools/bigwigAverage.py
+++ python-deeptools/deeptools/bigwigAverage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 import argparse
 import sys
--- python-deeptools.orig/deeptools/cm.py
+++ python-deeptools/deeptools/cm.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # This file comes from the seaborn project and is under a BSD license:
 
--- python-deeptools.orig/deeptools/estimateScaleFactor.py
+++ python-deeptools/deeptools/estimateScaleFactor.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import argparse