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|
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
|
