added support for warnings stdlib

deeptools/SES_scaleFactor.py

@@ -3,6 +3,8 @@
 
 import os
 import numpy as np
+import warnings
+np.warnings = warnings
 
 # own packages
 from deeptools import bamHandler

deeptools/bamCompare.py

@@ -3,6 +3,8 @@
 
 import argparse  # to parse command line arguments
 import numpy as np
+import warnings
+np.warnings = warnings
 import sys
 
 # my packages

deeptools/bamCoverage.py

@@ -5,6 +5,8 @@
 import argparse
 import sys
 import numpy as np
+import warnings
+np.warnings = warnings
 from deeptools import writeBedGraph  # This should be made directly into a bigWig
 from deeptools import parserCommon
 from deeptools.getScaleFactor import get_scale_factor

deeptools/bamPEFragmentSize.py

@@ -4,6 +4,8 @@
 import argparse
 import sys
 import numpy as np
+import warnings
+np.warnings = warnings
 
 import matplotlib
 matplotlib.use('Agg')

deeptools/bigwigAverage.py

@@ -3,6 +3,8 @@
 import argparse
 import sys
 import numpy as np
+import warnings
+np.warnings = warnings
 from deeptools import parserCommon
 from deeptools import writeBedGraph_bam_and_bw
 

deeptools/computeGCBias.py

@@ -5,6 +5,8 @@
 
 import multiprocessing
 import numpy as np
+import warnings
+np.warnings = warnings
 import argparse
 from scipy.stats import poisson
 import py2bit

deeptools/computeMatrixOperations.py

@@ -2,6 +2,8 @@
 import deeptools.heatmapper as heatmapper
 import deeptoolsintervals.parse as dti
 import numpy as np
+import warnings
+np.warnings = warnings
 import argparse
 import sys
 import os

deeptools/correctGCBias.py

@@ -11,6 +11,8 @@
 import pysam
 import multiprocessing
 import numpy as np
+import warnings
+np.warnings = warnings
 import argparse
 
 from scipy.stats import binom

deeptools/correlation.py

@@ -2,6 +2,8 @@
 import itertools
 import copy
 import numpy as np
+import warnings
+np.warnings = warnings
 import scipy.cluster.hierarchy as sch
 import scipy.stats
 import matplotlib as mpl

deeptools/correlation_heatmap.py

@@ -3,6 +3,8 @@
 from deeptools import cm  # noqa: F401
 import matplotlib.pyplot as plt
 import numpy as np
+import warnings
+np.warnings = warnings
 import scipy.cluster.hierarchy as sch
 from matplotlib import rcParams
 import matplotlib.colors as pltcolors

deeptools/countReadsPerBin.py

@@ -4,6 +4,8 @@
 import sys
 import multiprocessing
 import numpy as np
+import warnings
+np.warnings = warnings
 
 # deepTools packages
 import deeptools.utilities

deeptools/getFragmentAndReadSize.py

@@ -1,4 +1,6 @@
 import numpy as np
+import warnings
+np.warnings = warnings
 
 # own tools
 from deeptools import bamHandler

deeptools/getRatio.py

@@ -1,4 +1,6 @@
 import numpy as np
+import warnings
+np.warnings = warnings
 
 old_settings = np.seterr(all='ignore')
 

deeptools/getScaleFactor.py

@@ -2,6 +2,8 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
+import warnings
+np.warnings = warnings
 import deeptools.mapReduce as mapReduce
 from deeptools import bamHandler
 from deeptools import utilities

deeptools/getScorePerBigWigBin.py

@@ -1,5 +1,7 @@
 import pyBigWig
 import numpy as np
+import warnings
+np.warnings = warnings
 import os
 import sys
 import shutil

deeptools/heatmapper.py

@@ -2,6 +2,8 @@
 import gzip
 from collections import OrderedDict
 import numpy as np
+import warnings
+np.warnings = warnings
 from copy import deepcopy
 
 import pyBigWig

deeptools/heatmapper_utilities.py

@@ -1,4 +1,6 @@
 import numpy as np
+import warnings
+np.warnings = warnings
 import matplotlib
 matplotlib.use('Agg')
 matplotlib.rcParams['pdf.fonttype'] = 42

deeptools/multiBamSummary.py

@@ -5,6 +5,8 @@
 import sys
 import argparse
 import numpy as np
+import warnings
+np.warnings = warnings
 
 import deeptools.countReadsPerBin as countR
 from deeptools import parserCommon

deeptools/multiBigwigSummary.py

@@ -5,6 +5,8 @@
 import argparse
 import os.path
 import numpy as np
+import warnings
+np.warnings = warnings
 from deeptools import parserCommon
 from deeptools.utilities import smartLabels
 import deeptools.getScorePerBigWigBin as score_bw

deeptools/plotCorrelation.py

@@ -4,6 +4,8 @@
 import sys
 import argparse
 import numpy as np
+import warnings
+np.warnings = warnings
 import matplotlib
 matplotlib.use('Agg')
 matplotlib.rcParams['pdf.fonttype'] = 42

deeptools/plotCoverage.py

@@ -5,6 +5,8 @@
 import sys
 import argparse
 import numpy as np
+import warnings
+np.warnings = warnings
 
 import matplotlib
 matplotlib.use('Agg')

deeptools/plotEnrichment.py

@@ -4,6 +4,8 @@
 import sys
 import argparse
 import numpy as np
+import warnings
+np.warnings = warnings
 import matplotlib
 matplotlib.use('Agg')
 matplotlib.rcParams['pdf.fonttype'] = 42

deeptools/plotFingerprint.py

@@ -2,6 +2,8 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
+import warnings
+np.warnings = warnings
 import argparse
 import sys
 import matplotlib

deeptools/plotHeatmap.py

@@ -5,6 +5,8 @@
 import argparse
 from collections import OrderedDict
 import numpy as np
+import warnings
+np.warnings = warnings
 import matplotlib
 matplotlib.use('Agg')
 matplotlib.rcParams['pdf.fonttype'] = 42

deeptools/plotProfile.py

@@ -6,6 +6,8 @@
 
 import argparse
 import numpy as np
+import warnings
+np.warnings = warnings
 from math import ceil
 import matplotlib
 matplotlib.use('Agg')

deeptools/sumCoveragePerBin.py

@@ -1,4 +1,6 @@
 import numpy as np
+import warnings
+np.warnings = warnings
 import multiprocessing
 import time
 

deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py

@@ -1,6 +1,8 @@
 import deeptools.bigwigCompare as bwComp
 import deeptools.multiBigwigSummary as bwCorr
 import numpy as np
+import warnings
+np.warnings = warnings
 import numpy.testing as nt
 
 import os.path

deeptools/test/test_countReadsPerBin.py

@@ -2,6 +2,8 @@
 
 import deeptools.countReadsPerBin as cr
 import numpy as np
+import warnings
+np.warnings = warnings
 import numpy.testing as nt
 import os.path
 import pytest

deeptools/test/test_multiBamSummary.py

@@ -1,5 +1,7 @@
 import deeptools.multiBamSummary as mbs
 import numpy as np
+import warnings
+np.warnings = warnings
 import numpy.testing as nt
 
 import os.path

deeptools/utilities.py

@@ -6,6 +6,8 @@
 mpl.use('Agg')
 from deeptools import cm  # noqa: F401
 import numpy as np
+import warnings
+np.warnings = warnings
 
 
 debug = 0

deeptools/writeBedGraph.py

@@ -2,6 +2,8 @@
 import sys
 import shutil
 import numpy as np
+import warnings
+np.warnings = warnings
 import pyBigWig
 
 # own modules

deeptools/writeBedGraph_bam_and_bw.py

@@ -5,6 +5,8 @@
 import shutil
 import tempfile
 import numpy as np
+import warnings
+np.warnings = warnings
 import sys
 
 # NGS packages