Пример #1
0
def test_bedSizeFilter_cmdline():
    infn = 'inputfiles/multi.tracks.3.fields.bed'
    outfn = tempfile.mktemp()
    cmds = ' '.join([
        'python',
        '../bedSizeFilter.py',
        '-i',
        infn,
        '-o',
        outfn,
    ])
    os.system(cmds)
    assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(
        outfn).read()

    # make sure minlen works
    infile = open(infn)
    outfile = open(outfn, 'w')
    bedSizeFilter(infile, outfile, minlen=100, maxlen=None)
    outfile.close()
    assert open('inputfiles/expected.bedSizeFilter.1.bed').read() == open(
        outfn).read()

    # make sure minlen and maxlen work
    infile = open(infn)
    outfile = open(outfn, 'w')
    bedSizeFilter(infile, outfile, minlen=10, maxlen=500)
    outfile.close()
    assert open('inputfiles/expected.bedSizeFilter.2.bed').read() == open(
        outfn).read()
Пример #2
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def test_bedSizeFilter_importing():
    infn = 'inputfiles/multi.tracks.3.fields.bed'
    outfn = tempfile.mktemp()
    infile = open(infn)
    outfile = open(outfn,'w')
    bedSizeFilter(infile,outfile,minlen=None,maxlen=None)
    outfile.close()
    infile.close()
    assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(outfn).read()
Пример #3
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def test_bedSizeFilter_importing():
    infn = 'inputfiles/multi.tracks.3.fields.bed'
    outfn = tempfile.mktemp()
    infile = open(infn)
    outfile = open(outfn, 'w')
    bedSizeFilter(infile, outfile, minlen=None, maxlen=None)
    outfile.close()
    infile.close()
    assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(
        outfn).read()
Пример #4
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def test_bedSizeFilter_cmdline():
    infn = 'inputfiles/multi.tracks.3.fields.bed'
    outfn = tempfile.mktemp()
    cmds = ' '.join(['python',
                     '../bedSizeFilter.py',
                     '-i', infn,
                     '-o', outfn,
                     ])
    os.system(cmds)
    assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(outfn).read()

    # make sure minlen works
    infile = open(infn)
    outfile = open(outfn,'w')
    bedSizeFilter(infile,outfile,minlen=100,maxlen=None)
    outfile.close()
    assert open('inputfiles/expected.bedSizeFilter.1.bed').read() == open(outfn).read()

    # make sure minlen and maxlen work
    infile = open(infn)
    outfile = open(outfn,'w')
    bedSizeFilter(infile,outfile,minlen=10,maxlen=500)
    outfile.close()
    assert open('inputfiles/expected.bedSizeFilter.2.bed').read() == open(outfn).read()